Publications in the scientific literature

This list contains 1645 papers covering various topics of single cell sequencing. The list is compiled by searching for keywords in abstracts and titles using data from and The list is automatically updated once every 24h. Rows in blue indicate papers in "high impact" journals.

added within the last 24h to this list.

the study is about a computer software/algorithm/database/pure bioinformatics.

the study is about a new method.

the study is a review or comment.

the study does not involve mammalian scRNA-seq data or raw data are not public.

Include studies:

First author Journal Title Pub. date DOI Citations Action
Todorov Methods Mol. Biol. Network Inference from Single-Cell Transcriptomic Data. 2019-12-01 10.1007/978-1-4939-8882-2_10 view
Guthmiller Methods Mol. Biol. An Efficient Method to Generate Monoclonal Antibodies from Human B Cells. 2019-12-01 10.1007/978-1-4939-8958-4_5 view
Zwarycz Cell Mol Gastroenterol Hepatol IL22 Inhibits Epithelial Stem Cell Expansion in an Ileal Organoid Model. 2019-10-01 10.1016/j.jcmgh.2018.06.008 1 view
Rashid Bioinformatics Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data. 2019-02-15 10.1093/bioinformatics/btz095 view
Nowinski Environ. Microbiol. Microdiversity and Temporal Dynamics of Marine Bacterial Dimethylsulfoniopropionate Genes. 2019-02-14 10.1111/1462-2920.14560 view
Zhao Hepatology Tissue repair in the mouse liver following acute carbon tetrachloride depends on injury-induced Wnt/β-catenin signaling. 2019-02-14 10.1002/hep.30563 view
Monier PLoS Comput. Biol. IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis. 2019-02-14 10.1371/journal.pcbi.1006792 view
Haage Acta Neuropathol Commun Comprehensive gene expression meta-analysis identifies signature genes that distinguish microglia from peripheral monocytes/macrophages in health and glioma. 2019-02-14 10.1186/s40478-019-0665-y view
Dangi Cell. Mol. Immunol. Emerging approaches and technologies in transplantation: the potential game changers. 2019-02-13 10.1038/s41423-019-0207-3 view
Wu Mol. Cells Lineage Tracing: Computational Reconstruction Goes Beyond the Limit of Imaging. 2019-02-13 10.14348/molcells.2019.0006 view
Cui Cell Rep Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart. 2019-02-12 10.1016/j.celrep.2019.01.079 view
Tyler Cell Rep PyMINEr Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq. 2019-02-12 10.1016/j.celrep.2019.01.063 view
Choi Mol. Cells Dissecting Cellular Heterogeneity Using Single-Cell RNA Sequencing. 2019-02-12 10.14348/molcells.2019.2446 view
Linderman Nat. Methods Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data. 2019-02-11 10.1038/s41592-018-0308-4 view
Sato Genome Biol. CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing. 2019-02-11 10.1186/s13059-019-1639-x view
Kim Immunol. Cell Biol. Macrophages in wound healing: activation and plasticity. 2019-02-11 10.1111/imcb.12236 view
Rodriguez-Meira Mol. Cell Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing. 2019-02-11 10.1016/j.molcel.2019.01.009 view
Yu EMBO J. Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution. 2019-02-08 10.15252/embj.2018100164 view
Guerrero-Juarez Nat Commun Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds. 2019-02-08 10.1038/s41467-018-08247-x view
Gutierrez-Arcelus Nat Commun Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions. 2019-02-08 10.1038/s41467-019-08604-4 view
Koelwyn Trends Immunol. Defining Macrophages in the Heart One Cell at a Time. 2019-02-08 10.1016/ view
Wizeman Elife Specification of diverse cell types during early neurogenesis of the mouse cerebellum. 2019-02-08 10.7554/eLife.42388 view
Carr Cell Stem Cell Mesenchymal Precursor Cells in Adult Nerves Contribute to Mammalian Tissue Repair and Regeneration. 2019-02-07 10.1016/j.stem.2018.10.024 1 view
Tan Cell Stem Cell Human Spermatogonial Stem Cells Scrutinized under the Single-Cell Magnifying Glass. 2019-02-07 10.1016/j.stem.2019.01.010 view
Mayer Neuron Multimodal Single-Cell Analysis Reveals Physiological Maturation in the Developing Human Neocortex. 2019-02-07 10.1016/j.neuron.2019.01.027 view
Watcham Blood New Insights into Haematopoietic Differentiation Landscapes from scRNA-seq. 2019-02-06 10.1182/blood-2018-08-835355 view
Szczerba Nature Neutrophils escort circulating tumour cells to enable cell cycle progression. 2019-02-06 10.1038/s41586-019-0915-y view
Schreurs Immunity Human Fetal TNF-α-Cytokine-Producing CD4+ Effector Memory T Cells Promote Intestinal Development and Mediate Inflammation Early in Life. 2019-02-05 10.1016/j.immuni.2018.12.010 view
Ekiz JCI Insight MicroRNA-155 coordinates the immunological landscape within murine melanoma and correlates with immunity in human cancers. 2019-02-05 10.1172/jci.insight.126543 view
Mould JCI Insight Single cell RNA sequencing identifies unique inflammatory airspace macrophage subsets. 2019-02-05 10.1172/jci.insight.126556 view
Sohni Cell Rep The Neonatal and Adult Human Testis Defined at the Single-Cell Level. 2019-02-05 10.1016/j.celrep.2019.01.045 view
Poczobutt Am. J. Respir. Crit. Care Med. Defining the Cell Types That Drive IPF Using Single Cell RNA Sequencing. 2019-02-04 10.1164/rccm.201901-0197ED view
Ryu Plant Physiol. Single-cell RNA sequencing resolves molecular relationships among individual plant cells. 2019-02-04 10.1104/pp.18.01482 view
Borcherding Clin. Cancer Res. Single-cell profiling of cutaneous T-cell lymphoma reveals underlying heterogeneity associated with disease progression. 2019-02-04 10.1158/1078-0432.CCR-18-3309 view
Risso Nat Commun Publisher Correction: A general and flexible method for signal extraction from single-cell RNA-seq data. 2019-02-04 10.1038/s41467-019-08614-2 view
Tiklová Nat Commun Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development. 2019-02-04 10.1038/s41467-019-08453-1 view
Saint Nat Microbiol Single-cell imaging and RNA sequencing reveal patterns of gene expression heterogeneity during fission yeast growth and adaptation. 2019-02-04 10.1038/s41564-018-0330-4 view
Nadal-Ribelles Nat Microbiol Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations. 2019-02-04 10.1038/s41564-018-0346-9 view
Potter Methods Mol. Biol. Dissociation of Tissues for Single-Cell Analysis. 2019-02-01 10.1007/978-1-4939-9021-4_5 view
Brazovskaja Curr. Opin. Biotechnol. High-throughput single-cell transcriptomics on organoids. 2019-02-01 10.1016/j.copbio.2018.11.002 view
Jiang Methods Mol. Biol. Quality Control of Single-Cell RNA-seq. 2019-02-01 10.1007/978-1-4939-9057-3_1 view
Bacher Methods Mol. Biol. Normalization for Single-Cell RNA-Seq Data Analysis. 2019-02-01 10.1007/978-1-4939-9057-3_2 view
Kim Methods Mol. Biol. Analysis of Technical and Biological Variability in Single-Cell RNA Sequencing. 2019-02-01 10.1007/978-1-4939-9057-3_3 view
Shekhar Methods Mol. Biol. Identification of Cell Types from Single-Cell Transcriptomic Data. 2019-02-01 10.1007/978-1-4939-9057-3_4 view
Sun Methods Mol. Biol. scMCA: A Tool to Define Mouse Cell Types Based on Single-Cell Digital Expression. 2019-02-01 10.1007/978-1-4939-9057-3_6 view
Fan Methods Mol. Biol. Differential Pathway Analysis. 2019-02-01 10.1007/978-1-4939-9057-3_7 view
Ji Methods Mol. Biol. Pseudotime Reconstruction Using TSCAN. 2019-02-01 10.1007/978-1-4939-9057-3_8 view
Chen Methods Mol. Biol. Estimating Differentiation Potency of Single Cells Using Single-Cell Entropy (SCENT). 2019-02-01 10.1007/978-1-4939-9057-3_9 view
Lamere Methods Mol. Biol. Inference of Gene Co-expression Networks from Single-Cell RNA-Sequencing Data. 2019-02-01 10.1007/978-1-4939-9057-3_10 view
Dong Methods Mol. Biol. Single-Cell Allele-Specific Gene Expression Analysis. 2019-02-01 10.1007/978-1-4939-9057-3_11 view
Huang Methods Mol. Biol. Using BRIE to Detect and Analyze Splicing Isoforms in scRNA-Seq Data. 2019-02-01 10.1007/978-1-4939-9057-3_12 view
Lindeman Methods Mol. Biol. Antigen Receptor Sequence Reconstruction and Clonality Inference from scRNA-Seq Data. 2019-02-01 10.1007/978-1-4939-9057-3_15 view
Mongia Front Genet McImpute: Matrix Completion Based Imputation for Single Cell RNA-seq Data. 2019-02-01 10.3389/fgene.2019.00009 1 view
Winterhoff Curr. Opin. Obstet. Gynecol. Single-cell sequencing in ovarian cancer: a new frontier in precision medicine. 2019-02-01 10.1097/GCO.0000000000000516 view
Papadopoulos Bioinformatics PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. 2019-02-01 10.1093/bioinformatics/btz078 view
Zhou Stem Cells Int Stem Cells and Cellular Origins of Mammary Gland: Updates in Rationale, Controversies, and Cancer Relevance. 2019-02-01 10.1155/2019/4247168 view
Penaranda ACS Infect Dis Single-Cell RNA Sequencing to Understand Host-Pathogen Interactions. 2019-01-31 10.1021/acsinfecdis.8b00369 view
Stuart Nat. Rev. Genet. Integrative single-cell analysis. 2019-01-29 10.1038/s41576-019-0093-7 view
Zhu Genes (Basel) A Hybrid Clustering Algorithm for Identifying Cell Types from Single-Cell RNA-Seq Data. 2019-01-29 10.3390/genes10020098 view
Rosenzweig Nat Commun PD-1/PD-L1 checkpoint blockade harnesses monocyte-derived macrophages to combat cognitive impairment in a tauopathy mouse model. 2019-01-28 10.1038/s41467-019-08352-5 view
Schiebinger Cell Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. 2019-01-28 10.1016/j.cell.2019.01.006 view
Peng Cell Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina. 2019-01-28 10.1016/j.cell.2019.01.004 view
Lush Elife scRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling. 2019-01-25 10.7554/eLife.44431 view
Collin Stem Cells CRX expression in pluripotent stem cell derived photoreceptors marks a transplantable subpopulation of early cones. 2019-01-25 10.1002/stem.2974 view
Daughtry Genome Res. Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion. 2019-01-25 10.1101/gr.239830.118 view
Lawlor Elife Nephron progenitor commitment is a stochastic process influenced by cell migration. 2019-01-24 10.7554/eLife.41156 view
Williams Curr. Opin. Neurobiol. Neuronal cell types in the annelid Platynereis dumerilii. 2019-01-24 10.1016/j.conb.2018.12.008 view
Maehara Int J Oral Maxillofac Surg Clinical features and mechanistic insights regarding IgG4-related dacryoadenitis and sialoadenitis: a review. 2019-01-24 10.1016/j.ijom.2019.01.006 view
Sahara Dev. Cell Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract. 2019-01-24 10.1016/j.devcel.2019.01.005 view
Ba Funct. Integr. Genomics Single-cell transcriptome provides novel insights into antler stem cells, a cell type capable of mammalian organ regeneration. 2019-01-23 10.1007/s10142-019-00659-2 view
Hamza Proc. Natl. Acad. Sci. U.S.A. Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer. 2019-01-23 10.1073/pnas.1814102116 view
Eraslan Nat Commun Single-cell RNA-seq denoising using a deep count autoencoder. 2019-01-23 10.1038/s41467-018-07931-2 view
Miragaia Immunity Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation. 2019-01-23 10.1016/j.immuni.2019.01.001 view
Messmer Cell Rep Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution. 2019-01-22 10.1016/j.celrep.2018.12.099 view
Darde Bioinformatics The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community. 2019-01-22 10.1093/bioinformatics/btz047 view
Huss Hum. Hered. Comparison of SureSelect and Nextera Exome Capture Performance in Single-Cell Sequencing. 2019-01-22 10.1159/000490506 view
Yang BMC Syst Biol Correction to: MISC: missing imputation for single-cell RNA sequencing data. 2019-01-22 10.1186/s12918-019-0681-3 view
Wang Nat Commun Bulk tissue cell type deconvolution with multi-subject single-cell expression reference. 2019-01-22 10.1038/s41467-018-08023-x view
Chapuy Mucosal Immunol Two distinct colonic CD14+ subsets characterized by single-cell RNA profiling in Crohn's disease. 2019-01-22 10.1038/s41385-018-0126-0 view
Kiselev Nat. Rev. Genet. Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data. 2019-01-22 10.1038/s41576-019-0095-5 view
Li Nat. Immunol. Memory CD4+ T cells are generated in the human fetal intestine. 2019-01-21 10.1038/s41590-018-0294-9 view
Ntranos Nat. Methods A discriminative learning approach to differential expression analysis for single-cell RNA-seq. 2019-01-21 10.1038/s41592-018-0303-9 view
Wang BMC Bioinformatics Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data. 2019-01-18 10.1186/s12859-019-2599-6 view
Castro Dias Sci Rep Claudin-3-deficient C57BL/6J mice display intact brain barriers. 2019-01-18 10.1038/s41598-018-36731-3 view
Tambe BMC Bioinformatics Barcode identification for single cell genomics. 2019-01-17 10.1186/s12859-019-2612-0 1 view
Bassler Annu. Rev. Immunol. The Myeloid Cell Compartment-Cell by Cell. 2019-01-16 10.1146/annurev-immunol-042718-041728 view
Chowdhury IEEE/ACM Trans Comput Biol Bioinform (Differential) Co-Expression Analysis of Gene Expression: A Survey of Best Practices. 2019-01-16 10.1109/TCBB.2019.2893170 view
Adorjan J. Anat. Neuroserpin expression during human brain development and in adult brain revealed by immunohistochemistry and single cell RNA sequencing. 2019-01-15 10.1111/joa.12931 view
Kiser FASEB J. Conditional deletion of Des1 in the mouse retina does not impair the visual cycle in cones. 2019-01-15 10.1096/fj.201802493R view
Xu Elife Hedgehog signaling patterns the oral-aboral axis of the mandibular arch. 2019-01-14 10.7554/eLife.40315 view
Hernandez-Barco Clin. Cancer Res. No Cell Left Unturned: Intraductal Papillary Mucinous Neoplasm Heterogeneity. 2019-01-14 10.1158/1078-0432.CCR-18-3877 view
Aran Nat. Immunol. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. 2019-01-14 10.1038/s41590-018-0276-y view
Gao Bioinformatics ClusterMap: Compare multiple Single Cell RNA-Seq datasets across different experimental conditions. 2019-01-14 10.1093/bioinformatics/btz024 view
Rentzsch Curr. Opin. Neurobiol. Modern genomic tools reveal the structural and cellular diversity of cnidarian nervous systems. 2019-01-14 10.1016/j.conb.2018.12.004 view
Asante Environ Microbiol Rep Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: Advances and applications. 2019-01-13 10.1111/1758-2229.12735 view
Liu J Transl Med Single cell sequencing reveals gene expression signatures associated with bone marrow stromal cell subpopulations and time in culture. 2019-01-11 10.1186/s12967-018-1766-2 view
Loo Nat Commun Single-cell transcriptomic analysis of mouse neocortical development. 2019-01-11 10.1038/s41467-018-08079-9 view
Stratton J Vis Exp Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues. 2019-01-10 10.3791/58709 view
Davis Mol. Phylogenet. Evol. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi). 2019-01-10 10.1016/j.ympev.2019.01.006 view
Schmidt ILAR J Rational Design and In Vivo Characterization of Vaccine Adjuvants. 2019-01-09 10.1093/ilar/ily018 view
O'Neal J. Virol. West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type I interferon response within single cells. 2019-01-09 10.1128/JVI.01778-18 view
Takahashi Proc. Natl. Acad. Sci. U.S.A. Autocrine regulation of mesenchymal progenitor cell fates orchestrates tooth eruption. 2019-01-08 10.1073/pnas.1810200115 view
Mizrak Cell Rep Single-Cell Analysis of Regional Differences in Adult V-SVZ Neural Stem Cell Lineages. 2019-01-08 10.1016/j.celrep.2018.12.044 view
Manipur Int. J. Biochem. Cell Biol. Exploiting single-cell RNA sequencing data to link alternative splicing and cancer heterogeneity: a computational approach. 2019-01-08 10.1016/j.biocel.2018.12.015 view
Ciucci Immunity The Emergence and Functional Fitness of Memory CD4+ T Cells Require the Transcription Factor Thpok. 2019-01-08 10.1016/j.immuni.2018.12.019 view
Anaparthy Cold Spring Harb Perspect Med Single-Cell Applications of Next-Generation Sequencing. 2019-01-07 10.1101/cshperspect.a026898 view
Kiselev Nat. Rev. Genet. Challenges in unsupervised clustering of single-cell RNA-seq data. 2019-01-07 10.1038/s41576-018-0088-9 view
Liu Dev. Cell Neurog3-Independent Methylation Is the Earliest Detectable Mark Distinguishing Pancreatic Progenitor Identity. 2019-01-07 10.1016/j.devcel.2018.11.048 view
Crow Curr. Opin. Neurobiol. Single cell RNA-sequencing: replicability of cell types. 2019-01-06 10.1016/j.conb.2018.12.002 view
Wilson Pediatr. Nephrol. Kidney and organoid single-cell transcriptomics: the end of the beginning. 2019-01-04 10.1007/s00467-018-4177-y view
Jang Blood Cancer J Molecular signatures of multiple myeloma progression through single cell RNA-Seq. 2019-01-03 10.1038/s41408-018-0160-x view
Lang Cell Stem Cell Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes. 2019-01-03 10.1016/j.stem.2018.10.023 view
Satoh J. Mol. Cell. Cardiol. High-throughput single-molecule RNA imaging analysis reveals heterogeneous responses of cardiomyocytes to hemodynamic overload. 2019-01-03 10.1016/j.yjmcc.2018.12.018 view
Larsson Nature Genomic encoding of transcriptional burst kinetics. 2019-01-02 10.1038/s41586-018-0836-1 view
McCurdy PLoS ONE Deterministic column subset selection for single-cell RNA-Seq. 2019-01-01 10.1371/journal.pone.0210571 view
Torres Neurosurg. Clin. N. Am. Alterations in the Brain Microenvironment in Diffusely Infiltrating Low-Grade Glioma. 2019-01-01 10.1016/ view
Kim Methods Mol. Biol. Single-Cell Library Preparation of iPSC-Derived Neural Stem Cells. 2019-01-01 10.1007/978-1-4939-9007-8_10 view
Kim Methods Mol. Biol. Bioinformatics Analysis of Single-Cell RNA-Seq Raw Data from iPSC-Derived Neural Stem Cells. 2019-01-01 10.1007/978-1-4939-9007-8_11 view
Dick Nat. Immunol. Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction. 2019-01-01 10.1038/s41590-018-0272-2 view
Whitsett Physiol. Rev. Building and Regenerating the Lung Cell by Cell. 2019-01-01 10.1152/physrev.00001.2018 view
Ma BMC Bioinformatics Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes. 2018-12-31 10.1186/s12859-018-2519-1 view
Gan BMC Med Genomics Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method. 2018-12-31 10.1186/s12920-018-0433-z view
Saito Neuron Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function. 2018-12-28 10.1016/j.neuron.2018.12.019 view
Field Stem Cell Reports Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes. 2018-12-28 10.1016/j.stemcr.2018.12.006 view
Li Bioinformatics Single-cell RNA-seq Interpretations using Evolutionary Multiobjective Ensemble Pruning. 2018-12-28 10.1093/bioinformatics/bty1056 view
Andor Blood Single-cell RNA-Seq of lymphoma cancers reveals malignant B cell types and co-expression of T cell immune checkpoints. 2018-12-27 10.1182/blood-2018-08-862292 view
Li Neuron Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing. 2018-12-27 10.1016/j.neuron.2018.12.006 view
Romagnoli BMC Genomics ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data. 2018-12-24 10.1186/s12864-018-5249-x view
Higdon J. Immunol. Methods Optimization of single-cell plate sorting for high throughput sequencing applications. 2018-12-24 10.1016/j.jim.2018.12.006 view
Yuan Genome Biol. SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing. 2018-12-24 10.1186/s13059-018-1607-x view
Gasperini Cell A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. 2018-12-22 10.1016/j.cell.2018.11.029 view
Wang BMC Syst Biol The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: systems biology on diverse data types. 2018-12-21 10.1186/s12918-018-0648-9 view
Chiu BMC Syst Biol scdNet: a computational tool for single-cell differential network analysis. 2018-12-21 10.1186/s12918-018-0652-0 1 view
Büttner Nat. Methods A test metric for assessing single-cell RNA-seq batch correction. 2018-12-20 10.1038/s41592-018-0254-1 view
Neirijnck Endocrinology The tumor suppressor PTEN regulates negatively Sertoli cell proliferation, testis size and sperm production in vivo. 2018-12-20 10.1210/en.2018-00892 view
Li Cell Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma. 2018-12-20 10.1016/j.cell.2018.11.043 view
Mok Dev. Cell Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent. 2018-12-20 10.1016/j.devcel.2018.11.034 view
van der Wijst Genome Med An integrative approach for building personalized gene regulatory networks for precision medicine. 2018-12-19 10.1186/s13073-018-0608-4 view
Stoeckius Genome Biol. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. 2018-12-19 10.1186/s13059-018-1603-1 7 view
Karmaus Nature Metabolic heterogeneity underlies reciprocal fates of TH17 cell stemness and plasticity. 2018-12-19 10.1038/s41586-018-0806-7 view
Gupta Dev. Cell Single-Cell Analysis Reveals a Hair Follicle Dermal Niche Molecular Differentiation Trajectory that Begins Prior to Morphogenesis. 2018-12-19 10.1016/j.devcel.2018.11.032 view
Egli Immunogenetics The genomic organization and expression pattern of the low-affinity Fc gamma receptors (FcγR) in the Göttingen minipig. 2018-12-18 10.1007/s00251-018-01099-1 1 view
Garieri Proc. Natl. Acad. Sci. U.S.A. Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts. 2018-12-18 10.1073/pnas.1806811115 view
Henry Cell Rep A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. 2018-12-18 10.1016/j.celrep.2018.11.086 view
Wang Genomics Proteomics Bioinformatics VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder. 2018-12-18 10.1016/j.gpb.2018.08.003 view
Saikia Nat. Methods Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells. 2018-12-17 10.1038/s41592-018-0259-9 view
Shema Nat. Genet. Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution. 2018-12-17 10.1038/s41588-018-0290-x 1 view
Reyfman Am. J. Respir. Crit. Care Med. Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis. 2018-12-15 10.1164/rccm.201712-2410OC view
Westerlund Biochem. Biophys. Res. Commun. EPAS1/HIF2α correlates with features of low-risk neuroblastoma and with adrenal chromaffin cell differentiation during sympathoadrenal development. 2018-12-15 10.1016/j.bbrc.2018.12.076 view
Croote Science High-affinity allergen-specific human antibodies cloned from single IgE B cell transcriptomes. 2018-12-14 10.1126/science.aau2599 view
Yang BMC Syst Biol MISC: missing imputation for single-cell RNA sequencing data. 2018-12-14 10.1186/s12918-018-0638-y 1 view
Yu Cytometry A An integrated enrichment system to facilitate isolation and molecular characterization of single cancer cells from whole blood. 2018-12-14 10.1002/cyto.a.23599 1 view
Schlenner Ann. Rheum. Dis. NFIL3 mutations alter immune homeostasis and sensitise for arthritis pathology. 2018-12-14 10.1136/annrheumdis-2018-213764 view
Freedman Nephron Better Being Single? Omics Improves Kidney Organoids. 2018-12-14 10.1159/000496009 view
Wang Cell Metab. Single-Cell RNA-Seq of the Pancreatic Islets--a Promise Not yet Fulfilled? 2018-12-14 10.1016/j.cmet.2018.11.016 2 view
Wu Haematologica Long noncoding RNAs of single hematopoietic stem and progenitor cells in healthy and dysplastic human bone marrow. 2018-12-13 10.3324/haematol.2018.208926 view
Collin Stem Cells Deconstructing Retinal Organoids: Single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina. 2018-12-12 10.1002/stem.2963 view
Thier Cell Stem Cell Identification of Embryonic Neural Plate Border Stem Cells and Their Generation by Direct Reprogramming from Adult Human Blood Cells. 2018-12-12 10.1016/j.stem.2018.11.015 view
Sa Int. J. Cancer Hypermutagenesis in untreated adult gliomas due to inherited mismatch mutations. 2018-12-11 10.1002/ijc.32054 view
Mann Cell Rep Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli Are Altered with Age. 2018-12-11 10.1016/j.celrep.2018.11.056 view
Hao Bioinformatics Optimal Gene Filtering for Single-Cell data (OGFSC) - a gene filtering algorithm for single-cell RNA-seq data. 2018-12-10 10.1093/bioinformatics/bty1016 view
da Costa Urol. Oncol. Molecular tumor heterogeneity in muscle invasive bladder cancer: Biomarkers, subtypes, and implications for therapy. 2018-12-08 10.1016/j.urolonc.2018.11.015 view
Hochrein ACS Synth Biol Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology. 2018-12-07 10.1021/acssynbio.8b00424 1 view
Zanini Proc. Natl. Acad. Sci. U.S.A. Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue. 2018-12-07 10.1073/pnas.1813819115 view
Chen Bioinformatics DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data. 2018-12-07 10.1093/bioinformatics/bty1009 view
Kim Bioinformatics In silico error correction improves cfDNA mutation calling. 2018-12-06 10.1093/bioinformatics/bty1004 view
Oetjen JCI Insight Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry. 2018-12-06 10.1172/jci.insight.124928 view
Fujii Cell Stem Cell Human Intestinal Organoids Maintain Self-Renewal Capacity and Cellular Diversity in Niche-Inspired Culture Condition. 2018-12-06 10.1016/j.stem.2018.11.016 view
Li BMC Cancer EGF/EGFR upregulates and cooperates with Netrin-4 to protect glioblastoma cells from DNA damage-induced senescence. 2018-12-04 10.1186/s12885-018-5056-4 view
Leigh Nat Commun Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution. 2018-12-04 10.1038/s41467-018-07604-0 view
Singer Nat Commun Single-cell mutation identification via phylogenetic inference. 2018-12-04 10.1038/s41467-018-07627-7 view
Bartoschek Nat Commun Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing. 2018-12-04 10.1038/s41467-018-07582-3 1 view
Tepe Cell Rep Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons. 2018-12-04 10.1016/j.celrep.2018.11.034 view
Ren Genome Biol. Understanding tumor ecosystems by single-cell sequencing: promises and limitations. 2018-12-03 10.1186/s13059-018-1593-z view
Chen Nat. Med. Myelodysplastic syndrome progression to acute myeloid leukemia at the stem cell level. 2018-12-03 10.1038/s41591-018-0267-4 view
Wu J. Am. Soc. Nephrol. Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis. 2018-12-03 10.1681/ASN.2018090912 view
Becht Nat. Biotechnol. Dimensionality reduction for visualizing single-cell data using UMAP. 2018-12-03 10.1038/nbt.4314 view
McCracken Curr. Opin. Lipidol. Unravelling atherosclerotic heterogeneity by single cell RNA sequencing. 2018-12-01 10.1097/MOL.0000000000000559 view
Shih PLoS ONE Correction: Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq. 2018-12-01 10.1371/journal.pone.0208778 view
Yao PLoS ONE Exploiting antigen receptor information to quantify index switching in single-cell transcriptome sequencing experiments. 2018-12-01 10.1371/journal.pone.0208484 view
Huang Front Oncol Technical Advances in Single-Cell RNA Sequencing and Applications in Normal and Malignant Hematopoiesis. 2018-12-01 10.3389/fonc.2018.00582 view
Bakken PLoS ONE Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. 2018-12-01 10.1371/journal.pone.0209648 view
Sierant Genomics Inform Single-Cell Ssequencing in Cancer: Recent Applications to Immunogenomics and Multi-omics Tools. 2018-12-01 10.5808/GI.2018.16.4.e17 view
Lopez Nat. Methods Deep generative modeling for single-cell transcriptomics. 2018-12-01 10.1038/s41592-018-0229-2 1 view
Ledergor Nat. Med. Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma. 2018-12-01 10.1038/s41591-018-0269-2 view
Massaia Front Cardiovasc Med Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart. 2018-12-01 10.3389/fcvm.2018.00167 view
Peng Cell Inflammatory Cytokine TNFα Promotes the Long-Term Expansion of Primary Hepatocytes in 3D Culture. 2018-11-29 10.1016/j.cell.2018.11.012 1 view
Riemondy Nucleic Acids Res. Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries. 2018-11-29 10.1093/nar/gky1204 view
Barrett Stem Cells Dev. Human Wharton's Jelly Mesenchymal Stem Cells Show Unique Gene Expression Compared to Bone Marrow Mesenchymal Stem Cells Using Single-Cell RNA-Sequencing. 2018-11-28 10.1089/scd.2018.0132 view
Xin Nat Commun Single-cell RNA sequencing unveils an IL-10-producing helper subset that sustains humoral immunity during persistent infection. 2018-11-28 10.1038/s41467-018-07492-4 view
Wu Cell Syst Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding. 2018-11-28 10.1016/j.cels.2018.10.015 view
Garris Immunity Successful Anti-PD-1 Cancer Immunotherapy Requires T Cell-Dendritic Cell Crosstalk Involving the Cytokines IFN-γ and IL-12. 2018-11-27 10.1016/j.immuni.2018.09.024 view
Hadi Nat Commun Macrophage-derived netrin-1 promotes abdominal aortic aneurysm formation by activating MMP3 in vascular smooth muscle cells. 2018-11-27 10.1038/s41467-018-07495-1 view
Ariss Nat Commun Single cell RNA-sequencing identifies a metabolic aspect of apoptosis in Rbf mutant. 2018-11-27 10.1038/s41467-018-07540-z view
Kimmerling Genome Biol. Linking single-cell measurements of mass, growth rate, and gene expression. 2018-11-27 10.1186/s13059-018-1576-0 1 view
Zywitza Cell Rep Single-Cell Transcriptomics Characterizes Cell Types in the Subventricular Zone and Uncovers Molecular Defects Impairing Adult Neurogenesis. 2018-11-27 10.1016/j.celrep.2018.11.003 view
Bancells Nat Microbiol Revisiting the initial steps of sexual development in the malaria parasite Plasmodium falciparum. 2018-11-26 10.1038/s41564-018-0291-7 view
Zheng Mol. Immunol. A complex auxiliary: IL-17/Th17 signaling during type 1 diabetes progression. 2018-11-22 10.1016/j.molimm.2018.11.007 view
Sharma Nat Commun Longitudinal single-cell RNA sequencing of patient-derived primary cells reveals drug-induced infidelity in stem cell hierarchy. 2018-11-22 10.1038/s41467-018-07261-3 view
Alpár Curr. Opin. Neurobiol. Hypothalamic cell diversity: non-neuronal codes for long-distance volume transmission by neuropeptides. 2018-11-21 10.1016/j.conb.2018.10.012 view
Hammond Immunity Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes. 2018-11-21 10.1016/j.immuni.2018.11.004 4 view
Churko Nat Commun Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis. 2018-11-21 10.1038/s41467-018-07333-4 view
Singh Sci Rep Machine learning based classification of cells into chronological stages using single-cell transcriptomics. 2018-11-21 10.1038/s41598-018-35218-5 view
Poirion Nat Commun Using single nucleotide variations in single-cell RNA-seq to identify subpopulations and genotype-phenotype linkage. 2018-11-20 10.1038/s41467-018-07170-5 3 view
Seki DNA Res. Evaluation and application of RNA-Seq by MinION. 2018-11-20 10.1093/dnares/dsy038 2 view
Dura Nucleic Acids Res. scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3' mRNA profiling. 2018-11-20 10.1093/nar/gky1173 view
Czupalla Bio Protoc Collagenase-based Single Cell Isolation of Primary Murine Brain Endothelial Cells Using Flow Cytometry. 2018-11-20 10.21769/BioProtoc.3092 1 view
Lu Cell Rep The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. 2018-11-20 10.1016/j.celrep.2018.10.084 view
Jia Nat Commun Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement. 2018-11-19 10.1038/s41467-018-07307-6 view
Aulicino Nat Commun Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets. 2018-11-19 10.1038/s41467-018-07329-0 view
Lee Sci Rep Detection of correlated hidden factors from single cell transcriptomes using Iteratively Adjusted-SVA (IA-SVA). 2018-11-19 10.1038/s41598-018-35365-9 view
Nelson Nat Commun Publisher Correction: Single-cell RNA-seq reveals cell type-specific transcriptional signatures at the maternal-foetal interface during pregnancy. 2018-11-19 10.1038/ncomms16219 view
Heuvel Hum. Mol. Genet. Single-cell RNA-sequencing in facioscapulohumeral muscular dystrophy disease etiology and development. 2018-11-16 10.1093/hmg/ddy400 view
Chen Bioinformatics pyNVR: Investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction. 2018-11-16 10.1093/bioinformatics/bty950 1 view
Hernández Sci Immunol Single-cell transcriptional analysis reveals ILC-like cells in zebrafish. 2018-11-16 10.1126/sciimmunol.aau5265 view
Lafzi Nat Protoc Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies. 2018-11-16 10.1038/s41596-018-0073-y view
Kimura Cancer Sci. Immunomodulatory activity of lenvatinib contributes to antitumor activity in the Hepa1-6 hepatocellular carcinoma model. 2018-11-16 10.1111/cas.13806 1 view
Zhang Mol. Cell Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems. 2018-11-16 10.1016/j.molcel.2018.10.020 view
Moerman Bioinformatics GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks. 2018-11-15 10.1093/bioinformatics/bty916 view
Hinohara Cancer Cell KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. 2018-11-14 10.1016/j.ccell.2018.10.014 1 view
Nilsson Allergy New insights into the origin of mast cells. 2018-11-14 10.1111/all.13668 view
Kuboki J. Pathol. Single-cell sequencing defines genetic heterogeneity in pancreatic cancer precursor lesions. 2018-11-14 10.1002/path.5194 view
Shifrut Cell Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function. 2018-11-13 10.1016/j.cell.2018.10.024 view
Alavi Nat Commun A web server for comparative analysis of single-cell RNA-seq data. 2018-11-13 10.1038/s41467-018-07165-2 view
Parekh Cell Syst Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout. 2018-11-12 10.1016/j.cels.2018.10.008 view
Vuong PLoS Genet. Single-cell RNA-sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium. 2018-11-12 10.1371/journal.pgen.1007788 1 view
Chen Genome Biol. VIPER: variability-preserving imputation for accurate gene expression recovery in single-cell RNA sequencing studies. 2018-11-12 10.1186/s13059-018-1575-1 1 view
Behjati Ardakani Epigenetics Chromatin Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters. 2018-11-10 10.1186/s13072-018-0236-7 view
Balboa Elife Insulin mutations impair beta-cell development in a patient-derived iPSC model of neonatal diabetes. 2018-11-09 10.7554/eLife.38519 1 view
Zhu Elife T-ALL leukemia stem cell 'stemness' is epigenetically controlled by the master regulator SPI1. 2018-11-09 10.7554/eLife.38314 view
Khong Stem Cells Single-Cell Transcriptomics of Human Mesenchymal Stem Cells Reveal Age-Related Cellular Subpopulation Depletion and Impaired Regenerative Function. 2018-11-09 10.1002/stem.2934 view
Boroviak Development Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development. 2018-11-09 10.1242/dev.167833 1 view
Jindal Nat Commun Discovery of rare cells from voluminous single cell expression data. 2018-11-09 10.1038/s41467-018-07234-6 view
Lu J Mol Cell Biol Single-cell analyses identify distinct and intermediate states of zebrafish pancreatic islet development. 2018-11-08 10.1093/jmcb/mjy064 1 view
Jones Cell Stem Cell Quantitative Clonal Analysis and Single-Cell Transcriptomics Reveal Division Kinetics, Hierarchy, and Fate of Oral Epithelial Progenitor Cells. 2018-11-07 10.1016/j.stem.2018.10.015 view
Westoby Genome Biol. Simulation-based benchmarking of isoform quantification in single-cell RNA-seq. 2018-11-07 10.1186/s13059-018-1571-5 view
Yin J. Biol. Chem. Single-cell RNA-Seq analysis identifies a noncoding interleukin 4 (IL-4) RNA that post-transcriptionally up-regulates IL-4 production in T helper cells. 2018-11-07 10.1074/jbc.RA118.004111 view
Revinski Nat Commun CDC20B is required for deuterosome-mediated centriole production in multiciliated cells. 2018-11-07 10.1038/s41467-018-06768-z view
Kumar Cell Rep Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics. 2018-11-06 10.1016/j.celrep.2018.10.047 view
Talwar Sci Rep AutoImpute: Autoencoder based imputation of single-cell RNA-seq data. 2018-11-05 10.1038/s41598-018-34688-x view
Salzer Cell Identity Noise and Adipogenic Traits Characterize Dermal Fibroblast Aging. 2018-11-03 10.1016/j.cell.2018.10.012 2 view
Wang Sci Immunol Combination cancer immunotherapy targeting PD-1 and GITR can rescue CD8+ T cell dysfunction and maintain memory phenotype. 2018-11-02 10.1126/sciimmunol.aat7061 view
Bajpai Circ. Res. Tissue Resident CCR2- and CCR2+ Cardiac Macrophages Differentially Orchestrate Monocyte Recruitment and Fate Specification Following Myocardial Injury. 2018-11-02 10.1161/CIRCRESAHA.118.314028 1 view
Wu Cell Stem Cell Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics. 2018-11-01 10.1016/j.stem.2018.10.010 4 view
Durruthy-Durruthy Front Genet Single Cell Transcriptomics Reveal Abnormalities in Neurosensory Patterning of the Chd7 Mutant Mouse Ear. 2018-11-01 10.3389/fgene.2018.00473 view
Jusino J Cancer Metastasis Treat Centrosome aberrations and chromosome instability contribute to tumorigenesis and intra-tumor heterogeneity. 2018-11-01 10.20517/2394-4722.2018.24 view
Tasic Nature Shared and distinct transcriptomic cell types across neocortical areas. 2018-11-01 10.1038/s41586-018-0654-5 13 view
Bhaduri Nature Single-cell sequencing paints diverse pictures of the brain. 2018-11-01 10.1038/d41586-018-07027-3 view
Shih PLoS ONE Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq. 2018-11-01 10.1371/journal.pone.0206785 1 view
Moffitt Science Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region. 2018-11-01 10.1126/science.aau5324 11 view
Bernard Clin. Cancer Res. Single Cell Transcriptomics of Pancreatic Cancer Precursors Demonstrates Epithelial and Microenvironmental Heterogeneity as an Early Event in Neoplastic Progression. 2018-11-01 10.1158/1078-0432.CCR-18-1955 4 view
Dobnikar Nat Commun Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels. 2018-11-01 10.1038/s41467-018-06891-x view
Scott Cell Tissue Unit-ed: Lung Cells Team up to Drive Alveolar Macrophage Development. 2018-11-01 10.1016/j.cell.2018.10.031 view
Jerby-Arnon Cell A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. 2018-11-01 10.1016/j.cell.2018.09.006 2 view
Wallrapp Immunol. Rev. Type 2 innate lymphoid cells in the induction and resolution of tissue inflammation. 2018-11-01 10.1111/imr.12702 1 view
Uniken Venema Gastroenterology Single-cell RNA Sequencing of Blood and Ileal T cells From Patients With Crohn's Disease Reveals Tissue-specific Characteristics and Drug Targets. 2018-11-01 10.1053/j.gastro.2018.10.046 view
Jiang Cell Discov Maintenance of human haematopoietic stem and progenitor cells in vitro using a chemical cocktail. 2018-11-01 10.1038/s41421-018-0059-5 view
Yang NPJ Breast Cancer An assessment of prognostic immunity markers in breast cancer. 2018-11-01 10.1038/s41523-018-0088-0 view
McTaggart BioTechniques Chromium sequencing: the doors open for genomics of obligate plant pathogens. 2018-11-01 10.2144/btn-2018-0019 view
Ye Kidney Dis (Basel) Understanding the Biology and Pathogenesis of the Kidney by Single-Cell Transcriptomic Analysis. 2018-11-01 10.1159/000492470 view
Lieberman PLoS ONE Correction: CaSTLe - Classification of single cells by transfer learning: Harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments. 2018-11-01 10.1371/journal.pone.0208349 view
Valdes-Mora Front Immunol Single-Cell Transcriptomics in Cancer Immunobiology: The Future of Precision Oncology. 2018-11-01 10.3389/fimmu.2018.02582 view
See Front Immunol A Single-Cell Sequencing Guide for Immunologists. 2018-11-01 10.3389/fimmu.2018.02425 1 view
Wu PLoS ONE Characterization of sensory neuronal subtypes innervating mouse tongue. 2018-11-01 10.1371/journal.pone.0207069 view
Crinier Immunity High-Dimensional Single-Cell Analysis Identifies Organ-Specific Signatures and Conserved NK Cell Subsets in Humans and Mice. 2018-11-01 10.1016/j.immuni.2018.09.009 2 view
Freytag F1000Res Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data. 2018-11-01 10.12688/f1000research.15809.1 6 view
Bai PLoS ONE Evaluation of the capacities of mouse TCR profiling from short read RNA-seq data. 2018-11-01 10.1371/journal.pone.0207020 view
Bacon Front Immunol Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice. 2018-11-01 10.3389/fimmu.2018.02523 view
Hosoya J. Immunol. High-Throughput Single-Cell Sequencing of both TCR-β Alleles. 2018-10-31 10.4049/jimmunol.1800774 view
Scimone Curr. Biol. foxF-1 Controls Specification of Non-body Wall Muscle and Phagocytic Cells in Planarians. 2018-10-31 10.1016/j.cub.2018.10.030 view
Ackers-Johnson Nat Commun Following hearts, one cell at a time: recent applications of single-cell RNA sequencing to the understanding of heart disease. 2018-10-30 10.1038/s41467-018-06894-8 view
Cembrowski Elife The subiculum is a patchwork of discrete subregions. 2018-10-30 10.7554/eLife.37701 view
Codeluppi Nat. Methods Spatial organization of the somatosensory cortex revealed by osmFISH. 2018-10-30 10.1038/s41592-018-0175-z 3 view
Dominguez Gutierrez Endocrinology Gene Signature of the Human Pancreatic ε-Cell. 2018-10-30 10.1210/en.2018-00833 view
Zhu Nat. Biotechnol. Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. 2018-10-29 10.1038/nbt.4260 1 view
Gerber Science Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration. 2018-10-26 10.1126/science.aaq0681 3 view
Kim Circ. Res. Transcriptome Analysis Reveals Nonfoamy Rather Than Foamy Plaque Macrophages Are Proinflammatory in Atherosclerotic Murine Models. 2018-10-26 10.1161/CIRCRESAHA.118.312804 5 view
Tanaka Cancer Med Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63. 2018-10-26 10.1002/cam4.1828 1 view
Biton Cell T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. 2018-10-26 10.1016/j.cell.2018.10.008 view
Paul J Vis Exp Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing (DIVA-Seq). 2018-10-26 10.3791/58690 view
Suber Respir. Res. FBXO17 promotes cell proliferation through activation of Akt in lung adenocarcinoma cells. 2018-10-25 10.1186/s12931-018-0910-0 view
Sommarin J Vis Exp A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations. 2018-10-25 10.3791/57831 view
Fan J. Exp. Med. CD49b defines functionally mature Treg cells that survey skin and vascular tissues. 2018-10-24 10.1084/jem.20181442 view
Hagai Nature Gene expression variability across cells and species shapes innate immunity. 2018-10-24 10.1038/s41586-018-0657-2 3 view
Athar Nucleic Acids Res. ArrayExpress update - from bulk to single-cell expression data. 2018-10-24 10.1093/nar/gky964 1 view
Raj Nat Protoc Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT. 2018-10-23 10.1038/s41596-018-0058-x view
Mok Cell Rep More Than the Sum of Its Parts: Single-Cell Transcriptomics Reveals Epidermal Cell States. 2018-10-23 10.1016/j.celrep.2018.10.041 view
Cheng Cell Rep Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution. 2018-10-23 10.1016/j.celrep.2018.09.006 2 view
Liu PLoS Biol. Quantitative assessment of cell population diversity in single-cell landscapes. 2018-10-22 10.1371/journal.pbio.2006687 1 view
MacParland Nat Commun Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. 2018-10-22 10.1038/s41467-018-06318-7 1 view
Graham Nat. Med. Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. 2018-10-22 10.1038/s41591-018-0203-7 view
D'Gama Nat. Neurosci. Somatic mosaicism and neurodevelopmental disease. 2018-10-22 10.1038/s41593-018-0257-3 view
Yuan Nucleic Acids Res. CancerSEA: a cancer single-cell state atlas. 2018-10-17 10.1093/nar/gky939 view
Xiao Genome Biol. Holo-Seq: single-cell sequencing of holo-transcriptome. 2018-10-17 10.1186/s13059-018-1553-7 view
Müller Nature Genome organization and DNA accessibility control antigenic variation in trypanosomes. 2018-10-17 10.1038/s41586-018-0619-8 3 view
Cheung Endocrinology Single-cell RNA sequencing reveals novel markers of male pituitary stem cells and hormone-producing cell-types. 2018-10-17 10.1210/en.2018-00750 view
Joost Cell Rep Single-Cell Transcriptomics of Traced Epidermal and Hair Follicle Stem Cells Reveals Rapid Adaptations during Wound Healing. 2018-10-16 10.1016/j.celrep.2018.09.059 2 view
Gubin Cell High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy. 2018-10-16 10.1016/j.cell.2018.09.030 4 view
Subramanian Parimalam Anal. Chem. Electrical Lysis and RNA Extraction from Single Cells Fixed by Dithiobis(succinimidyl propionate). 2018-10-16 10.1021/acs.analchem.8b02338 view
Liu Cancer Res. Circulating glioma cells exhibit stem cell-like properties. 2018-10-15 10.1158/0008-5472.CAN-18-0650 view
Marie Proc. Natl. Acad. Sci. U.S.A. Single-molecule DNA-mapping and whole-genome sequencing of individual cells. 2018-10-15 10.1073/pnas.1804194115 1 view
Owen Nat Commun Single cell RNA-seq reveals profound transcriptional similarity between Barrett's oesophagus and oesophageal submucosal glands. 2018-10-15 10.1038/s41467-018-06796-9 view
Matson J Vis Exp Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing. 2018-10-12 10.3791/58413 view
Guo Cell Res. The adult human testis transcriptional cell atlas. 2018-10-12 10.1038/s41422-018-0099-2 view
Molenaar Circ. Res. Single-Cell Sequencing of the Mammalian Heart. 2018-10-12 10.1161/CIRCRESAHA.118.313531 view
Ó hAinmhire Am. J. Physiol. Renal Physiol. A conditionally immortalized Gli1-positive kidney mesenchymal cell line models myofibroblast transition. 2018-10-10 10.1152/ajprenal.00460.2018 view
Gao Analyst Recent advances in single cell manipulation and biochemical analysis on microfluidics. 2018-10-09 10.1039/c8an01186a view
Sharma Mol. Immunol. Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges. 2018-10-06 10.1016/j.molimm.2018.09.020 view
Shi Brief. Bioinformatics Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures. 2018-10-05 10.1093/bib/bby093 view
Zhang Nucleic Acids Res. CellMarker: a manually curated resource of cell markers in human and mouse. 2018-10-05 10.1093/nar/gky900 1 view
Manh Nguyen Appl. Environ. Microbiol. Effective soil extraction method for cultivating previously uncultured soil bacteria. 2018-10-05 10.1128/AEM.01145-18 view
Upadhaya J. Exp. Med. Kinetics of adult hematopoietic stem cell differentiation in vivo. 2018-10-05 10.1084/jem.20180136 2 view
Kilian J. Biol. Chem. Role of phospholipid synthesis in the development and differentiation of malaria parasites in the blood. 2018-10-04 10.1074/jbc.R118.003213 view
Svensson Mol. Cell RNA Velocity: Molecular Kinetics from Single-Cell RNA-Seq. 2018-10-04 10.1016/j.molcel.2018.09.026 view
Boulais Immunity The Majority of CD45- Ter119- CD31- Bone Marrow Cell Fraction Is of Hematopoietic Origin and Contains Erythroid and Lymphoid Progenitors. 2018-10-04 10.1016/j.immuni.2018.08.019 1 view
Wurmus Gigascience PiGx: Reproducible genomics analysis pipelines with GNU Guix. 2018-10-02 10.1093/gigascience/giy123 view
Bradley Cell Rep Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency. 2018-10-02 10.1016/j.celrep.2018.09.020 view
Qiu Nat. Med. Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease. 2018-10-01 10.1038/s41591-018-0194-4 7 view
Bresciani MethodsX An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae. 2018-10-01 10.1016/j.mex.2018.10.009 1 view
Peng F1000Res Regulatory network characterization in development: challenges and opportunities. 2018-10-01 10.12688/f1000research.15271.1 view
Cho Lett Biomath Modelling acute myeloid leukaemia in a continuum of differentiation states. 2018-10-01 10.1080/23737867.2018.1472532 1 view
Brancucci Wellcome Open Res Probing Plasmodium falciparum sexual commitment at the single-cell level. 2018-10-01 10.12688/wellcomeopenres.14645.4 view
Duò F1000Res A systematic performance evaluation of clustering methods for single-cell RNA-seq data. 2018-10-01 10.12688/f1000research.15666.2 6 view
Liang Comput Struct Biotechnol J A Review of Matched-pairs Feature Selection Methods for Gene Expression Data Analysis. 2018-10-01 10.1016/j.csbj.2018.02.005 2 view
Guo Nat. Med. Publisher Correction: Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. 2018-10-01 10.1038/s41591-018-0167-7 1 view
Lieberman PLoS ONE CaSTLe - Classification of single cells by transfer learning: Harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments. 2018-10-01 10.1371/journal.pone.0205499 1 view
Suryawanshi Sci Adv A single-cell survey of the human first-trimester placenta and decidua. 2018-10-01 10.1126/sciadv.aau4788 1 view
Apostolidis Front Immunol Single Cell RNA Sequencing Identifies HSPG2 and APLNR as Markers of Endothelial Cell Injury in Systemic Sclerosis Skin. 2018-10-01 10.3389/fimmu.2018.02191 view
Bryan Hum. Mol. Genet. Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks. 2018-10-01 10.1093/hmg/ddy239 view
Mays PLoS ONE Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression. 2018-10-01 10.1371/journal.pone.0205883 1 view
Tripathy Front Mol Neurosci Assessing Transcriptome Quality in Patch-Seq Datasets. 2018-10-01 10.3389/fnmol.2018.00363 view
Li J Vis Exp Single-cell Transcriptomic Analyses of Mouse Pancreatic Endocrine Cells. 2018-09-30 10.3791/58000 view
Chambers Respirology Transcriptomics and single-cell RNA-sequencing. 2018-09-28 10.1111/resp.13412 view
Hepler Elife Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice. 2018-09-28 10.7554/eLife.39636 3 view
Nirmal Cancer Immunol Res Immune cell gene signatures for profiling the microenvironment of solid tumors. 2018-09-28 10.1158/2326-6066.CIR-18-0342 1 view
Meilhac Nat Rev Cardiol The deployment of cell lineages that form the mammalian heart. 2018-09-28 10.1038/s41569-018-0086-9 1 view
Biase iScience Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos. 2018-09-28 10.1016/j.isci.2018.08.009 view
Daniszewski iScience Single-Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media. 2018-09-28 10.1016/j.isci.2018.08.016 view
Cohen Cell Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting. 2018-09-28 10.1016/j.cell.2018.09.009 5 view
Ranu Nucleic Acids Res. Targeting individual cells by barcode in pooled sequence libraries. 2018-09-26 10.1093/nar/gky856 1 view
Tischler EMBO J. Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate. 2018-09-26 10.15252/embj.201899518 1 view
Arneson Nat Commun Single cell molecular alterations reveal target cells and pathways of concussive brain injury. 2018-09-25 10.1038/s41467-018-06222-0 view
Byrnes Nat Commun Lineage dynamics of murine pancreatic development at single-cell resolution. 2018-09-25 10.1038/s41467-018-06176-3 2 view
Pezoldt Nat Commun Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes. 2018-09-25 10.1038/s41467-018-06423-7 view
Wang Cell Rep Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing. 2018-09-25 10.1016/j.celrep.2018.08.056 3 view
Avey Cell Rep Single-Cell RNA-Seq Uncovers a Robust Transcriptional Response to Morphine by Glia. 2018-09-25 10.1016/j.celrep.2018.08.080 view
Paulson Nat Commun Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA. 2018-09-24 10.1038/s41467-018-06300-3 3 view
AlJanahi Mol Ther Methods Clin Dev An Introduction to the Analysis of Single-Cell RNA-Sequencing Data. 2018-09-21 10.1016/j.omtm.2018.07.003 4 view
Jin JCI Insight Chronic infection stunts macrophage heterogeneity and disrupts immune-mediated myogenesis. 2018-09-20 10.1172/jci.insight.121549 view
Farhadian JCI Insight Single-cell RNA sequencing reveals microglia-like cells in cerebrospinal fluid during virologically suppressed HIV. 2018-09-20 10.1172/jci.insight.121718 view
Florian PLoS Biol. Aging alters the epigenetic asymmetry of HSC division. 2018-09-20 10.1371/journal.pbio.2003389 2 view
Leung Genome Med Single-cell transcriptomics reveal that PD-1 mediates immune tolerance by regulating proliferation of regulatory T cells. 2018-09-20 10.1186/s13073-018-0581-y view
Elias J. Pathol. Primordial germ cells as a potential shared cell of origin for mucinous cystic neoplasms of the pancreas and mucinous ovarian tumors. 2018-09-19 10.1002/path.5161 view
Tong Cancer Commun (Lond) Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells. 2018-09-19 10.1186/s40880-018-0326-8 1 view
Song Sci Rep Genetic and scRNA-seq Analysis Reveals Distinct Cell Populations that Contribute to Salivary Gland Development and Maintenance. 2018-09-19 10.1038/s41598-018-32343-z view
Horie Genes Dev. Regulatory cocktail for dopaminergic neurons in a protovertebrate identified by whole-embryo single-cell transcriptomics. 2018-09-18 10.1101/gad.317669.118 2 view
Shang Gigascience Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation. 2018-09-18 10.1093/gigascience/giy117 view
Lindström Am. J. Kidney Dis. Single-Cell RNA Sequencing of the Adult Mouse Kidney: From Molecular Cataloging of Cell Types to Disease-Associated Predictions. 2018-09-18 10.1053/j.ajkd.2018.07.002 view
Halpern Nat. Biotechnol. Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells. 2018-09-17 10.1038/nbt.4231 3 view
Cunha Cell LC3-Associated Phagocytosis in Myeloid Cells Promotes Tumor Immune Tolerance. 2018-09-17 10.1016/j.cell.2018.08.061 3 view
Wu Cancer Lett. Single-cell RNA sequencing reveals diverse intratumoral heterogeneities and gene signatures of two types of esophageal cancers. 2018-09-14 10.1016/j.canlet.2018.09.017 view
Zeng Stem Cell Res Ther Revealing cellular and molecular complexity of the central nervous system using single cell sequencing. 2018-09-13 10.1186/s13287-018-0985-z view
Duan Neuron PDGFRβ Cells Rapidly Relay Inflammatory Signal from the Circulatory System to Neurons via Chemokine CCL2. 2018-09-12 10.1016/j.neuron.2018.08.030 1 view
Petitpré Nat Commun Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system. 2018-09-12 10.1038/s41467-018-06033-3 2 view
Li Stem Cells Transl Med Generation of Functional Hepatocytes from Human Adipose-Derived MYC+ KLF4+ GMNN+ Stem Cells Analyzed by Single-Cell RNA-Seq Profiling. 2018-09-11 10.1002/sctm.17-0273 view
Lukassen Sci Data Single-cell RNA sequencing of adult mouse testes. 2018-09-11 10.1038/sdata.2018.192 view
Grootens Blood Adv Deciphering the differentiation trajectory from hematopoietic stem cells to mast cells. 2018-09-11 10.1182/bloodadvances.2018019539 1 view
Sousa EMBO Rep. Single-cell transcriptomics reveals distinct inflammation-induced microglia signatures. 2018-09-11 10.15252/embr.201846171 view
Costa Nat Commun GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge. 2018-09-11 10.1038/s41467-018-05988-7 view
Gruber Nat. Methods Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. 2018-09-10 10.1038/s41592-018-0114-z view
Sloan Nat Protoc Generation and assembly of human brain region-specific three-dimensional cultures. 2018-09-10 10.1038/s41596-018-0032-7 2 view
Carter Curr. Biol. A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum. 2018-09-10 10.1016/j.cub.2018.07.062 1 view
Yang Bioinformatics SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data. 2018-09-08 10.1093/bioinformatics/bty793 2 view
Birnbaum Annu. Rev. Genet. Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues. 2018-09-07 10.1146/annurev-genet-120417-031247 1 view
Gokey JCI Insight MEG3 is increased in idiopathic pulmonary fibrosis and regulates epithelial cell differentiation. 2018-09-06 10.1172/jci.insight.122490 view
Sabbagh Elife Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells. 2018-09-06 10.7554/eLife.36187 1 view
Fan Dev. Cell Single Cell and Open Chromatin Analysis Reveals Molecular Origin of Epidermal Cells of the Skin. 2018-09-06 10.1016/j.devcel.2018.08.010 2 view
Volpato Stem Cell Reports Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study. 2018-09-06 10.1016/j.stemcr.2018.08.013 1 view
Tay Acta Neuropathol Commun Unique microglia recovery population revealed by single-cell RNAseq following neurodegeneration. 2018-09-05 10.1186/s40478-018-0584-3 1 view
Chiu Development A novel role for Lyl1 in primitive erythropoiesis. 2018-09-05 10.1242/dev.162990 view
Karaayvaz Nat Commun Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. 2018-09-04 10.1038/s41467-018-06052-0 5 view
Sena Sci Rep Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis. 2018-09-03 10.1038/s41598-018-31064-7 view
Kadnikov Syst. Appl. Microbiol. Phylogeny and physiology of candidate phylum BRC1 inferred from the first complete metagenome-assembled genome obtained from deep subsurface aquifer. 2018-09-03 10.1016/j.syapm.2018.08.013 view
Camp Nat. Methods Single-cell genomics to guide human stem cell and tissue engineering. 2018-09-01 10.1038/s41592-018-0113-0 1 view
Bloom PeerJ Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments. 2018-09-01 10.7717/peerj.5578 view
Mars Brisbin Front Microbiol Intra-host Symbiont Diversity and Extended Symbiont Maintenance in Photosymbiotic Acantharea (Clade F). 2018-09-01 10.3389/fmicb.2018.01998 view
Lythe Immunol. Rev. Some deterministic and stochastic mathematical models of naïve T-cell homeostasis. 2018-09-01 10.1111/imr.12696 1 view
Nguyen Front Cell Dev Biol Experimental Considerations for Single-Cell RNA Sequencing Approaches. 2018-09-01 10.3389/fcell.2018.00108 2 view
Vanlandewijck Methods Mol. Biol. Single-Cell mRNA Sequencing of the Mouse Brain Vasculature. 2018-09-01 10.1007/978-1-4939-8712-2_21 view
El-Kebir Bioinformatics SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error. 2018-09-01 10.1093/bioinformatics/bty589 view
Miura Bioinformatics Computational enhancement of single-cell sequences for inferring tumor evolution. 2018-09-01 10.1093/bioinformatics/bty571 view
Puram Mol Cell Oncol Single cell RNA-seq highlights a role for a partial EMT in head and neck cancer. 2018-09-01 10.1080/23723556.2018.1448244 view
Menon Development Single-cell analysis of progenitor cell dynamics and lineage specification in the human fetal kidney. 2018-08-30 10.1242/dev.164038 view
Klum EMBO Rep. Sequentially acting SOX proteins orchestrate astrocyte- and oligodendrocyte-specific gene expression. 2018-08-30 10.15252/embr.201846635 view
Cacchiarelli Cell Syst Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. 2018-08-30 10.1016/j.cels.2018.07.006 view
Eling Cell Syst Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data. 2018-08-29 10.1016/j.cels.2018.06.011 1 view
Zhu Cell Rep Identification of an Early Unipotent Neutrophil Progenitor with Pro-tumoral Activity in Mouse and Human Bone Marrow. 2018-08-28 10.1016/j.celrep.2018.07.097 2 view
Karki Cell Rep Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories. 2018-08-28 10.1016/j.celrep.2018.07.091 1 view
Buus Blood Adv Single-cell heterogeneity in Sézary syndrome. 2018-08-28 10.1182/bloodadvances.2018022608 view
Liu Genome Res. Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos. 2018-08-28 10.1101/gr.233437.117 view
Brummelman J. Exp. Med. High-dimensional single cell analysis identifies stem-like cytotoxic CD8+ T cells infiltrating human tumors. 2018-08-28 10.1084/jem.20180684 view
Hu Blood A cloning and expression system to probe T cell receptor specificity and assess functional avidity to neoantigens. 2018-08-27 10.1182/blood-2018-04-843763 3 view
Wang Cell Stem Cell Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis. 2018-08-24 10.1016/j.stem.2018.08.007 2 view
Swapna Genome Biol. Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. 2018-08-24 10.1186/s13059-018-1498-x view
Habiel JCI Insight CCR10+ epithelial cells from idiopathic pulmonary fibrosis lungs drive remodeling. 2018-08-23 10.1172/jci.insight.122211 view
Wu BMC Genomics Long non-coding RNAs potentially function synergistically in the cellular reprogramming of SCNT embryos. 2018-08-23 10.1186/s12864-018-5021-2 view
Crow Trends Genet. Co-expression in Single-Cell Analysis: Saving Grace or Original Sin? 2018-08-23 10.1016/j.tig.2018.07.007 1 view
Lall J. Comput. Biol. Structure-Aware Principal Component Analysis for Single-Cell RNA-seq Data. 2018-08-22 10.1089/cmb.2018.0027 1 view
Scavuzzo Nat Commun Endocrine lineage biases arise in temporally distinct endocrine progenitors during pancreatic morphogenesis. 2018-08-22 10.1038/s41467-018-05740-1 1 view
Kim Brief. Bioinformatics Impact of similarity metrics on single-cell RNA-seq data clustering. 2018-08-22 10.1093/bib/bby076 1 view
He Sci Data Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types. 2018-08-21 10.1038/sdata.2018.160 3 view
Muñoz-Manchado Cell Rep Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq. 2018-08-21 10.1016/j.celrep.2018.07.053 3 view
Green Dev. Cell A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq. 2018-08-21 10.1016/j.devcel.2018.07.025 6 view
Hines Protist Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records. 2018-08-20 10.1016/j.protis.2018.08.001 view
Wimmers Nat Commun Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells. 2018-08-20 10.1038/s41467-018-05784-3 1 view
Chen Protein Cell Dgcr8 deletion in the primitive heart uncovered novel microRNA regulating the balance of cardiac-vascular gene program. 2018-08-20 10.1007/s13238-018-0572-1 view
Mazza Cytometry A Background fluorescence and spreading error are major contributors of variability in high-dimensional flow cytometry data visualization by t-distributed stochastic neighboring embedding. 2018-08-14 10.1002/cyto.a.23566 1 view
Vanuytsel Blood Adv Induced pluripotent stem cell-based mapping of β-globin expression throughout human erythropoietic development. 2018-08-14 10.1182/bloodadvances.2018020560 view
Balan Cell Rep Large-Scale Human Dendritic Cell Differentiation Revealing Notch-Dependent Lineage Bifurcation and Heterogeneity. 2018-08-14 10.1016/j.celrep.2018.07.033 2 view
Moussa BMC Genomics Single cell RNA-seq data clustering using TF-IDF based methods. 2018-08-13 10.1186/s12864-018-4922-4 3 view
Zhang PLoS Comput. Biol. SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks. 2018-08-13 10.1371/journal.pcbi.1006369 view
Kim Sci Rep In situ transcriptome characteristics are lost following culture adaptation of adult cardiac stem cells. 2018-08-13 10.1038/s41598-018-30551-1 3 view
Tian PLoS Comput. Biol. scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data. 2018-08-10 10.1371/journal.pcbi.1006361 8 view
Oldham Cell Sequencing Diversity One Cell at a Time. 2018-08-09 10.1016/j.cell.2018.07.024 2 view
La Manno Nature RNA velocity of single cells. 2018-08-08 10.1038/s41586-018-0414-6 view
Kim Nucleic Acids Res. CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type. 2018-08-08 10.1093/nar/gky698 view
Pellegrino Genome Res. High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics. 2018-08-07 10.1101/gr.232272.117 view
Hwang Exp. Mol. Med. Single-cell RNA sequencing technologies and bioinformatics pipelines. 2018-08-07 10.1038/s12276-018-0071-8 3 view
Ngara Exp. Cell Res. Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum parasites. 2018-08-07 10.1016/j.yexcr.2018.08.003 view
Yu PLoS Comput. Biol. A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data. 2018-08-06 10.1371/journal.pcbi.1006391 view
Li Mol. Cancer Res. Dissecting lncRNA Roles in Renal Cell Carcinoma Metastasis and Characterizing Genomic Heterogeneity by Single-cell RNA-seq. 2018-08-06 10.1158/1541-7786.MCR-17-0776 1 view
McDonald Cell Stem Cell Endothelial Regeneration of Large Vessels Is a Biphasic Process Driven by Local Cells with Distinct Proliferative Capacities. 2018-08-02 10.1016/j.stem.2018.07.011 11 view
Montoro Nature A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. 2018-08-01 10.1038/s41586-018-0393-7 19 view
Horie Nature Shared evolutionary origin of vertebrate neural crest and cranial placodes. 2018-08-01 10.1038/s41586-018-0385-7 3 view
Lee Nature Human glioblastoma arises from subventricular zone cells with low-level driver mutations. 2018-08-01 10.1038/s41586-018-0389-3 8 view
De Simone Front Immunol Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges. 2018-08-01 10.3389/fimmu.2018.01638 view
Schalck Trends Mol Med Resident Breast T Cells: The Troops Are Already There. 2018-08-01 10.1016/j.molmed.2018.07.006 view
Marques Dev. Cell Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development. 2018-08-01 10.1016/j.devcel.2018.07.005 3 view
Roy Sci Adv Accelerating a paradigm shift: The Common Fund Single Cell Analysis Program. 2018-08-01 10.1126/sciadv.aat8573 view
Sampath Front Immunol Monocyte Subsets: Phenotypes and Function in Tuberculosis Infection. 2018-08-01 10.3389/fimmu.2018.01726 1 view
Parsons Mutat. Res. Multiclonal tumor origin: Evidence and implications. 2018-08-01 10.1016/j.mrrev.2018.05.001 2 view
Kramer eNeuro Combinatorial Expression of Grp and Neurod6 Defines Dopamine Neuron Populations with Distinct Projection Patterns and Disease Vulnerability. 2018-08-01 10.1523/ENEURO.0152-18.2018 view
van den Hurk Front Mol Neurosci Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells. 2018-08-01 10.3389/fnmol.2018.00261 view
Elion Trends Mol Med Genetic and Phenotypic Diversification of Heterogeneous Tumor Populations. 2018-08-01 10.1016/j.molmed.2018.06.003 view
Lindeman Nat. Methods BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq. 2018-08-01 10.1038/s41592-018-0082-3 4 view
Nawy Nat. Methods Tumor genetic analysis from single-cell RNA-seq data. 2018-08-01 10.1038/s41592-018-0089-9 view
Simpson Hum. Gene Ther. New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina. 2018-07-31 10.1089/hum.2018.118 1 view
Yamashita PLoS Genet. High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor. 2018-07-31 10.1371/journal.pgen.1007552 view
Tao Biomed. Pharmacother. Inhibition of EP300 and DDR1 synergistically alleviates pulmonary fibrosis in vitro and in vivo. 2018-07-30 10.1016/j.biopha.2018.07.132 view
Ho Genome Res. Single-cell RNA-seq analysis identifies markers of resistance to targeted BRAF inhibitors in melanoma cell populations. 2018-07-30 10.1101/gr.234062.117 1 view
Chen Cell Res. Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis. 2018-07-30 10.1038/s41422-018-0074-y 5 view
Salehi Hear. Res. Detection of single mRNAs in individual cells of the auditory system. 2018-07-29 10.1016/j.heares.2018.07.008 view
Spangler Stem Cell Res A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo. 2018-07-29 10.1016/j.scr.2018.07.022 view
Shrestha Cell Sensory Neuron Diversity in the Inner Ear Is Shaped by Activity. 2018-07-28 10.1016/j.cell.2018.07.007 8 view
Sadahiro Cell Stem Cell Tbx6 Induces Nascent Mesoderm from Pluripotent Stem Cells and Temporally Controls Cardiac versus Somite Lineage Diversification. 2018-07-26 10.1016/j.stem.2018.07.001 2 view
Dziewulska Genes (Basel) High-Throughput Approaches onto Uncover (Epi)Genomic Architecture of Type 2 Diabetes. 2018-07-26 10.3390/genes9080374 3 view
Bagnoli Nat Commun Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq. 2018-07-26 10.1038/s41467-018-05347-6 3 view
Strauß Bioinformatics GPseudoRank: a permutation sampler for single cell orderings. 2018-07-25 10.1093/bioinformatics/bty664 view
Gracz Gastroenterology SOX4 Promotes ATOH1-independent Intestinal Secretory Differentiation Toward Tuft and Enteroendocrine Fates. 2018-07-25 10.1053/j.gastro.2018.07.023 2 view
Liu Micromachines (Basel) The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms. 2018-07-25 10.3390/mi9080367 1 view
Yuan Genome Med Single-cell transcriptome analysis of lineage diversity in high-grade glioma. 2018-07-24 10.1186/s13073-018-0567-9 4 view
Liu Cell Res. Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta. 2018-07-24 10.1038/s41422-018-0066-y 5 view
Severo Proc. Natl. Acad. Sci. U.S.A. Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging. 2018-07-23 10.1073/pnas.1803062115 5 view
Gao Nat. Cell Biol. Publisher Correction: Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. 2018-07-23 10.1038/s41556-018-0165-5 view
Gillies Am. J. Hum. Genet. An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome. 2018-07-20 10.1016/j.ajhg.2018.07.004 7 view
Ji Ann. Rheum. Dis. Single-cell RNA-seq analysis reveals the progression of human osteoarthritis. 2018-07-19 10.1136/annrheumdis-2017-212863 1 view
Lee Semin. Cancer Biol. Comparison of glioblastoma (GBM) molecular classification methods. 2018-07-19 10.1016/j.semcancer.2018.07.006 4 view
Zhao Reprod. Fertil. Dev. Single-cell RNA sequencing reveals distinct gene expression patterns in glucose metabolism of human preimplantation embryos. 2018-07-18 10.1071/RD18178 view
Bornstein Nature Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells. 2018-07-18 10.1038/s41586-018-0346-1 3 view
Chen J Transl Med PBMC fixation and processing for Chromium single-cell RNA sequencing. 2018-07-17 10.1186/s12967-018-1578-4 view
Rheaume Nat Commun Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes. 2018-07-17 10.1038/s41467-018-05134-3 9 view
Lauridsen Cell Rep Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment. 2018-07-17 10.1016/j.celrep.2018.06.057 1 view
Winkels Curr. Opin. Lipidol. Atherosclerosis in the single-cell era. 2018-07-16 10.1097/MOL.0000000000000537 view
Wang J. Clin. Invest. Expansion of hedgehog disrupts mesenchymal identity and induces emphysema phenotype. 2018-07-12 10.1172/JCI99435 view
Kretzler J. Am. Soc. Nephrol. Single-Cell Sequencing the Glomerulus, Unraveling the Molecular Programs of Glomerular Filtration, One Cell at a Time. 2018-07-12 10.1681/ASN.2018060626 1 view
Suyama J Physiol Sci New insight into GABAergic neurons in the hypothalamic feeding regulation. 2018-07-12 10.1007/s12576-018-0622-8 view
Rulands Cell Syst Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency. 2018-07-12 10.1016/j.cels.2018.06.012 2 view
Ayabe Stem Cell Reports Optimal Hypoxia Regulates Human iPSC-Derived Liver Bud Differentiation through Intercellular TGFB Signaling. 2018-07-12 10.1016/j.stemcr.2018.06.015 1 view
Donlin Arthritis Res. Ther. Methods for high-dimensonal analysis of cells dissociated from cyropreserved synovial tissue. 2018-07-11 10.1186/s13075-018-1631-y 2 view
Packer Trends Genet. Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation. 2018-07-11 10.1016/j.tig.2018.06.001 view
Zappia Gigascience Clustering trees: a visualisation for evaluating clusterings at multiple resolutions. 2018-07-11 10.1093/gigascience/giy083 5 view
Dominguez Gutierrez Endocrinology Gene Signature of Proliferating Human Pancreatic α-Cells. 2018-07-11 10.1210/en.2018-00469 view
Dasgupta Biophys. J. Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics. 2018-07-11 10.1016/j.bpj.2018.07.003 view
Moroz ACS Chem Neurosci NeuroSystematics and Periodic System of Neurons: Model vs Reference Species at Single-cell Resolution. 2018-07-10 10.1021/acschemneuro.8b00100 4 view
Griffiths Nat Commun Detection and removal of barcode swapping in single-cell RNA-seq data. 2018-07-10 10.1038/s41467-018-05083-x 2 view
Paik Circ. Res. Large-Scale Single-Cell RNA-Seq Reveals Molecular Signatures of Heterogeneous Populations of Human Induced Pluripotent Stem Cell-Derived Endothelial Cells. 2018-07-09 10.1161/CIRCRESAHA.118.312913 5 view
Wu Proc. Natl. Acad. Sci. U.S.A. Scleral hypoxia is a target for myopia control. 2018-07-09 10.1073/pnas.1721443115 1 view
Duren Proc. Natl. Acad. Sci. U.S.A. Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations. 2018-07-09 10.1073/pnas.1805681115 2 view
Yang Sci Immunol Metabolic signaling directs the reciprocal lineage decisions of αβ and γδ T cells. 2018-07-06 10.1126/sciimmunol.aas9818 5 view
Wu J. Am. Soc. Nephrol. Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response. 2018-07-06 10.1681/ASN.2018020125 9 view
Rambow Cell Toward Minimal Residual Disease-Directed Therapy in Melanoma. 2018-07-06 10.1016/j.cell.2018.06.025 9 view
Stosch Br. J. Haematol. Gene mutations and clonal architecture in myelodysplastic syndromes and changes upon progression to acute myeloid leukaemia and under treatment. 2018-07-05 10.1111/bjh.15461 view
Su Nature Single-cell analysis of early progenitor cells that build coronary arteries. 2018-07-04 10.1038/s41586-018-0288-7 5 view
Patel Bioinformatics iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data. 2018-07-04 10.1093/bioinformatics/bty517 view
Okawa Nat Commun Transcriptional synergy as an emergent property defining cell subpopulation identity enables population shift. 2018-07-03 10.1038/s41467-018-05016-8 view
Smithey Proc. Natl. Acad. Sci. U.S.A. Lifelong CMV infection improves immune defense in old mice by broadening the mobilized TCR repertoire against third-party infection. 2018-07-02 10.1073/pnas.1719451115 4 view
Tang-Huau Nat Commun Human in vivo-generated monocyte-derived dendritic cells and macrophages cross-present antigens through a vacuolar pathway. 2018-07-02 10.1038/s41467-018-04985-0 5 view
Tekin Nat Biomed Eng Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons. 2018-07-01 10.1038/s41551-018-0219-9 6 view
Nguyen Front Immunol Single Cell RNA Sequencing of Rare Immune Cell Populations. 2018-07-01 10.3389/fimmu.2018.01553 6 view
Liang Evid Based Complement Alternat Med Zuo Gui Wan Alters Expression of Energy Metabolism Genes and Prevents Cell Death in High-Glucose Loaded Mouse Embryos. 2018-07-01 10.1155/2018/2409471 view
Clement Bioinformatics AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. 2018-07-01 10.1093/bioinformatics/bty264 view
Mukherjee Bioinformatics Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge. 2018-07-01 10.1093/bioinformatics/bty293 2 view
Pouyan Bioinformatics Random forest based similarity learning for single cell RNA sequencing data. 2018-07-01 10.1093/bioinformatics/bty260 2 view
Menon Brief Funct Genomics Clustering single cells: a review of approaches on high-and low-depth single-cell RNA-seq data. 2018-07-01 10.1093/bfgp/elx044 10 view
Borensztein Methods Mol. Biol. Transcriptome Profiling of Single Mouse Oocytes. 2018-07-01 10.1007/978-1-4939-8603-3_7 view
Bradley Front Immunol Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis. 2018-07-01 10.3389/fimmu.2018.01444 view
Ho Front Cell Neurosci A Guide to Single-Cell Transcriptomics in Adult Rodent Brain: The Medium Spiny Neuron Transcriptome Revisited. 2018-07-01 10.3389/fncel.2018.00159 view
Chen Conf Proc IEEE Eng Med Biol Soc Single-Cell Transcriptomics Reveals Heterogeneity and Drug Response of Human Colorectal Cancer Organoids. 2018-07-01 10.1109/EMBC.2018.8512784 view
Mukherjee Conf Proc IEEE Eng Med Biol Soc Identifying progressive gene network perturbation from single-cell RNA-seq data. 2018-07-01 10.1109/EMBC.2018.8513444 view
Li Neuroreport A novel long noncoding RNA lnc158 promotes the differentiation of mouse neural precursor cells into oligodendrocytes by targeting nuclear factor-IB. 2018-06-30 10.1097/WNR.0000000000001083 view
Lin Acta Neuropathol Commun Non-inflammatory tumor microenvironment of diffuse intrinsic pontine glioma. 2018-06-28 10.1186/s40478-018-0553-x 6 view
Baron Nat Commun Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta. 2018-06-28 10.1038/s41467-018-04893-3 3 view
Lukowski J. Invest. Dermatol. Detection of HPV E7 transcription at single-cell resolution in epidermis. 2018-06-28 10.1016/j.jid.2018.06.169 view
Fletcher Bioessays Creating Lineage Trajectory Maps Via Integration of Single-Cell RNA-Sequencing and Lineage Tracing: Integrating transgenic lineage tracing and single-cell RNA-sequencing is a robust approach for mapping developmental lineage trajectories and cell fate changes. 2018-06-26 10.1002/bies.201800056 3 view
Wang Proc. Natl. Acad. Sci. U.S.A. Gene expression distribution deconvolution in single-cell RNA sequencing. 2018-06-26 10.1073/pnas.1721085115 7 view
Cristea Nat Commun Dissecting the mammary gland one cell at a time. 2018-06-26 10.1038/s41467-018-04905-2 view
Zhang Biophys. J. Recent Developments in Single-Cell RNA-Seq of Microorganisms. 2018-06-26 10.1016/j.bpj.2018.06.008 1 view
Zappia PLoS Comput. Biol. Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database. 2018-06-25 10.1371/journal.pcbi.1006245 19 view
Huang Nat. Methods SAVER: gene expression recovery for single-cell RNA sequencing. 2018-06-25 10.1038/s41592-018-0033-z 18 view
Sebé-Pedrós Nat Ecol Evol Early metazoan cell type diversity and the evolution of multicellular gene regulation. 2018-06-25 10.1038/s41559-018-0575-6 6 view
Savas Nat. Med. Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis. 2018-06-25 10.1038/s41591-018-0078-7 25 view
Guo Nat. Med. Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing. 2018-06-25 10.1038/s41591-018-0045-3 8 view
Azizi Cell Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment. 2018-06-25 10.1016/j.cell.2018.05.060 32 view
van Dijk Cell Recovering Gene Interactions from Single-Cell Data Using Data Diffusion. 2018-06-22 10.1016/j.cell.2018.05.061 view
Schwalie Nature A stromal cell population that inhibits adipogenesis in mammalian fat depots. 2018-06-20 10.1038/s41586-018-0226-8 14 view
Zhang IEEE/ACM Trans Comput Biol Bioinform Comparison of computational methods for imputing single-cell RNA-sequencing data. 2018-06-19 10.1109/TCBB.2018.2848633 6 view
Chen BMC Bioinformatics Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data. 2018-06-19 10.1186/s12859-018-2217-z 6 view
Street BMC Genomics Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. 2018-06-19 10.1186/s12864-018-4772-0 28 view
Petukhov Genome Biol. dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. 2018-06-19 10.1186/s13059-018-1449-6 7 view
Lu Cell Cycle Transcriptome analysis of PCOS arrested 2-cell embryos. 2018-06-18 10.1080/15384101.2018.1467678 view
Harris PLoS Biol. Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics. 2018-06-18 10.1371/journal.pbio.2006387 12 view
Barshad Genome Res. Human primitive brain displays negative mitochondrial-nuclear expression correlation of respiratory genes. 2018-06-14 10.1101/gr.226324.117 1 view
Zeng Cell Prospectively Isolated Tetraspanin+ Neoblasts Are Adult Pluripotent Stem Cells Underlying Planaria Regeneration. 2018-06-14 10.1016/j.cell.2018.05.006 view
Fan Genome Res. Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data. 2018-06-13 10.1101/gr.228080.117 5 view
Feng IEEE/ACM Trans Comput Biol Bioinform ELF: Extract Landmark Features by optimizing topology maintenance, redundancy, and specificity. 2018-06-12 10.1109/TCBB.2018.2846225 view
Park Lab Chip Isolation and genome sequencing of individual circulating tumor cells using hydrogel encapsulation and laser capture microdissection. 2018-06-12 10.1039/c8lc00184g view
Zhang J. Clin. Invest. Ca2+-binding protein NECAB2 facilitates inflammatory pain hypersensitivity. 2018-06-12 10.1172/JCI120913 view
Goodrum MBio A Single-Cell Approach to the Elusive Latent Human Cytomegalovirus Transcriptome. 2018-06-12 10.1128/mBio.01001-18 view
Worrall Cell Rep Non-random Mis-segregation of Human Chromosomes. 2018-06-12 10.1016/j.celrep.2018.05.047 6 view
Zhao Cell Stem Cell Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming. 2018-06-12 10.1016/j.stem.2018.05.025 3 view
Dalal Sci Rep Transcriptome analysis highlights nuclear control of chloroplast development in the shoot apex. 2018-06-11 10.1038/s41598-018-27305-4 view
Konstantinides Cell Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features. 2018-06-09 10.1016/j.cell.2018.05.021 10 view
Burl Cell Metab. Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling. 2018-06-09 10.1016/j.cmet.2018.05.025 5 view
Gong BMC Bioinformatics DrImpute: imputing dropout events in single cell RNA sequencing data. 2018-06-08 10.1186/s12859-018-2226-y 7 view
Ortiz Trends Cell Biol. Analyzing Circulating Tumor Cells One at a Time. 2018-06-08 10.1016/j.tcb.2018.05.004 5 view
Abdelmoez Genome Biol. SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology. 2018-06-06 10.1186/s13059-018-1446-9 4 view
Mead BMC Biol. Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. 2018-06-05 10.1186/s12915-018-0527-2 4 view
Yao Circulation Histone Variant H2A.Z is Required for the Maintenance of Smooth Muscle Cell Identity as Revealed by Single-Cell Transcriptomics. 2018-06-05 10.1161/CIRCULATIONAHA.117.033114 1 view
Lindström Dev. Cell Progressive Recruitment of Mesenchymal Progenitors Reveals a Time-Dependent Process of Cell Fate Acquisition in Mouse and Human Nephrogenesis. 2018-06-04 10.1016/j.devcel.2018.05.010 9 view
Fan Cell Res. Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis. 2018-06-04 10.1038/s41422-018-0053-3 10 view
Steuerman Cell Syst Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing. 2018-06-01 10.1016/j.cels.2018.05.008 10 view
Sainio Neurol Genet Absence of NEFL in patient-specific neurons in early-onset Charcot-Marie-Tooth neuropathy. 2018-06-01 10.1212/NXG.0000000000000244 view
Yang Oncol Lett Single-cell whole-genome sequencing identifies human papillomavirus integration in cervical tumour cells prior to and following radiotherapy. 2018-06-01 10.3892/ol.2018.8567 view
Do Cell Discov SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements. 2018-06-01 10.1038/s41421-018-0032-3 2 view
Belokhvostova Int. J. Dev. Biol. Homeostasis, regeneration and tumour formation in the mammalian epidermis. 2018-06-01 10.1387/ijdb.170341fw view
Gao Nat. Cell Biol. Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. 2018-06-01 10.1038/s41556-018-0105-4 4 view
Fu Adv. Exp. Med. Biol. Single-Cell Non-coding RNA in Embryonic Development. 2018-06-01 10.1007/978-981-13-0502-3_3 1 view
Huang Adv. Exp. Med. Biol. High Throughput Single Cell RNA Sequencing, Bioinformatics Analysis and Applications. 2018-06-01 10.1007/978-981-13-0502-3_4 1 view
Shi Adv. Exp. Med. Biol. The Potential Roles and Advantages of Single Cell Sequencing in the Diagnosis and Treatment of Hematological Malignancies. 2018-06-01 10.1007/978-981-13-0502-3_10 1 view
Yu Adv. Exp. Med. Biol. Application of Single Cell Sequencing in Cancer. 2018-06-01 10.1007/978-981-13-0502-3_11 1 view
Luo Adv. Exp. Med. Biol. Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq. 2018-06-01 10.1007/978-981-13-0502-3_12 view
Yao Adv. Exp. Med. Biol. Is Pooled CRISPR-Screening the Dawn of a New Era for Functional Genomics. 2018-06-01 10.1007/978-981-13-0502-3_14 view
Zeng Adv. Exp. Med. Biol. Roles of Single Cell Systems Biomedicine in Lung Diseases. 2018-06-01 10.1007/978-981-13-0502-3_15 view
Buggert Sci Immunol Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue. 2018-06-01 10.1126/sciimmunol.aar4526 view
Kageyama Front Neurosci ShinyCortex: Exploring Single-Cell Transcriptome Data From the Developing Human Cortex. 2018-06-01 10.3389/fnins.2018.00315 1 view
Lu Arthritis Rheumatol. T cell-dependent affinity maturation and innate immune pathways differentially drive autoreactive B cell responses in rheumatoid arthritis. 2018-05-31 10.1002/art.40578 3 view
Chen Genome Biol. UMI-count modeling and differential expression analysis for single-cell RNA sequencing. 2018-05-31 10.1186/s13059-018-1438-9 2 view
Sebé-Pedrós Cell Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq. 2018-05-31 10.1016/j.cell.2018.05.019 9 view
Tierney Methods Mol. Biol. Assessing Muscle Stem Cell Clonal Complexity During Aging. 2018-05-30 10.1007/7651_2018_139 view
Boukouvalas Genome Biol. BGP: identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process. 2018-05-29 10.1186/s13059-018-1440-2 2 view
Parekh Gigascience zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs. 2018-05-26 10.1093/gigascience/giy059 13 view
Kernfeld Immunity A Single-Cell Transcriptomic Atlas of Thymus Organogenesis Resolves Cell Types and Developmental Maturation. 2018-05-25 10.1016/j.immuni.2018.04.015 7 view
Nötzel Trends Parasitol. Single-Cell Transcriptome Profiling of Protozoan and Metazoan Parasites. 2018-05-25 10.1016/ 1 view
Demaree J Vis Exp An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing. 2018-05-23 10.3791/57598 1 view
Nguyen Nat Commun Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity. 2018-05-23 10.1038/s41467-018-04334-1 16 view
Potter Nat Rev Nephrol Single-cell RNA sequencing for the study of development, physiology and disease. 2018-05-22 10.1038/s41581-018-0021-7 8 view
Wuidart Nat. Cell Biol. Early lineage segregation of multipotent embryonic mammary gland progenitors. 2018-05-21 10.1038/s41556-018-0095-2 10 view
Ding Nat Commun Interpretable dimensionality reduction of single cell transcriptome data with deep generative models. 2018-05-21 10.1038/s41467-018-04368-5 13 view
Skene Nat. Genet. Genetic identification of brain cell types underlying schizophrenia. 2018-05-21 10.1038/s41588-018-0129-5 28 view
Srivastava Nucleic Acids Res. CellAtlasSearch: a scalable search engine for single cells. 2018-05-21 10.1093/nar/gky421 5 view
Jiang Bioinformatics Single Cell Clustering Based on Cell-Pair Differentiability Correlation and Variance Analysis. 2018-05-16 10.1093/bioinformatics/bty390 3 view
Deng Biol. Reprod. Long noncoding RNAs exchange during zygotic genome activation in goat. 2018-05-15 10.1093/biolre/ioy118 4 view
Rodda Immunity Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity. 2018-05-15 10.1016/j.immuni.2018.04.006 14 view
Czerniecki Cell Stem Cell High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping. 2018-05-15 10.1016/j.stem.2018.04.022 7 view
Vértesy Nat Commun Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells. 2018-05-14 10.1038/s41467-018-04215-7 view
Jay Nat Microbiol Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats. 2018-05-14 10.1038/s41564-018-0163-1 3 view
Jaff Neuroradiology Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy. 2018-05-14 10.1007/s00234-018-2033-1 2 view
Schiaffino FEBS J. Muscle fiber type diversity revealed by anti-myosin heavy chain antibodies. 2018-05-14 10.1111/febs.14502 3 view
Sisakhtnezhad J. Cell. Biochem. In silico analysis of single-cell RNA sequencing data from 3 and 7 days old mouse spermatogonial stem cells to identify their differentially expressed genes and transcriptional regulators. 2018-05-11 10.1002/jcb.27066 view
Nguyen Genome Res. Single-cell RNA-seq of human induced pluripotent stem cells reveals cellular heterogeneity and cell state transitions between subpopulations. 2018-05-11 10.1101/gr.223925.117 5 view
Pu Antiviral Res. Feasibility and biological rationale of repurposing sunitinib and erlotinib for dengue treatment. 2018-05-10 10.1016/j.antiviral.2018.05.001 1 view
Tasic Curr. Opin. Neurobiol. Single cell transcriptomics in neuroscience: cell classification and beyond. 2018-05-05 10.1016/j.conb.2018.04.021 3 view
Lu Cell Metab. The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes. 2018-05-04 10.1016/j.cmet.2018.04.013 6 view
Kester Cell Stem Cell Single-Cell Transcriptomics Meets Lineage Tracing. 2018-05-03 10.1016/j.stem.2018.04.014 15 view
Kramann JCI Insight Parabiosis and single-cell RNA sequencing reveal a limited contribution of monocytes to myofibroblasts in kidney fibrosis. 2018-05-03 10.1172/jci.insight.99561 5 view
Lun PLoS Comput. Biol. beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types. 2018-05-03 10.1371/journal.pcbi.1006135 view
Iacono Genome Res. bigSCale: an analytical framework for big-scale single-cell data. 2018-05-03 10.1101/gr.230771.117 3 view
Shah Cell Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function. 2018-05-03 10.1016/j.cell.2018.03.063 5 view
Sarkar Cell Stem Cell Efficient Generation of CA3 Neurons from Human Pluripotent Stem Cells Enables Modeling of Hippocampal Connectivity In Vitro. 2018-05-03 10.1016/j.stem.2018.04.009 8 view
Tosches Science Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles. 2018-05-03 10.1126/science.aar4237 13 view
Ortega Curr. Opin. Genet. Dev. Functional genetics of early human development. 2018-05-02 10.1016/j.gde.2018.04.005 view
Wu J. Invest. Dermatol. Research Techniques Made Simple: Single-Cell RNA Sequencing and its Applications in Dermatology. 2018-05-01 10.1016/j.jid.2018.01.026 3 view
Matern Front Cell Dev Biol Transcriptomic Profiling of Zebrafish Hair Cells Using RiboTag. 2018-05-01 10.3389/fcell.2018.00047 2 view
Bayega Methods Mol. Biol. Current and Future Methods for mRNA Analysis: A Drive Toward Single Molecule Sequencing. 2018-05-01 10.1007/978-1-4939-7834-2_11 2 view
Rivron Nature Blastocyst-like structures generated solely from stem cells. 2018-05-01 10.1038/s41586-018-0051-0 23 view
Tran Semin. Cell Dev. Biol. A lineage CLOUD for neoblasts. 2018-05-01 10.1016/j.semcdb.2018.04.012 1 view
Hu Front Cell Dev Biol Single Cell Multi-Omics Technology: Methodology and Application. 2018-05-01 10.3389/fcell.2018.00028 6 view
Chen Nucleic Acids Res. BCseq: accurate single cell RNA-seq quantification with bias correction. 2018-04-30 10.1093/nar/gky308 1 view
Wirka Circ. Res. Advances in Transcriptomics: Investigating Cardiovascular Disease at Unprecedented Resolution. 2018-04-27 10.1161/CIRCRESAHA.117.310910 3 view
Wagner Science Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. 2018-04-26 10.1126/science.aar4362 46 view
Heintze Nat Rev Nephrol Whole-kidney single-cell transcriptomics identifies new cell types. 2018-04-25 10.1038/s41581-018-0013-7 view
Lukassen Sci Rep Characterization of germ cell differentiation in the male mouse through single-cell RNA sequencing. 2018-04-25 10.1038/s41598-018-24725-0 4 view
Buenrostro Cell Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation. 2018-04-25 10.1016/j.cell.2018.03.074 21 view
Miao Bioinformatics DEsingle for detecting three types of differential expression in single-cell RNA-seq data. 2018-04-24 10.1093/bioinformatics/bty332 1 view
Wu Bioinformatics Two-phase differential expression analysis for single cell RNA-seq. 2018-04-24 10.1093/bioinformatics/bty329 5 view
Golumbeanu Cell Rep Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells. 2018-04-24 10.1016/j.celrep.2018.03.102 4 view
Wang Methods SigEMD: A powerful method for differential gene expression analysis in single-cell RNA sequencing data. 2018-04-24 10.1016/j.ymeth.2018.04.017 view
Häring Nat. Neurosci. Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types. 2018-04-23 10.1038/s41593-018-0141-1 8 view
Xiao Dev. Cell Hippo Signaling Plays an Essential Role in Cell State Transitions during Cardiac Fibroblast Development. 2018-04-23 10.1016/j.devcel.2018.03.019 7 view
Filbin Science Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. 2018-04-20 10.1126/science.aao4750 14 view
Müller Bioinformatics CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones. 2018-04-20 10.1093/bioinformatics/bty316 3 view
Croset Elife Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomics. 2018-04-19 10.7554/eLife.34550 16 view
Plass Science Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics. 2018-04-19 10.1126/science.aaq1723 30 view
Fincher Science Cell type transcriptome atlas for the planarian Schmidtea mediterranea. 2018-04-19 10.1126/science.aaq1736 30 view
De Bie Leukemia Single-cell sequencing reveals the origin and the order of mutation acquisition in T-cell acute lymphoblastic leukemia. 2018-04-18 10.1038/s41375-018-0127-8 view
He BMC Genomics Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation. 2018-04-17 10.1186/s12864-018-4649-2 1 view
Sun J. Biol. Chem. Single-cell RNA-Seq reveals cell heterogeneity and hierarchy within mouse mammary epithelia. 2018-04-17 10.1074/jbc.RA118.002297 3 view
Xu Genomics Where are we going with genomics in plant pathogenic bacteria? 2018-04-17 10.1016/j.ygeno.2018.04.011 view
Wang J. Med. Genet. Genetic and phenotypic difference in CD8+ T cell exhaustion between chronic hepatitis B infection and hepatocellular carcinoma. 2018-04-17 10.1136/jmedgenet-2018-105267 view
Pijuan-Sala Nat. Rev. Mol. Cell Biol. Single-cell transcriptional profiling: a window into embryonic cell-type specification. 2018-04-17 10.1038/s41580-018-0002-5 6 view
Pflug Bioinformatics TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers. 2018-04-16 10.1093/bioinformatics/bty283 2 view
Alves Genome Med Sensitivity to sequencing depth in single-cell cancer genomics. 2018-04-16 10.1186/s13073-018-0537-2 view
Kim Cell Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing. 2018-04-13 10.1016/j.cell.2018.03.041 28 view
Simoni Curr. Opin. Immunol. Mass cytometry: a powerful tool for dissecting the immune landscape. 2018-04-11 10.1016/j.coi.2018.03.023 3 view
Cembrowski Cell Dissociable Structural and Functional Hippocampal Outputs via Distinct Subiculum Cell Classes. 2018-04-10 10.1016/j.cell.2018.03.031 6 view
Johnson Curr Oncol Rep Single-Cell RNA-Sequencing in Glioma. 2018-04-10 10.1007/s11912-018-0673-2 4 view
Herman Nat. Methods FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data. 2018-04-09 10.1038/nmeth.4662 12 view
Zhang PLoS Comput. Biol. A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa. 2018-04-09 10.1371/journal.pcbi.1006053 2 view
Spanjaard Nat. Biotechnol. Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. 2018-04-09 10.1038/nbt.4124 53 view
Tata Cell Stem Cell Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury. 2018-04-07 10.1016/j.stem.2018.03.018 7 view
Rizzetto Bioinformatics B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle. 2018-04-05 10.1093/bioinformatics/bty203 4 view
Han Genome Biol. Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. 2018-04-05 10.1186/s13059-018-1426-0 5 view
Park Science Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. 2018-04-05 10.1126/science.aar2131 38 view
Loeffler-Wirth Biology (Basel) Pseudotime Dynamics in Melanoma Single-Cell Transcriptomes Reveals Different Mechanisms of Tumor Progression. 2018-04-03 10.3390/biology7020023 view
Targa Curr. Opin. Cell Biol. Cancer: a CINful evolution. 2018-04-03 10.1016/ 4 view
Haghverdi Nat. Biotechnol. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. 2018-04-02 10.1038/nbt.4091 34 view
Butler Nat. Biotechnol. Integrating single-cell transcriptomic data across different conditions, technologies, and species. 2018-04-02 10.1038/nbt.4096 237 view
Kiselev Nat. Methods scmap: projection of single-cell RNA-seq data across data sets. 2018-04-02 10.1038/nmeth.4644 33 view
van der Wijst Nat. Genet. Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs. 2018-04-02 10.1038/s41588-018-0089-9 view
Hen-Avivi Curr. Opin. Microbiol. Immune cell type 'fingerprints' at the basis of outcome diversity of human infection. 2018-04-01 10.1016/j.mib.2017.09.012 1 view
Tawil Thromb. Res. Single cell coagulomes as constituents of the oncogene-driven coagulant phenotype in brain tumours. 2018-04-01 10.1016/j.thromres.2018.01.021 view
Hu J. Invest. Dermatol. A Fibroblast Is Not a Fibroblast Is Not a Fibroblast. 2018-04-01 10.1016/j.jid.2017.10.012 1 view
Hu Front Immunol Impaired CD27+IgD+ B Cells With Altered Gene Signature in Rheumatoid Arthritis. 2018-04-01 10.3389/fimmu.2018.00626 view
Sagar Methods Mol. Biol. High-Throughput Single-Cell RNA Sequencing and Data Analysis. 2018-04-01 10.1007/978-1-4939-7768-0_15 view
Levitin Trends Cancer Single-Cell Transcriptomic Analysis of Tumor Heterogeneity. 2018-04-01 10.1016/j.trecan.2018.02.003 4 view
Svensson Nat Protoc Exponential scaling of single-cell RNA-seq in the past decade. 2018-04-01 10.1038/nprot.2017.149 44 view
DeLaughter Curr Protoc Mol Biol The Use of the Fluidigm C1 for RNA Expression Analyses of Single Cells. 2018-04-01 10.1002/cpmb.55 view
Olsen Curr Protoc Mol Biol Introduction to Single-Cell RNA Sequencing. 2018-04-01 10.1002/cpmb.57 view
Yi Bioinformatics Detecting hidden batch factors through data-adaptive adjustment for biological effects. 2018-04-01 10.1093/bioinformatics/btx635 1 view
Nässel Front Cell Neurosci Substrates for Neuronal Cotransmission With Neuropeptides and Small Molecule Neurotransmitters in Drosophila. 2018-04-01 10.3389/fncel.2018.00083 8 view
Ichinohe Front Immunol Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host-Gut Microbiome Interactions. 2018-04-01 10.3389/fimmu.2018.00668 view
Alemany Nature Whole-organism clone tracing using single-cell sequencing. 2018-03-28 10.1038/nature25969 40 view
Raj Nat. Biotechnol. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. 2018-03-28 10.1038/nbt.4103 45 view
Reid Elife Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites. 2018-03-27 10.7554/eLife.33105 16 view
Dahlin Blood A single cell hematopoietic landscape resolves eight lineage trajectories and defects in Kit mutant mice. 2018-03-27 10.1182/blood-2017-12-821413 12 view
Xie Cell Rep Single-Cell Deconvolution of Fibroblast Heterogeneity in Mouse Pulmonary Fibrosis. 2018-03-27 10.1016/j.celrep.2018.03.010 8 view
Liu Cancer Biol. Ther. Comparison of EpCAMhighCD44+ cancer stem cells with EpCAMhighCD44- tumor cells in colon cancer by single-cell sequencing. 2018-03-26 10.1080/15384047.2018.1456605 view
Aevermann Hum. Mol. Genet. Big data and single cell transcriptomics: implications for ontological representation. 2018-03-24 10.1093/hmg/ddy100 view
Severson Nat Commun BEARscc determines robustness of single-cell clusters using simulated technical replicates. 2018-03-22 10.1038/s41467-018-03608-y 5 view
Ziegenhain Brief Funct Genomics Quantitative single-cell transcriptomics. 2018-03-22 10.1093/bfgp/ely009 9 view
Verheijen Trends Genet. Understanding Alzheimer Disease at the Interface between Genetics and Transcriptomics. 2018-03-21 10.1016/j.tig.2018.02.007 11 view
Chen Sci Rep Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms. 2018-03-21 10.1038/s41598-018-23325-2 view
Bergiers Elife Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis. 2018-03-20 10.7554/eLife.29312 3 view
Upadhyay Genome Med BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data. 2018-03-20 10.1186/s13073-018-0528-3 4 view
Yu Development Dynamics of chromatin marks and the role of JMJD3 during pancreatic endocrine cell fate commitment. 2018-03-20 10.1242/dev.163162 5 view
Edsgärd Nat. Methods Identification of spatial expression trends in single-cell gene expression data. 2018-03-19 10.1038/nmeth.4634 11 view
Wang Sci Rep Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. 2018-03-19 10.1038/s41598-018-22297-7 13 view
Cristinelli Curr Opin Virol The use of single-cell RNA-Seq to understand virus-host interactions. 2018-03-17 10.1016/j.coviro.2018.03.001 3 view
Cochain Circ. Res. Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis. 2018-03-15 10.1161/CIRCRESAHA.117.312509 28 view
Winkels Circ. Res. Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry. 2018-03-15 10.1161/CIRCRESAHA.117.312513 23 view
Zheng Mol. Syst. Biol. Molecular transitions in early progenitors during human cord blood hematopoiesis. 2018-03-15 10.15252/msb.20178041 9 view
Rosenberg Science Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. 2018-03-15 10.1126/science.aam8999 66 view
Ding PLoS Comput. Biol. iDREM: Interactive visualization of dynamic regulatory networks. 2018-03-14 10.1371/journal.pcbi.1006019 view
Zhong Nature A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. 2018-03-14 10.1038/nature25980 27 view
Dong Genome Biol. Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis. 2018-03-14 10.1186/s13059-018-1416-2 11 view
Vegh Brief Funct Genomics The impact of single-cell RNA sequencing on understanding the functional organization of the immune system. 2018-03-14 10.1093/bfgp/ely003 view
Cole Nucleic Acids Res. Tn5Prime, a Tn5 based 5' capture method for single cell RNA-seq. 2018-03-14 10.1093/nar/gky182 view
Ziller Cell Stem Cell Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology. 2018-03-14 10.1016/j.stem.2018.02.012 6 view
Treen Curr. Biol. Depletion of Maternal Cyclin B3 Contributes to Zygotic Genome Activation in the Ciona Embryo. 2018-03-14 10.1016/j.cub.2018.02.046 4 view
Strell FEBS J. Placing RNA in Context and Space - Methods for Spatially Resolved Transcriptomics. 2018-03-14 10.1111/febs.14435 5 view
Shnayder MBio Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing. 2018-03-13 10.1128/mBio.00013-18 5 view
Alpert Nat. Methods Alignment of single-cell trajectories to compare cellular expression dynamics. 2018-03-12 10.1038/nmeth.4628 6 view
Langer Stem Cell Reports Retinal Ganglion Cell Diversity and Subtype Specification from Human Pluripotent Stem Cells. 2018-03-10 10.1016/j.stemcr.2018.02.010 7 view
Pandey Curr. Biol. Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq. 2018-03-09 10.1016/j.cub.2018.02.040 11 view
Zhang BMC Bioinformatics An interpretable framework for clustering single-cell RNA-Seq datasets. 2018-03-09 10.1186/s12859-018-2092-7 3 view
Sasagawa Genome Biol. Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads. 2018-03-09 10.1186/s13059-018-1407-3 10 view
Li Nat Commun An accurate and robust imputation method scImpute for single-cell RNA-seq data. 2018-03-08 10.1038/s41467-018-03405-7 44 view
Lavagi Sci Rep Single-cell RNA sequencing reveals developmental heterogeneity of blastomeres during major genome activation in bovine embryos. 2018-03-06 10.1038/s41598-018-22248-2 5 view
Donega Cell Rep Transcriptional Dysregulation in Postnatal Glutamatergic Progenitors Contributes to Closure of the Cortical Neurogenic Period. 2018-03-06 10.1016/j.celrep.2018.02.030 1 view
Mayer Nature Developmental diversification of cortical inhibitory interneurons. 2018-03-05 10.1038/nature25999 36 view
Gao Methods Mol. Biol. Data Analysis in Single-Cell Transcriptome Sequencing. 2018-03-01 10.1007/978-1-4939-7717-8_18 3 view
Pillonel Front Microbiol Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle. 2018-03-01 10.3389/fmicb.2018.00079 1 view
Ronen F1000Res netSmooth: Network-smoothing based imputation for single cell RNA-seq. 2018-03-01 10.12688/f1000research.13511.2 6 view
Xu Methods Mol. Biol. Applications of Single-Cell Sequencing for Multiomics. 2018-03-01 10.1007/978-1-4939-7717-8_19 2 view
Lummertz da Rocha Nat Commun Reconstruction of complex single-cell trajectories using CellRouter. 2018-03-01 10.1038/s41467-018-03214-y view
Hook Am. J. Hum. Genet. Single-Cell RNA-Seq of Mouse Dopaminergic Neurons Informs Candidate Gene Selection for Sporadic Parkinson Disease. 2018-03-01 10.1016/j.ajhg.2018.02.001 8 view
Pensold J Exp Neurosci Single-Cell Transcriptomics Reveals Regulators of Neuronal Migration and Maturation During Brain Development. 2018-03-01 10.1177/1179069518760783 2 view
Terryn F1000Res Recent advances in lineage differentiation from stem cells: hurdles and opportunities? 2018-03-01 10.12688/f1000research.12596.1 1 view
Guo Methods Mol. Biol. Single-Cell Transcriptome Analysis Using SINCERA Pipeline. 2018-03-01 10.1007/978-1-4939-7710-9_15 view
Crow Nat Commun Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. 2018-02-28 10.1038/s41467-018-03282-0 20 view
Zhao Antioxid. Redox Signal. Single-cell transcriptomics of human oocytes: environment-driven metabolic competition and compensatory mechanisms during oocyte maturation. 2018-02-27 10.1089/ars.2017.7151 view
Vu Bioinformatics Isoform-level gene expression patterns in single-cell RNA-sequencing data. 2018-02-27 10.1093/bioinformatics/bty100 3 view
Van den Berge Genome Biol. Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. 2018-02-26 10.1186/s13059-018-1406-4 view
Soneson Nat. Methods Bias, robustness and scalability in single-cell differential expression analysis. 2018-02-26 10.1038/nmeth.4612 28 view
Hockley Gut Single-cell RNAseq reveals seven classes of colonic sensory neuron. 2018-02-26 10.1136/gutjnl-2017-315631 10 view
Kayaba Int. Immunol. Bone Marrow PDGFR+Sca-1+ Enriched Mesenchymal Stem Cells Support Survival of and Antibody Production by Plasma Cells in vitro through IL-6. 2018-02-24 10.1093/intimm/dxy018 view
Stephenson Nat Commun Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. 2018-02-23 10.1038/s41467-017-02659-x 25 view
Mizoguchi Nat Commun Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis. 2018-02-23 10.1038/s41467-018-02892-y 22 view
Kashima Sci Rep Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response. 2018-02-22 10.1038/s41598-018-21161-y 3 view
Han Cell Mapping the Mouse Cell Atlas by Microwell-Seq. 2018-02-22 10.1016/j.cell.2018.02.001 92 view
Mi Science Early emergence of cortical interneuron diversity in the mouse embryo. 2018-02-22 10.1126/science.aar6821 20 view
Clark Nat Commun scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. 2018-02-22 10.1038/s41467-018-03149-4 39 view
Sereti Nat Commun Analysis of cardiomyocyte clonal expansion during mouse heart development and injury. 2018-02-21 10.1038/s41467-018-02891-z 5 view
Yip Brief. Bioinformatics Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data. 2018-02-21 10.1093/bib/bby011 4 view
Tusi Nature Population snapshots predict early haematopoietic and erythroid hierarchies. 2018-02-21 10.1038/nature25741 23 view
Munson-McGee ISME J A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments. 2018-02-21 10.1038/s41396-018-0071-7 10 view
Wang Proc. Natl. Acad. Sci. U.S.A. Pulmonary alveolar type I cell population consists of two distinct subtypes that differ in cell fate. 2018-02-20 10.1073/pnas.1719474115 8 view
DeWitt Mol. Biol. Evol. Using genotype abundance to improve phylogenetic inference. 2018-02-20 10.1093/molbev/msy020 4 view
Hill Nat. Methods On the design of CRISPR-based single-cell molecular screens. 2018-02-19 10.1038/nmeth.4604 18 view
Sun Oncotarget Single-cell RNA sequencing reveals gene expression signatures of breast cancer-associated endothelial cells. 2018-02-16 10.18632/oncotarget.23760 1 view
Zanini Elife Single-cell transcriptional dynamics of flavivirus infection. 2018-02-16 10.7554/eLife.32942 16 view
Barron Nucleic Acids Res. A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data. 2018-02-16 10.1093/nar/gkx1113 view
Lin PLoS Comput. Biol. A stochastic and dynamical view of pluripotency in mouse embryonic stem cells. 2018-02-16 10.1371/journal.pcbi.1006000 8 view
Zhao Cancer Res. Single-cell transcriptome analyses reveal endothelial cell heterogeneity in tumors and changes following anti-angiogenic treatment. 2018-02-15 10.1158/0008-5472.CAN-17-2728 6 view
Vanlandewijck Nature A molecular atlas of cell types and zonation in the brain vasculature. 2018-02-14 10.1038/nature25739 72 view
Wang BMC Genomics Predictors of breast cancer cell types and their prognostic power in breast cancer patients. 2018-02-13 10.1186/s12864-018-4527-y 2 view
Daniszewski Sci Data Single cell RNA sequencing of stem cell-derived retinal ganglion cells. 2018-02-13 10.1038/sdata.2018.13 5 view
Delley Sci Rep Combined aptamer and transcriptome sequencing of single cells. 2018-02-13 10.1038/s41598-018-21153-y 2 view
Zemmour Nat. Immunol. Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR. 2018-02-12 10.1038/s41590-018-0051-0 12 view
Moon Lab Chip Inertial-ordering-assisted droplet microfluidics for high-throughput single-cell RNA-sequencing. 2018-02-09 10.1039/c7lc01284e 8 view
Miyai Genes Dev. Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells. 2018-02-09 10.1101/gad.309575.117 5 view
Park Bioinformatics Spectral clustering based on learning similarity matrix. 2018-02-08 10.1093/bioinformatics/bty050 view
Qin PLoS Genet. Gli3 is a negative regulator of Tas1r3-expressing taste cells. 2018-02-07 10.1371/journal.pgen.1007058 view
Torre Cell Syst Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. 2018-02-07 10.1016/j.cels.2018.01.014 20 view
Stévant Cell Rep Deciphering Cell Lineage Specification during Male Sex Determination with Single-Cell RNA Sequencing. 2018-02-06 10.1016/j.celrep.2018.01.043 16 view
Dumdie Dev. Cell Chromatin Modification and Global Transcriptional Silencing in the Oocyte Mediated by the mRNA Decay Activator ZFP36L2. 2018-02-05 10.1016/j.devcel.2018.01.006 2 view
Jin Bioinformatics scEpath: Energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. 2018-02-05 10.1093/bioinformatics/bty058 10 view
Sen Methods Mol. Biol. Single-Cell RNA Sequencing of Glioblastoma Cells. 2018-02-01 10.1007/978-1-4939-7659-1_12 1 view
Li Neurosci Bull Somatosensory Neuron Typing with High-Coverage Single-Cell RNA Sequencing and Functional Analysis. 2018-02-01 10.1007/s12264-017-0147-9 11 view
Dharampuriya Curr. Opin. Cell Biol. Tracking the origin, development, and differentiation of hematopoietic stem cells. 2018-02-01 10.1016/ 1 view
Sagner PLoS Biol. Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics. 2018-02-01 10.1371/journal.pbio.2003127 7 view
Naidoo Curr Issues Mol Biol Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel. 2018-02-01 10.21775/cimb.027.127 view
Durruthy-Durruthy Methods Mol. Biol. Using Fluidigm C1 to Generate Single-Cell Full-Length cDNA Libraries for mRNA Sequencing. 2018-02-01 10.1007/978-1-4939-7471-9_11 1 view
Carter F1000Res Recent advances in understanding evolution of the placenta: insights from transcriptomics. 2018-02-01 10.12688/f1000research.13115.1 3 view
DiStefano Methods Mol. Biol. Identification of Disease Susceptibility Alleles in the Next Generation Sequencing Era. 2018-02-01 10.1007/978-1-4939-7471-9_1 view
Kiniwa J. Dermatol. Sci. Diversity of circulating tumor cells in peripheral blood: Detection of heterogeneous BRAF mutations in a patient with advanced melanoma by single-cell analysis. 2018-02-01 10.1016/j.jdermsci.2018.01.011 1 view
Mamedov Immunity A Macrophage Colony-Stimulating Factor-Producing γδ T Cell Subset Prevents Malarial Parasitemic Recurrence. 2018-02-01 10.1016/j.immuni.2018.01.009 11 view
Tian PLoS ONE Single cell on-chip whole genome amplification via micropillar arrays for reduced amplification bias. 2018-02-01 10.1371/journal.pone.0191520 view
Wang Cell Biol. Toxicol. Can single-cell RNA sequencing crack the mystery of cells? 2018-02-01 10.1007/s10565-017-9404-y 24 view
Cai IEEE Trans Biomed Eng WaveDec: A Wavelet Approach to Identify Both Shared and Individual Patterns of Copy-Number Variations. 2018-02-01 10.1109/TBME.2017.2769677 2 view
Hedlund Mol. Aspects Med. Single-cell RNA sequencing: Technical advancements and biological applications. 2018-02-01 10.1016/j.mam.2017.07.003 15 view
Jeong Front Neurosci Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics. 2018-02-01 10.3389/fnins.2018.00031 1 view
Ramos-Ibeas Curr. Top. Dev. Biol. States and Origins of Mammalian Embryonic Pluripotency In Vivo and in a Dish. 2018-02-01 10.1016/bs.ctdb.2017.11.002 view
Dang PLoS Genet. Coordination of olfactory receptor choice with guidance receptor expression and function in olfactory sensory neurons. 2018-01-31 10.1371/journal.pgen.1007164 1 view
Dal Molin Brief. Bioinformatics How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives. 2018-01-31 10.1093/bib/bby007 view
Hayashi Neuron Graded Arrays of Spinal and Supraspinal V2a Interneuron Subtypes Underlie Forelimb and Hindlimb Motor Control. 2018-01-31 10.1016/j.neuron.2018.01.023 9 view
Vierra Mol Metab TALK-1 reduces delta-cell endoplasmic reticulum and cytoplasmic calcium levels limiting somatostatin secretion. 2018-01-31 10.1016/j.molmet.2018.01.016 1 view
Gladka Circulation Single-Cell Sequencing of the Healthy and Diseased Heart Reveals Ckap4 as a New Modulator of Fibroblasts Activation. 2018-01-31 10.1161/CIRCULATIONAHA.117.030742 12 view
Lu Stem Cell Res Single-cell RNA sequencing reveals metallothionein heterogeneity during hESC differentiation to definitive endoderm. 2018-01-31 10.1016/j.scr.2018.01.015 view
Chiang J. Allergy Clin. Immunol. Single cell profiling of peanut-responsive T cells in peanut allergic subjects reveals heterogeneous effector Th2 subsets. 2018-01-30 10.1016/j.jaci.2017.11.060 view
Wu Cancer Lett. Single-cell Transcriptome Analyses Reveal Molecular Signals to Intrinsic and Acquired Paclitaxel Resistance in Esophageal Squamous Cancer Cells. 2018-01-30 10.1016/j.canlet.2018.01.059 3 view
Khoramian Tusi Exp. Hematol. High throughput single-cell fate potential assay of murine hematopoietic progenitors in vitro. 2018-01-30 10.1016/j.exphem.2018.01.005 view
Martin-Gayo Genome Biol. A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers. 2018-01-29 10.1186/s13059-017-1385-x 5 view
Sarrach Sci Rep Spatiotemporal patterning of EpCAM is important for murine embryonic endo- and mesodermal differentiation. 2018-01-29 10.1038/s41598-018-20131-8 5 view
Wu Cell. Mol. Immunol. Epigenetic regulation in B-cell maturation and its dysregulation in autoimmunity. 2018-01-29 10.1038/cmi.2017.133 11 view
Xiong Oncotarget Novel mutational landscapes and expression signatures of lung squamous cell carcinoma. 2018-01-26 10.18632/oncotarget.23716 1 view
Cui Nucleic Acids Res. Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells. 2018-01-25 10.1093/nar/gkx874 6 view
Murray Wiley Interdiscip Rev Dev Biol Systems biology of embryonic development: Prospects for a complete understanding of the Caenorhabditis elegans embryo. 2018-01-25 10.1002/wdev.314 5 view
Lescroart Science Defining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq. 2018-01-25 10.1126/science.aao4174 24 view
Blum Eur. J. Immunol. Circulating plasmablasts are elevated and produce pathogenic anti-endothelial cell autoantibodies in idiopathic pulmonary arterial hypertension. 2018-01-25 10.1002/eji.201747460 1 view
Leija-Salazar Neuropathol. Appl. Neurobiol. Somatic mutations in neurodegeneration. 2018-01-25 10.1111/nan.12465 5 view
Achim Mol. Biol. Evol. Whole-body single-cell sequencing reveals transcriptional domains in the annelid larval body. 2018-01-24 10.1093/molbev/msx336 5 view
Betsholtz EMBO Mol Med Cell-cell signaling in blood vessel development and function. 2018-01-23 10.15252/emmm.201708610 1 view
Stévant Mol. Cell. Endocrinol. Single cell transcriptome sequencing: A new approach for the study of mammalian sex determination. 2018-01-22 10.1016/j.mce.2018.01.013 3 view
Patil Sci Immunol Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis. 2018-01-19 10.1126/sciimmunol.aan8664 2 view
Risso Nat Commun A general and flexible method for signal extraction from single-cell RNA-seq data. 2018-01-18 10.1038/s41467-017-02554-5 36 view
Sinha Nucleic Acids Res. dropClust: efficient clustering of ultra-large scRNA-seq data. 2018-01-18 10.1093/nar/gky007 9 view
Kalish Proc. Natl. Acad. Sci. U.S.A. Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement. 2018-01-17 10.1073/pnas.1717871115 6 view
Muliaditan Clin. Cancer Res. Repurposing tin mesoporphyrin as an immune checkpoint inhibitor shows therapeutic efficacy in preclinical models of cancer. 2018-01-16 10.1158/1078-0432.CCR-17-2587 4 view
Skelly Cell Rep Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart. 2018-01-16 10.1016/j.celrep.2017.12.072 27 view
Ghahramani Genome Biol. Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells. 2018-01-15 10.1186/s13059-017-1384-y 7 view
Hochgerner Nat. Neurosci. Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing. 2018-01-15 10.1038/s41593-017-0056-2 20 view
Pace Science The epigenetic control of stemness in CD8+ T cell fate commitment. 2018-01-12 10.1126/science.aah6499 view
Miragaia Sci Rep Single-cell RNA-sequencing resolves self-antigen expression during mTEC development. 2018-01-12 10.1038/s41598-017-19100-4 3 view
Fiers Brief Funct Genomics Mapping gene regulatory networks from single-cell omics data. 2018-01-12 10.1093/bfgp/elx046 20 view
Rodriguez-Fraticelli Nature Clonal analysis of lineage fate in native haematopoiesis. 2018-01-11 10.1038/nature25168 43 view
Tirosh Neuro-oncology Dissecting human gliomas by single-cell RNA sequencing. 2018-01-10 10.1093/neuonc/nox126 4 view
Maurer-Alcalá MBio Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics). 2018-01-09 10.1128/mBio.01836-17 4 view
Ding Genome Res. Reconstructing differentiation networks and their regulation from time series single cell expression data. 2018-01-09 10.1101/gr.225979.117 4 view
Chevée Cell Rep Variation in Activity State, Axonal Projection, and Position Define the Transcriptional Identity of Individual Neocortical Projection Neurons. 2018-01-09 10.1016/j.celrep.2017.12.046 18 view
Liang Nucleic Acids Res. Polysome-profiling in small tissue samples. 2018-01-09 10.1093/nar/gkx940 5 view
Das J. Clin. Invest. Early B cell changes predict autoimmunity following combination immune checkpoint blockade. 2018-01-08 10.1172/JCI96798 20 view
Basak Proc. Natl. Acad. Sci. U.S.A. Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy. 2018-01-08 10.1073/pnas.1715911114 view
Chen Proc. Natl. Acad. Sci. U.S.A. Reply to Edemir: Physiological regulation and single-cell RNA sequencing. 2018-01-08 10.1073/pnas.1720333115 view
Ibarra-Soria Nat. Cell Biol. Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation. 2018-01-08 10.1038/s41556-017-0013-z 11 view
Conrad Adv. Exp. Med. Biol. Single-Cell Expression Profiling and Proteomics of Primordial Germ Cells, Spermatogonial Stem Cells, Adult Germ Stem Cells, and Oocytes. 2018-01-04 10.1007/5584_2017_117 view
van den Bos Int. J. Biochem. Cell Biol. Single-cell sequencing to quantify genomic integrity in cancer. 2018-01-01 10.1016/j.biocel.2017.09.016 view
Barroso Genetics The Evolution of Gene-Specific Transcriptional Noise Is Driven by Selection at the Pathway Level. 2018-01-01 10.1534/genetics.117.300467 3 view
Fergusson Front Immunol Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens. 2018-01-01 10.3389/fimmu.2018.02902 view
Slowikowski Curr Opin Rheumatol Functional genomics of stromal cells in chronic inflammatory diseases. 2018-01-01 10.1097/BOR.0000000000000455 2 view
Malone Semin. Nephrol. Bringing Renal Biopsy Interpretation Into the Molecular Age With Single-Cell RNA Sequencing. 2018-01-01 10.1016/j.semnephrol.2017.09.005 7 view
Renthal Cephalalgia Localization of migraine susceptibility genes in human brain by single-cell RNA sequencing. 2018-01-01 10.1177/0333102418762476 2 view
Arlauckas Theranostics Arg1 expression defines immunosuppressive subsets of tumor-associated macrophages. 2018-01-01 10.7150/thno.26888 1 view
D'Gama Cell Rep Somatic Mutations Activating the mTOR Pathway in Dorsal Telencephalic Progenitors Cause a Continuum of Cortical Dysplasias. 2017-12-26 10.1016/j.celrep.2017.11.106 view
Tang Interdiscip Sci visnormsc: A Graphical User Interface to Normalize Single-cell RNA Sequencing Data. 2017-12-26 10.1007/s12539-017-0277-9 view
Yuzwa Cell Rep Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling. 2017-12-26 10.1016/j.celrep.2017.12.017 16 view
Zong Genome Biol. Single-cell RNA-seq study determines the ontogeny of macrophages in glioblastomas. 2017-12-21 10.1186/s13059-017-1375-z 1 view
Zhao Blood Single-cell RNA-seq reveals a distinct transcriptome signature of aneuploid hematopoietic cells. 2017-12-21 10.1182/blood-2017-08-803353 9 view
Bakken BMC Bioinformatics Cell type discovery and representation in the era of high-content single cell phenotyping. 2017-12-21 10.1186/s12859-017-1977-1 7 view
Wu DNA Cell Biol. Clinical Applications of and Challenges in Single-Cell Analysis of Circulating Tumor Cells. 2017-12-21 10.1089/dna.2017.3981 3 view
Müller Genome Biol. Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment. 2017-12-20 10.1186/s13059-017-1362-4 24 view
Nguyen Genome Med Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders. 2017-12-20 10.1186/s13073-017-0497-y 8 view
Cho Gene Single cell transcriptome analysis of muscle satellite cells reveals widespread transcriptional heterogeneity. 2017-12-15 10.1016/j.gene.2017.09.014 3 view
Alberti-Servera EMBO J. Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors. 2017-12-15 10.15252/embj.201797105 15 view
Casasent Cell Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing. 2017-12-14 10.1016/j.cell.2017.12.007 33 view
Gasch PLoS Biol. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. 2017-12-14 10.1371/journal.pbio.2004050 9 view
Bonnardel Curr. Opin. Immunol. Developmental control of macrophage function. 2017-12-13 10.1016/j.coi.2017.12.001 9 view
Chen Circulation Pathologic Stimulus Determines Lineage Commitment of Cardiac C-kit+ Cells. 2017-12-12 10.1161/CIRCULATIONAHA.117.030137 view
Phillips Stem Cells A novel approach to single cell RNA-seq analysis facilitates in silico gene reporting of human pluripotent stem cell-derived retinal cell types. 2017-12-12 10.1002/stem.2755 view
Horning Cancer Res. Single-cell RNA-seq reveals a subpopulation of prostate cancer cells with enhanced cell cycle-related transcription and attenuated androgen response. 2017-12-12 10.1158/0008-5472.CAN-17-1924 6 view
Artegiani Cell Rep A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche. 2017-12-12 10.1016/j.celrep.2017.11.050 19 view
Gomes Fernandes Hum. Reprod. Human-specific subcellular compartmentalization of P-element induced wimpy testis-like (PIWIL) granules during germ cell development and spermatogenesis. 2017-12-11 10.1093/humrep/dex365 view
Bach Nat Commun Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing. 2017-12-11 10.1038/s41467-017-02001-5 22 view
Kang Nat. Biotechnol. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. 2017-12-11 10.1038/nbt.4042 62 view
Athanasiadis Nat Commun Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis. 2017-12-11 10.1038/s41467-017-02305-6 17 view
Schwartzentruber Nat. Genet. Molecular and functional variation in iPSC-derived sensory neurons. 2017-12-11 10.1038/s41588-017-0005-8 26 view
Schelker Nat Commun Estimation of immune cell content in tumour tissue using single-cell RNA-seq data. 2017-12-11 10.1038/s41467-017-02289-3 28 view
Hrvatin Nat. Neurosci. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. 2017-12-11 10.1038/s41593-017-0029-5 40 view
Cheng Curr Opin Oncol Medical bioinformatics in melanoma. 2017-12-08 10.1097/CCO.0000000000000428 view
Medaglia Science Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq. 2017-12-07 10.1126/science.aao4277 24 view
Hu Mol. Cell Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq. 2017-12-07 10.1016/j.molcel.2017.11.017 11 view
Trevino Genome Biol Evol High-resolution single-cell sequencing of malaria parasites. 2017-12-06 10.1093/gbe/evx256 8 view
Tabib J. Invest. Dermatol. SFRP2/DPP4 and FMO1/LSP1 Define Major Fibroblast Populations in Human Skin. 2017-12-06 10.1016/j.jid.2017.09.045 10 view
Yeldell Org. Biomol. Chem. Oligonucleotide modifications enhance probe stability for single cell transcriptome in vivo analysis (TIVA). 2017-12-06 10.1039/c7ob02353g 3 view
Zhu Genome Med Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists. 2017-12-05 10.1186/s13073-017-0492-3 15 view
Cao Genes (Basel) scRNASeqDB: A Database for RNA-Seq Based Gene Expression Profiles in Human Single Cells. 2017-12-05 10.3390/genes8120368 7 view
Han Genome Res. SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells. 2017-12-05 10.1101/gr.223263.117 7 view
Swisa Cell Metab. Transcriptional Noise and Somatic Mutations in the Aging Pancreas. 2017-12-05 10.1016/j.cmet.2017.11.009 1 view
Su BMC Genomics Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development. 2017-12-04 10.1186/s12864-017-4342-x 6 view
Wang Clin Transl Med Single cell sequencing: a distinct new field. 2017-12-01 10.1186/s40169-017-0139-4 24 view
Fonseka Curr. Opin. Immunol. Leveraging blood and tissue CD4+ T cell heterogeneity at the single cell level to identify mechanisms of disease in rheumatoid arthritis. 2017-12-01 10.1016/j.coi.2017.08.005 view
Ellsworth Clin Transl Med Single-cell sequencing and tumorigenesis: improved understanding of tumor evolution and metastasis. 2017-12-01 10.1186/s40169-017-0145-6 18 view
Cadwell Nat Protoc Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq. 2017-12-01 10.1038/nprot.2017.120 12 view
Cuevas-Diaz Duran Clin Transl Med Single-cell RNA-sequencing of the brain. 2017-12-01 10.1186/s40169-017-0150-9 view
Shah Mol Oncol APE1/Ref-1 knockdown in pancreatic ductal adenocarcinoma - characterizing gene expression changes and identifying novel pathways using single-cell RNA sequencing. 2017-12-01 10.1002/1878-0261.12138 5 view
Sisakhtnezhad J. Cell. Physiol. Comparative analysis of single-cell RNA sequencing data from mouse spermatogonial and mesenchymal stem cells to identify differentially expressed genes and transcriptional regulators of germline cells. 2017-12-01 10.1002/jcp.26303 1 view
Schwalie Stem Cells Cross-Tissue Identification of Somatic Stem and Progenitor Cells Using a Single-Cell RNA-Sequencing Derived Gene Signature. 2017-12-01 10.1002/stem.2719 view
Mancarci eNeuro Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. 2017-12-01 10.1523/ENEURO.0212-17.2017 13 view
Haliburton PLoS ONE Genetic interaction mapping with microfluidic-based single cell sequencing. 2017-12-01 10.1371/journal.pone.0171302 6 view
van Bruggen Curr. Opin. Neurobiol. Single-cell transcriptomic analysis of oligodendrocyte lineage cells. 2017-12-01 10.1016/j.conb.2017.10.005 view
Wu Kidney Int. The promise of single-cell RNA sequencing for kidney disease investigation. 2017-12-01 10.1016/j.kint.2017.06.033 7 view
Toledo Br. J. Pharmacol. Translation of WNT developmental programs into stem cell replacement strategies for the treatment of Parkinson's disease. 2017-12-01 10.1111/bph.13871 view
Pfeffer Front Cell Neurosci Correlating Anatomy and Function with Gene Expression in Individual Neurons by Combining in Vivo Labeling, Patch Clamp, and Single Cell RNA-seq. 2017-12-01 10.3389/fncel.2017.00376 1 view
Han Biomed Res Int Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns. 2017-12-01 10.1155/2017/3035481 2 view
Sun Parasite Phylogenomic analysis of Balantidium ctenopharyngodoni (Ciliophora, Litostomatea) based on single-cell transcriptome sequencing. 2017-12-01 10.1051/parasite/2017043 1 view
Sun Nat Commun Inference of differentiation time for single cell transcriptomes using cell population reference data. 2017-11-30 10.1038/s41467-017-01860-2 6 view
Shi J. Neurosci. Neuromedin B Expression Defines the Mouse Retrotrapezoid Nucleus. 2017-11-29 10.1523/JNEUROSCI.2055-17.2017 4 view
Hochgerner Sci Rep STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array. 2017-11-27 10.1038/s41598-017-16546-4 view
Boufaied Sci Rep Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics. 2017-11-27 10.1038/s41598-017-16685-8 view
Griffiths BMC Genomics Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data. 2017-11-25 10.1186/s12864-017-4253-x view
Magella Dev. Biol. Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf. 2017-11-25 10.1016/j.ydbio.2017.11.006 20 view
Easton BMC Genomics Genome-wide segregation of single nucleotide and structural variants into single cancer cells. 2017-11-25 10.1186/s12864-017-4286-1 view
Cook Nucleic Acids Res. The European Bioinformatics Institute in 2017: data coordination and integration. 2017-11-25 10.1093/nar/gkx1154 10 view
Chen Mol. Aspects Med. Constructing cell lineages from single-cell transcriptomes. 2017-11-24 10.1016/j.mam.2017.10.004 3 view
Liu BMC Cancer Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer. 2017-11-23 10.1186/s12885-017-3777-4 3 view
Spanjaard Curr. Opin. Cell Biol. Methods for lineage tracing on the organism-wide level. 2017-11-22 10.1016/ 5 view
Zhu Cell Biol. Toxicol. Progress and challenges of sequencing and analyzing circulating tumor cells. 2017-11-22 10.1007/s10565-017-9418-5 10 view
Faure Cell Syst Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells. 2017-11-22 10.1016/j.cels.2017.10.003 7 view
Ivanovitch J Cardiovasc Dev Dis Growth and Morphogenesis during Early Heart Development in Amniotes. 2017-11-22 10.3390/jcdd4040020 1 view
Wang Anal. Chem. Raman-Activated Droplet Sorting (RADS) for Label-Free High-Throughput Screening of Microalgal Single-Cells. 2017-11-21 10.1021/acs.analchem.7b03884 8 view
Prykhozhij Curr Gene Ther New Developments in CRISPR/Cas-based Functional Genomics and their Implications for Research using Zebrafish. 2017-11-21 10.2174/1566523217666171121164132 6 view
Turaj Cancer Cell Antibody Tumor Targeting Is Enhanced by CD27 Agonists through Myeloid Recruitment. 2017-11-21 10.1016/j.ccell.2017.11.001 9 view
Herbach BMC Syst Biol Inferring gene regulatory networks from single-cell data: a mechanistic approach. 2017-11-21 10.1186/s12918-017-0487-0 12 view
Allison Nat Rev Nephrol Gene expression: Single-cell RNA sequencing of collecting duct cells. 2017-11-20 10.1038/nrneph.2017.163 view
Kurata J. Hum. Genet. CRISPR/Cas9 library screening for drug target discovery. 2017-11-20 10.1038/s10038-017-0376-9 5 view
McCormick Antioxid. Redox Signal. Recent Advances in the Systems Biology of Aging. 2017-11-20 10.1089/ars.2017.7367 1 view
Yip Nucleic Acids Res. Linnorm: improved statistical analysis for single cell RNA-seq expression data. 2017-11-17 10.1093/nar/gkx1189 10 view
Li Cell Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing. 2017-11-16 10.1016/j.cell.2017.10.019 29 view
Angelos Stem Cells Single Cell Resolution of Human Hematoendothelial Cells Defines Transcriptional Signatures of Hemogenic Endothelium. 2017-11-15 10.1002/stem.2739 2 view
Chen Proc. Natl. Acad. Sci. U.S.A. Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq. 2017-11-14 10.1073/pnas.1710964114 30 view
Racle Elife Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. 2017-11-13 10.7554/eLife.26476 21 view
Zhao BMC Genomics Characteristics of allelic gene expression in human brain cells from single-cell RNA-seq data analysis. 2017-11-10 10.1186/s12864-017-4261-x 2 view
Baran-Gale Brief Funct Genomics Experimental design for single-cell RNA sequencing. 2017-11-08 10.1093/bfgp/elx035 14 view
Dagogo-Jack Nat Rev Clin Oncol Tumour heterogeneity and resistance to cancer therapies. 2017-11-08 10.1038/nrclinonc.2017.166 93 view
Ma Curr. Opin. Neurobiol. Neural lineage tracing in the mammalian brain. 2017-11-07 10.1016/j.conb.2017.10.013 6 view
Acosta Stem Cell Res Ther Single cell transcriptomics suggest that human adipocyte progenitor cells constitute a homogeneous cell population. 2017-11-07 10.1186/s13287-017-0701-4 6 view
Buettner Genome Biol. f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq. 2017-11-07 10.1186/s13059-017-1334-8 17 view
Herring Cell Syst Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. 2017-11-07 10.1016/j.cels.2017.10.012 22 view
King Nat. Med. IRF3 and type I interferons fuel a fatal response to myocardial infarction. 2017-11-06 10.1038/nm.4428 41 view
Hicks Biostatistics Missing data and technical variability in single-cell RNA-sequencing experiments. 2017-11-06 10.1093/biostatistics/kxx053 33 view
Porubsky Nat Commun Dense and accurate whole-chromosome haplotyping of individual genomes. 2017-11-03 10.1038/s41467-017-01389-4 16 view
Rantalainen Brief Funct Genomics Application of single-cell sequencing in human cancer. 2017-11-02 10.1093/bfgp/elx036 6 view
Calderon Am. J. Hum. Genet. Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression. 2017-11-02 10.1016/j.ajhg.2017.09.009 11 view
Li Nucleic Acids Res. Network embedding-based representation learning for single cell RNA-seq data. 2017-11-02 10.1093/nar/gkx750 4 view
Jia Nucleic Acids Res. Accounting for technical noise in differential expression analysis of single-cell RNA sequencing data. 2017-11-02 10.1093/nar/gkx754 6 view
Liu Nature Single-cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte. 2017-11-02 10.1038/nature24454 28 view
Poran Nature Single-cell RNA sequencing reveals a signature of sexual commitment in malaria parasites. 2017-11-02 10.1038/nature24280 30 view
Lu Kidney Int. Genome-wide identification of genes essential for podocyte cytoskeletons based on single-cell RNA sequencing. 2017-11-01 10.1016/j.kint.2017.04.022 12 view
Balakrishnan Biol. Blood Marrow Transplant. Proinflammatory Dual Receptor T Cells in Chronic Graft-versus-Host Disease. 2017-11-01 10.1016/j.bbmt.2017.07.016 1 view
Heintze Nat Rev Nephrol Developmental biology: Single-cell RNA sequencing identifies novel kidney cell types in zebrafish. 2017-11-01 10.1038/nrneph.2017.137 view
Yamamoto Nat. Methods Long-term expansion of alveolar stem cells derived from human iPS cells in organoids. 2017-11-01 10.1038/nmeth.4448 20 view
Kuipers Genome Res. Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors. 2017-11-01 10.1101/gr.220707.117 15 view
Schiffer Kidney Int. Going single but not solo with podocytes: potentials, limitations, and pitfalls of single-cell analysis. 2017-11-01 10.1016/j.kint.2017.05.033 view
Gawronski Wiley Interdiscip Rev RNA Single cell transcriptomics of noncoding RNAs and their cell-specificity. 2017-11-01 10.1002/wrna.1433 1 view
Liu Stem Cells Dev. Single-Cell Sequencing Technologies for Cardiac Stem Cell Studies. 2017-11-01 10.1089/scd.2017.0050 3 view
Nguyen PLoS ONE Diversity amongst trigeminal neurons revealed by high throughput single cell sequencing. 2017-11-01 10.1371/journal.pone.0185543 12 view
Lun Genome Res. Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data. 2017-11-01 10.1101/gr.222877.117 13 view
Wang Genome Res. Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons. 2017-11-01 10.1101/gr.223313.117 5 view
Brady Nat Commun Combating subclonal evolution of resistant cancer phenotypes. 2017-11-01 10.1038/s41467-017-01174-3 14 view
Vieth Bioinformatics powsimR: power analysis for bulk and single cell RNA-seq experiments. 2017-11-01 10.1093/bioinformatics/btx435 16 view
Aibar Nat. Methods SCENIC: single-cell regulatory network inference and clustering. 2017-11-01 10.1038/nmeth.4463 68 view
Wei Int. J. Biochem. Cell Biol. A short review of variants calling for single-cell-sequencing data with applications. 2017-11-01 10.1016/j.biocel.2017.09.018 view
Darmanis Cell Rep Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma. 2017-10-31 10.1016/j.celrep.2017.10.030 27 view
Woyke Nat. Methods The trajectory of microbial single-cell sequencing. 2017-10-31 10.1038/nmeth.4469 10 view
Savage Cell Rep A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer. 2017-10-31 10.1016/j.celrep.2017.10.015 9 view
Walker Nat. Rev. Immunol. TH2 cell development and function. 2017-10-30 10.1038/nri.2017.118 view
Lu Mol. Ther. An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors. 2017-10-28 10.1016/j.ymthe.2017.10.018 9 view
Avital Genome Biol. scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing. 2017-10-27 10.1186/s13059-017-1340-x 9 view
Bick Proc. Natl. Acad. Sci. U.S.A. Cardiovascular homeostasis dependence on MICU2, a regulatory subunit of the mitochondrial calcium uniporter. 2017-10-24 10.1073/pnas.1711303114 4 view
Semrau Nat Commun Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells. 2017-10-23 10.1038/s41467-017-01076-4 24 view
Chen Sci Rep Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes. 2017-10-19 10.1038/s41598-017-13665-w 6 view
Abugessaisa Nucleic Acids Res. SCPortalen: human and mouse single-cell centric database. 2017-10-17 10.1093/nar/gkx949 4 view
Golkaram Sci Rep The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation. 2017-10-17 10.1038/s41598-017-13731-3 2 view
Aarts Genes Dev. Coupling shRNA screens with single-cell RNA-seq identifies a dual role for mTOR in reprogramming-induced senescence. 2017-10-15 10.1101/gad.297796.117 7 view
Chlis Bioinformatics Model-based branching point detection in single-cell data by K-branches clustering. 2017-10-15 10.1093/bioinformatics/btx325 5 view
Karaiskos Science The Drosophila embryo at single-cell transcriptome resolution. 2017-10-13 10.1126/science.aan3235 64 view
Gilligan Lab Chip Single cell sequencing: An engineer and business person's perspective on how we got here. 2017-10-11 10.1039/c7lc90095c view
Wu Neuron Detecting Activated Cell Populations Using Single-Cell RNA-Seq. 2017-10-11 10.1016/j.neuron.2017.09.026 31 view
Honda Elife Molecular architecture underlying fluid absorption by the developing inner ear. 2017-10-10 10.7554/eLife.26851 1 view
Mathys Cell Rep Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution. 2017-10-10 10.1016/j.celrep.2017.09.039 53 view
Briggs Elife Mouse embryonic stem cells can differentiate via multiple paths to the same state. 2017-10-09 10.7554/eLife.26945 19 view
Stubbington Science Single-cell transcriptomics to explore the immune system in health and disease. 2017-10-06 10.1126/science.aan6828 58 view
Lein Science The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing. 2017-10-06 10.1126/science.aan6827 54 view
Rizzetto Sci Rep Impact of sequencing depth and read length on single cell RNA sequencing data of T cells. 2017-10-06 10.1038/s41598-017-12989-x 11 view
Enge Cell Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns. 2017-10-05 10.1016/j.cell.2017.09.004 43 view
Guo Cell Stem Cell Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development. 2017-10-05 10.1016/j.stem.2017.09.003 22 view
Yang BMC Genomics SAIC: an iterative clustering approach for analysis of single cell RNA-seq data. 2017-10-03 10.1186/s12864-017-4019-5 2 view
Zhao BMC Genomics The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics. 2017-10-03 10.1186/s12864-017-4018-6 view
Hayashi Oncotarget Size-based detection of sarcoma circulating tumor cells and cell clusters. 2017-10-03 10.18632/oncotarget.20697 2 view
Dvoryanchikov Nat Commun Transcriptomes and neurotransmitter profiles of classes of gustatory and somatosensory neurons in the geniculate ganglion. 2017-10-02 10.1038/s41467-017-01095-1 4 view
Tang J. Exp. Med. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. 2017-10-02 10.1084/jem.20170976 17 view
Adam Development Psychrophilic proteases dramatically reduce single-cell RNA-seq artifacts: a molecular atlas of kidney development. 2017-10-01 10.1242/dev.151142 18 view
Johnson J. Neurovirol. Lack of human cytomegalovirus expression in single cells from glioblastoma tumors and cell lines. 2017-10-01 10.1007/s13365-017-0543-y 3 view
Natarajan Curr. Opin. Genet. Dev. Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation. 2017-10-01 10.1016/j.gde.2017.06.003 5 view
Tripathy PLoS Comput. Biol. Transcriptomic correlates of neuron electrophysiological diversity. 2017-10-01 10.1371/journal.pcbi.1005814 9 view
Behjati Nat Rev Clin Oncol Genetics: Taking single-cell transcriptomics to the bedside. 2017-10-01 10.1038/nrclinonc.2017.117 2 view
Medeiros Mol. Ecol. Single-cell sequencing unveils the lifestyle and CRISPR-based population history of Hydrotalea sp. in acid mine drainage. 2017-10-01 10.1111/mec.14294 2 view
Tripathi Int. J. Biochem. Cell Biol. A computational integrative approach based on alternative splicing analysis to compare immortalized and primary cancer cells. 2017-10-01 10.1016/j.biocel.2017.07.010 view
Glass Mol Metab Single-cell RNA-sequencing reveals a distinct population of proglucagon-expressing cells specific to the mouse upper small intestine. 2017-10-01 10.1016/j.molmet.2017.07.014 14 view
Rato PLoS Pathog. Single-cell analysis identifies cellular markers of the HIV permissive cell. 2017-10-01 10.1371/journal.ppat.1006678 4 view
Gardeux Bioinformatics ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data. 2017-10-01 10.1093/bioinformatics/btx337 18 view
Weaver BioTechniques SEQUENCING BRAIN CELLS. 2017-10-01 10.2144/000114600 view
Xiao Stem Cell Res Ther Microbiota regulates bone marrow mesenchymal stem cell lineage differentiation and immunomodulation. 2017-09-29 10.1186/s13287-017-0670-7 2 view
Lin Nucleic Acids Res. Using neural networks for reducing the dimensions of single-cell RNA-Seq data. 2017-09-29 10.1093/nar/gkx681 28 view
van den Brink Nat. Methods Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations. 2017-09-29 10.1038/nmeth.4437 view
Felmlee Hepatology Zooming in on Liver Zonation. 2017-09-27 10.1002/hep.29554 view
Wallrapp Nature The neuropeptide NMU amplifies ILC2-driven allergic lung inflammation. 2017-09-21 10.1038/nature24029 82 view
Shalek Sci Transl Med Single-cell analyses to tailor treatments. 2017-09-20 10.1126/scitranslmed.aan4730 16 view
Afik Nucleic Acids Res. Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state. 2017-09-19 10.1093/nar/gkx615 17 view
Zafar Genome Biol. SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models. 2017-09-19 10.1186/s13059-017-1311-2 17 view
Zappia Genome Biol. Splatter: simulation of single-cell RNA sequencing data. 2017-09-12 10.1186/s13059-017-1305-0 32 view
Chen Curr Protoc Mouse Biol Profiling of Single-Cell Transcriptomes. 2017-09-08 10.1002/cpmo.30 2 view
Zhou Cell Tissue Res. Lessons from single-cell transcriptome analysis of oxygen-sensing cells. 2017-09-08 10.1007/s00441-017-2682-0 2 view
Moreira de Mello Sci Rep Early X chromosome inactivation during human preimplantation development revealed by single-cell RNA-sequencing. 2017-09-07 10.1038/s41598-017-11044-z view
Zepp Cell Distinct Mesenchymal Lineages and Niches Promote Epithelial Self-Renewal and Myofibrogenesis in the Lung. 2017-09-07 10.1016/j.cell.2017.07.034 52 view
Xiang Cell Stem Cell Fusion of Regionally Specified hPSC-Derived Organoids Models Human Brain Development and Interneuron Migration. 2017-09-07 10.1016/j.stem.2017.07.007 32 view
Lee Cell Anatomically and Functionally Distinct Lung Mesenchymal Populations Marked by Lgr5 and Lgr6. 2017-09-07 10.1016/j.cell.2017.07.028 47 view
Benitez Int. J. Biochem. Cell Biol. Revealing allele-specific gene expression by single-cell transcriptomics. 2017-09-01 10.1016/j.biocel.2017.05.029 5 view
Khomtchouk PLoS ONE shinyheatmap: Ultra fast low memory heatmap web interface for big data genomics. 2017-09-01 10.1371/journal.pone.0176334 9 view
Arzalluz-Luque Int. J. Biochem. Cell Biol. Delineating biological and technical variance in single cell expression data. 2017-09-01 10.1016/j.biocel.2017.07.006 2 view
Cao Int. J. Biochem. Cell Biol. Current research development of single cell genome in urological tumor. 2017-09-01 10.1016/j.biocel.2017.08.003 1 view
Perland Open Biol Characteristics of 29 novel atypical solute carriers of major facilitator superfamily type: evolutionary conservation, predicted structure and neuronal co-expression. 2017-09-01 10.1098/rsob.170142 10 view
Park Toxicol. Appl. Pharmacol. Single-cell RNA sequencing reveals an altered gene expression pattern as a result of CRISPR/cas9-mediated deletion of Gene 33/Mig6 and chronic exposure to hexavalent chromium in human lung epithelial cells. 2017-09-01 10.1016/j.taap.2017.07.003 3 view
Shugay Nucleic Acids Res. VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. 2017-09-01 10.1093/nar/gkx760 36 view
Tritschler Mol Metab Systematic single-cell analysis provides new insights into heterogeneity and plasticity of the pancreas. 2017-09-01 10.1016/j.molmet.2017.06.021 9 view
Kang Mol. Biol. Evol. Between a Pod and a Hard Test: The Deep Evolution of Amoebae. 2017-09-01 10.1093/molbev/msx162 39 view
Jaakkola Brief. Bioinformatics Comparison of methods to detect differentially expressed genes between single-cell populations. 2017-09-01 10.1093/bib/bbw057 29 view
Kidd Trends Immunol. Environments Tune and Select Cellular Diversity. 2017-09-01 10.1016/ view
Wu Curr Top Med Chem Single-Cell Sequencing for Drug Discovery and Drug Development. 2017-09-01 10.2174/1568026617666161116145358 1 view
Liu Int. J. Biol. Sci. Current Progresses of Single Cell DNA Sequencing in Breast Cancer Research. 2017-09-01 10.7150/ijbs.19627 2 view
Stoeckius Nat. Methods Simultaneous epitope and transcriptome measurement in single cells. 2017-09-01 10.1038/nmeth.4380 81 view
Dai J. Assist. Reprod. Genet. Time-lapse observation and transcriptome analysis of a case with repeated multiple pronuclei after IVF/ICSI. 2017-09-01 10.1007/s10815-017-0972-9 view
Kato R Soc Open Sci Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer. 2017-09-01 10.1098/rsos.171060 view
Zhang Biosci. Rep. The comparison of the performance of four whole genome amplification kits on ion proton platform in copy number variation detection. 2017-08-31 10.1042/BSR20170252 2 view
Mitchell Semin. Cell Dev. Biol. Enhancing our brains: Genomic mechanisms underlying cortical evolution. 2017-08-31 10.1016/j.semcdb.2017.08.045 7 view
Zhang Sci Rep A Total-variation Constrained Permutation Model for Revealing Common Copy Number Patterns. 2017-08-29 10.1038/s41598-017-09139-8 view
Baslan Nat. Rev. Cancer Unravelling biology and shifting paradigms in cancer with single-cell sequencing. 2017-08-24 10.1038/nrc.2017.58 34 view
Mackenzie Nature cGAS surveillance of micronuclei links genome instability to innate immunity. 2017-08-24 10.1038/nature23449 127 view
Zhou Sci Rep Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes. 2017-08-18 10.1038/s41598-017-09307-w 6 view
Haque Genome Med A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. 2017-08-18 10.1186/s13073-017-0467-4 60 view
Sloan Neuron Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells. 2017-08-16 10.1016/j.neuron.2017.07.035 48 view
Shaham Bioinformatics Removal of batch effects using distribution-matching residual networks. 2017-08-15 10.1093/bioinformatics/btx196 32 view
Rashid Bioinformatics TASIC: determining branching models from time series single cell data. 2017-08-15 10.1093/bioinformatics/btx173 12 view
Gao Nat Commun Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer. 2017-08-09 10.1038/s41467-017-00244-w 22 view
Sukumaran Sci Rep Whole transcriptome profiling of taste bud cells. 2017-08-08 10.1038/s41598-017-07746-z 6 view
Zhu Oncotarget Advances in single-cell RNA sequencing and its applications in cancer research. 2017-08-08 10.18632/oncotarget.17893 18 view
Kokkinopoulos Stem Cell Reports Adventitial SCA-1+ Progenitor Cell Gene Sequencing Reveals the Mechanisms of Cell Migration in Response to Hyperlipidemia. 2017-08-08 10.1016/j.stemcr.2017.06.011 7 view
Papalexi Nat. Rev. Immunol. Single-cell RNA sequencing to explore immune cell heterogeneity. 2017-08-07 10.1038/nri.2017.76 88 view
Sun Bioinformatics DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data. 2017-08-02 10.1093/bioinformatics/btx490 6 view
Hunter Front Genet Evidence for Loss in Identity, De-Differentiation, and Trans-Differentiation of Islet β-Cells in Type 2 Diabetes. 2017-08-01 10.3389/fgene.2017.00035 7 view
Lu Kidney Int. Single-cell RNA-sequence analysis of mouse glomerular mesangial cells uncovers mesangial cell essential genes. 2017-08-01 10.1016/j.kint.2017.01.016 13 view
Phipson F1000Res Gene length and detection bias in single cell RNA sequencing protocols. 2017-08-01 10.12688/f1000research.11290.1 9 view
Basu SLAS Technol Digital Assays Part II: Digital Protein and Cell Assays. 2017-08-01 10.1177/2472630317705681 5 view
Dal Molin Front Genet Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods. 2017-08-01 10.3389/fgene.2017.00062 view
Müller Front Genet Single-Cell mRNA Sequencing in Cancer Research: Integrating the Genomic Fingerprint. 2017-08-01 10.3389/fgene.2017.00073 9 view
Gao Genome Res. Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells. 2017-08-01 10.1101/gr.216788.116 13 view
Dentro Cold Spring Harb Perspect Med Principles of Reconstructing the Subclonal Architecture of Cancers. 2017-08-01 10.1101/cshperspect.a026625 5 view
E Hirbec Front Aging Neurosci Microglia Responses in Acute and Chronic Neurological Diseases: What Microglia-Specific Transcriptomic Studies Taught (and did Not Teach) Us. 2017-08-01 10.3389/fnagi.2017.00227 view
Rostom FEBS Lett. Computational approaches for interpreting scRNA-seq data. 2017-08-01 10.1002/1873-3468.12684 23 view
Vandin Front Genet Computational Methods for Characterizing Cancer Mutational Heterogeneity. 2017-08-01 10.3389/fgene.2017.00083 3 view
Xue Nat. Med. An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer. 2017-08-01 10.1038/nm.4369 view
Mohammed Cell Rep Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation. 2017-08-01 10.1016/j.celrep.2017.07.009 36 view
Zhu PeerJ Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization. 2017-08-01 10.7717/peerj.2888 15 view
Matsumoto Bioinformatics SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. 2017-08-01 10.1093/bioinformatics/btx194 21 view
Kim Exp. Hematol. CBP/Catenin antagonists: Targeting LSCs' Achilles heel. 2017-08-01 10.1016/j.exphem.2017.04.010 view
Rahman J. Clin. Invest. Inflammatory Ly6Chi monocytes and their conversion to M2 macrophages drive atherosclerosis regression. 2017-08-01 10.1172/JCI75005 20 view
Shi Protein Cell Single-cell transcriptomics reveals gene signatures and alterations associated with aging in distinct neural stem/progenitor cell subpopulations. 2017-07-26 10.1007/s13238-017-0450-2 6 view
Klein Lab Chip InDrops and Drop-seq technologies for single-cell sequencing. 2017-07-25 10.1039/c7lc90070h 2 view
Weitz Lab Chip Perspective on droplet-based single-cell sequencing. 2017-07-25 10.1039/c7lc90069d 1 view
Zhang Proc. Natl. Acad. Sci. U.S.A. Functional characterization of human pluripotent stem cell-derived arterial endothelial cells. 2017-07-25 10.1073/pnas.1702295114 24 view
Rato Virus Res. Exploring viral infection using single-cell sequencing. 2017-07-15 10.1016/j.virusres.2016.10.016 11 view
Malenczyk EMBO J. A TRPV1-to-secretagogin regulatory axis controls pancreatic β-cell survival by modulating protein turnover. 2017-07-14 10.15252/embj.201695347 7 view
Hosokawa Sci Rep Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics. 2017-07-12 10.1038/s41598-017-05436-4 14 view
Hupe Sci Signal Gene expression profiles of brain endothelial cells during embryonic development at bulk and single-cell levels. 2017-07-11 10.1126/scisignal.aag2476 13 view
Dorajoo Sci Rep Single-cell transcriptomics of East-Asian pancreatic islets cells. 2017-07-10 10.1038/s41598-017-05266-4 1 view
Goldstein BMC Genomics Massively parallel nanowell-based single-cell gene expression profiling. 2017-07-07 10.1186/s12864-017-3893-1 19 view
Zhang Brief. Bioinformatics SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data. 2017-07-07 10.1093/bib/bbx074 1 view
Cadwell BMC Biol. Q&A: using Patch-seq to profile single cells. 2017-07-06 10.1186/s12915-017-0396-0 927 view
Lechner Cell Stem Cell Recruited Monocytes and Type 2 Immunity Promote Lung Regeneration following Pneumonectomy. 2017-07-06 10.1016/j.stem.2017.03.024 21 view
Ding G3 (Bethesda) Assessment of Single Cell RNA-Seq Normalization Methods. 2017-07-05 10.1534/g3.117.040683 1 view
Perkel Nature Single-cell sequencing made simple. 2017-07-03 10.1038/547125a 6 view
Zhang Arch. Toxicol. Precision toxicology based on single cell sequencing: an evolving trend in toxicological evaluations and mechanism exploration. 2017-07-01 10.1007/s00204-017-1971-4 3 view
Krabberød Mol. Biol. Evol. Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria. 2017-07-01 10.1093/molbev/msx075 12 view
Lee Trends Mol Med De Novo Gene Expression Reconstruction in Space. 2017-07-01 10.1016/j.molmed.2017.05.004 3 view
Krasnitz Trends Mol Med Early Detection of Cancer in Blood Using Single-Cell Analysis: A Proposal. 2017-07-01 10.1016/j.molmed.2017.05.005 view
Santoferrara Mol. Phylogenet. Evol. Phylogeny, classification and diversity of Choreotrichia and Oligotrichia (Ciliophora, Spirotrichea). 2017-07-01 10.1016/j.ympev.2017.03.010 12 view
Lun Biostatistics Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data. 2017-07-01 10.1093/biostatistics/kxw055 11 view
Farmer Development Defining epithelial cell dynamics and lineage relationships in the developing lacrimal gland. 2017-07-01 10.1242/dev.150789 8 view
Doud FEMS Microbiol. Rev. Novel approaches in function-driven single-cell genomics. 2017-07-01 10.1093/femsre/fux009 3 view
Suffiotti Immunogenetics Identification of innate lymphoid cells in single-cell RNA-Seq data. 2017-07-01 10.1007/s00251-017-1002-x 3 view
Shi J. Comput. Biol. Identifying Cell Subpopulations and Their Genetic Drivers from Single-Cell RNA-Seq Data Using a Biclustering Approach. 2017-07-01 10.1089/cmb.2017.0049 3 view
Cerosaletti J. Immunol. Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes. 2017-07-01 10.4049/jimmunol.1700172 view
Mpina J. Immunol. Controlled Human Malaria Infection Leads to Long-Lasting Changes in Innate and Innate-like Lymphocyte Populations. 2017-07-01 10.4049/jimmunol.1601989 15 view
Nirschl Cell IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment. 2017-06-29 10.1016/j.cell.2017.06.016 31 view
Huang Genome Biol. BRIE: transcriptome-wide splicing quantification in single cells. 2017-06-27 10.1186/s13059-017-1248-5 11 view
Kar Nat Commun Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression. 2017-06-26 10.1038/s41467-017-00052-2 18 view
Camp Nature Multilineage communication regulates human liver bud development from pluripotency. 2017-06-22 10.1038/nature22796 76 view
Wang J Genet Genomics Differential gene network analysis from single cell RNA-seq. 2017-06-20 10.1016/j.jgg.2017.03.001 3 view
Liu Nat Commun Reconstructing cell cycle pseudo time-series via single-cell transcriptome data. 2017-06-19 10.1038/s41467-017-00039-z 10 view
Antolović Curr. Biol. Generation of Single-Cell Transcript Variability by Repression. 2017-06-19 10.1016/j.cub.2017.05.028 10 view
Li Sci Rep Dosage compensation in the process of inactivation/reactivation during both germ cell development and early embryogenesis in mouse. 2017-06-16 10.1038/s41598-017-03829-z view
Zheng Cell Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing. 2017-06-15 10.1016/j.cell.2017.05.035 128 view
Wu Annu Rev Anal Chem (Palo Alto Calif) Single-Cell Transcriptional Analysis. 2017-06-12 10.1146/annurev-anchem-061516-045228 18 view
Wen J. Biol. Chem. Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos. 2017-06-09 10.1074/jbc.M117.780585 8 view
Kang Dev. Cell Lineage Establishment and Progression within the Inner Cell Mass of the Mouse Blastocyst Requires FGFR1 and FGFR2. 2017-06-05 10.1016/j.devcel.2017.05.003 38 view
Picardi RNA Single-cell transcriptomics reveals specific RNA editing signatures in the human brain. 2017-06-01 10.1261/rna.058271.116 18 view
Hawkins J. Clin. Invest. Prospective isolation of NKX2-1-expressing human lung progenitors derived from pluripotent stem cells. 2017-06-01 10.1172/JCI89950 21 view
Vallejos Nat. Methods Normalizing single-cell RNA sequencing data: challenges and opportunities. 2017-06-01 10.1038/nmeth.4292 79 view
Teschendorff Nat Commun Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome. 2017-06-01 10.1038/ncomms15599 view
Ofengeim Trends Mol Med Single-Cell RNA Sequencing: Unraveling the Brain One Cell at a Time. 2017-06-01 10.1016/j.molmed.2017.04.006 23 view
Wu PLoS Comput. Biol. Independent regulation of gene expression level and noise by histone modifications. 2017-06-01 10.1371/journal.pcbi.1005585 10 view
Sanders Nat Protoc Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs. 2017-06-01 10.1038/nprot.2017.029 10 view
Bacher Nat. Methods SCnorm: robust normalization of single-cell RNA-seq data. 2017-06-01 10.1038/nmeth.4263 35 view
Luo Harmful Algae Adding new pieces to the Azadinium (Dinophyceae) diversity and biogeography puzzle: Non-toxigenic Azadinium zhuanum sp. nov. from China, toxigenic A. poporum from the Mediterranean, and a non-toxigenic A. dalianense from the French Atlantic. 2017-06-01 10.1016/j.hal.2017.05.001 14 view
Rizvi Nat. Biotechnol. Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development. 2017-06-01 10.1038/nbt.3854 62 view
Teng Neuro-oncology Dissecting inherent intratumor heterogeneity in patient-derived glioblastoma culture models. 2017-06-01 10.1093/neuonc/now253 7 view
Giustacchini Nat. Med. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia. 2017-06-01 10.1038/nm.4336 67 view
Li Cell Stem Cell Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. 2017-06-01 10.1016/j.stem.2017.03.007 56 view
Fletcher Cell Stem Cell Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution. 2017-06-01 10.1016/j.stem.2017.04.003 31 view
Qi J. Neurosci. Hierarchical Specification of Pruriceptors by Runt-Domain Transcription Factor Runx1. 2017-05-31 10.1523/JNEUROSCI.0094-17.2017 3 view
Batiuk J. Biol. Chem. An immunoaffinity-based method for isolating ultrapure adult astrocytes based on ATP1B2 targeting by the ACSA-2 antibody. 2017-05-26 10.1074/jbc.M116.765313 9 view
Chung Nature Identification of preoptic sleep neurons using retrograde labelling and gene profiling. 2017-05-25 10.1038/nature22350 66 view
Kirschner Cell Rep Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment. 2017-05-23 10.1016/j.celrep.2017.04.074 10 view
Wang BMC Bioinformatics DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data. 2017-05-23 10.1186/s12859-017-1647-3 2 view
Laboissonniere J Vis Exp Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells. 2017-05-22 10.3791/55229 2 view
Alles BMC Biol. Cell fixation and preservation for droplet-based single-cell transcriptomics. 2017-05-19 10.1186/s12915-017-0383-5 36 view
Lasrado Science Lineage-dependent spatial and functional organization of the mammalian enteric nervous system. 2017-05-19 10.1126/science.aam7511 18 view
Cabezas-Wallscheid Cell Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy. 2017-05-18 10.1016/j.cell.2017.04.018 41 view
Dai Proc. Natl. Acad. Sci. U.S.A. Conditional knockin of Dnmt3a R878H initiates acute myeloid leukemia with mTOR pathway involvement. 2017-05-16 10.1073/pnas.1703476114 9 view
Mildner Immunity Genomic Characterization of Murine Monocytes Reveals C/EBPβ Transcription Factor Dependence of Ly6C- Cells. 2017-05-16 10.1016/j.immuni.2017.04.018 40 view
Blasi Phys Biol cgCorrect: a method to correct for confounding cell-cell variation due to cell growth in single-cell transcriptomics. 2017-05-11 10.1088/1478-3975/aa609a view
Karlsson Mol. Syst. Biol. Alternative TSSs are co-regulated in single cells in the mouse brain. 2017-05-11 10.15252/msb.20167374 4 view
Gouti Dev. Cell A Gene Regulatory Network Balances Neural and Mesoderm Specification during Vertebrate Trunk Development. 2017-05-08 10.1016/j.devcel.2017.04.002 27 view
Chung Nat Commun Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer. 2017-05-05 10.1038/ncomms15081 92 view
Picelli RNA Biol Single-cell RNA-sequencing: The future of genome biology is now. 2017-05-04 10.1080/15476286.2016.1201618 37 view
Der JCI Insight Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis. 2017-05-04 10.1172/jci.insight.93009 28 view
Pruitt J Vis Exp Isolation of the Side Population in Myc-induced T-cell Acute Lymphoblastic Leukemia in Zebrafish. 2017-05-04 10.3791/55711 1 view
Zeng Cell Metab. Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation. 2017-05-02 10.1016/j.cmet.2017.04.014 22 view
Liu ISME J Single-cell transcriptomics of small microbial eukaryotes: limitations and potential. 2017-05-01 10.1038/ismej.2016.190 7 view
Kiselev Nat. Methods SC3: consensus clustering of single-cell RNA-seq data. 2017-05-01 10.1038/nmeth.4236 186 view
Lam Mol Metab Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing. 2017-05-01 10.1016/j.molmet.2017.02.007 27 view
Camp Development Human organomics: a fresh approach to understanding human development using single-cell transcriptomics. 2017-05-01 10.1242/dev.150458 6 view
Ner-Gaon J. Immunol. JingleBells: A Repository of Immune-Related Single-Cell RNA-Sequencing Datasets. 2017-05-01 10.4049/jimmunol.1700272 6 view
Li Nat. Genet. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. 2017-05-01 10.1038/ng.3818 112 view
Lane Cell Syst Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation. 2017-04-26 10.1016/j.cels.2017.03.010 28 view
Jiang Genome Biol. SCALE: modeling allele-specific gene expression by single-cell RNA sequencing. 2017-04-26 10.1186/s13059-017-1200-8 11 view
Villani Science Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. 2017-04-21 10.1126/science.aah4573 298 view
van Arensbergen Mol. Cell Functional Enhancer Screening in Single Cells. 2017-04-20 10.1016/j.molcel.2017.03.018 view
Yang Cell Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices. 2017-04-20 10.1016/j.cell.2017.03.038 54 view
Guo Nucleic Acids Res. SLICE: determining cell differentiation and lineage based on single cell entropy. 2017-04-20 10.1093/nar/gkw1278 26 view
Arguel Nucleic Acids Res. A cost effective 5΄ selective single cell transcriptome profiling approach with improved UMI design. 2017-04-20 10.1093/nar/gkw1242 10 view
Campbell Bioinformatics switchde: inference of switch-like differential expression along single-cell trajectories. 2017-04-15 10.1093/bioinformatics/btw798 10 view
McCarthy Bioinformatics Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R. 2017-04-15 10.1093/bioinformatics/btw777 125 view
Bershteyn Cell Stem Cell Human iPSC-Derived Cerebral Organoids Model Cellular Features of Lissencephaly and Reveal Prolonged Mitosis of Outer Radial Glia. 2017-04-06 10.1016/j.stem.2016.12.007 97 view
Hu Autophagy Single-cell RNA sequencing highlights transcription activity of autophagy-related genes during hematopoietic stem cell formation in mouse embryos. 2017-04-03 10.1080/15548627.2016.1278093 6 view
Qian Semin. Cell Dev. Biol. Detection of single cell heterogeneity in cancer. 2017-04-01 10.1016/j.semcdb.2016.09.003 26 view
Svensson Nat. Methods Power analysis of single-cell RNA-sequencing experiments. 2017-04-01 10.1038/nmeth.4220 137 view
Kakaradov Nat. Immunol. Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA sequencing. 2017-04-01 10.1038/ni.3688 24 view
Yu Cancer Res. Modeling the Genetic Regulation of Cancer Metabolism: Interplay between Glycolysis and Oxidative Phosphorylation. 2017-04-01 10.1158/0008-5472.CAN-16-2074 17 view
Kuipers Biochim. Biophys. Acta Advances in understanding tumour evolution through single-cell sequencing. 2017-04-01 10.1016/j.bbcan.2017.02.001 22 view
Woodworth Nat. Rev. Genet. Building a lineage from single cells: genetic techniques for cell lineage tracking. 2017-04-01 10.1038/nrg.2016.159 67 view
Gierahn Nat. Methods Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. 2017-04-01 10.1038/nmeth.4179 124 view
Wang Nat. Methods Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. 2017-04-01 10.1038/nmeth.4207 102 view
Li Curr Pharmacol Rep Single-Cell Transcriptome Analysis of Neural Stem Cells. 2017-04-01 10.1007/s40495-017-0084-3 view
Martinez-Jimenez Science Aging increases cell-to-cell transcriptional variability upon immune stimulation. 2017-03-31 10.1126/science.aah4115 51 view
Chen Sci Rep Single-cell RNA sequencing identifies distinct mouse medial ganglionic eminence cell types. 2017-03-31 10.1038/srep45656 13 view
Venteicher Science Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. 2017-03-31 10.1126/science.aai8478 104 view
Chen Cell Rep Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity. 2017-03-28 10.1016/j.celrep.2017.03.004 68 view
Lin Genome Biol. CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data. 2017-03-28 10.1186/s13059-017-1188-0 62 view
Vieira Braga Genome Biol. Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments. 2017-03-24 10.1186/s13059-017-1192-4 view
Furchtgott Elife Discovering sparse transcription factor codes for cell states and state transitions during development. 2017-03-15 10.7554/eLife.20488 15 view
Jang Elife Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states. 2017-03-15 10.7554/eLife.20487 19 view
Campbell Wellcome Open Res Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers. 2017-03-15 10.12688/wellcomeopenres.11087.1 8 view
Wurtzel Dev. Cell Planarian Epidermal Stem Cells Respond to Positional Cues to Promote Cell-Type Diversity. 2017-03-13 10.1016/j.devcel.2017.02.008 22 view
Close Neuron Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation. 2017-03-08 10.1016/j.neuron.2017.02.014 16 view
Tang Proc. Natl. Acad. Sci. U.S.A. High-throughput screening of rare metabolically active tumor cells in pleural effusion and peripheral blood of lung cancer patients. 2017-03-07 10.1073/pnas.1612229114 14 view
Chakravarthy Cell Metab. Converting Adult Pancreatic Islet α Cells into β Cells by Targeting Both Dnmt1 and Arx. 2017-03-07 10.1016/j.cmet.2017.01.009 28 view
Lönnberg Sci Immunol Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria. 2017-03-03 10.1126/sciimmunol.aal2192 64 view
Bifari Cell Stem Cell Neurogenic Radial Glia-like Cells in Meninges Migrate and Differentiate into Functionally Integrated Neurons in the Neonatal Cortex. 2017-03-02 10.1016/j.stem.2016.10.020 25 view
Santoni Am. J. Hum. Genet. Detection of Imprinted Genes by Single-Cell Allele-Specific Gene Expression. 2017-03-02 10.1016/j.ajhg.2017.01.028 10 view
Kunz Cancer Metastasis Rev. The impact of melanoma genetics on treatment response and resistance in clinical and experimental studies. 2017-03-01 10.1007/s10555-017-9657-1 11 view
Yan Oncol Lett Single-cell genomic profiling of acute myeloid leukemia for clinical use: A pilot study. 2017-03-01 10.3892/ol.2017.5669 8 view
Borensztein Nat. Struct. Mol. Biol. Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. 2017-03-01 10.1038/nsmb.3365 36 view
Sheng Nat. Methods Effective detection of variation in single-cell transcriptomes using MATQ-seq. 2017-03-01 10.1038/nmeth.4145 24 view
Qiu Nat. Methods Single-cell mRNA quantification and differential analysis with Census. 2017-03-01 10.1038/nmeth.4150 124 view
Winterhoff Gynecol. Oncol. Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells. 2017-03-01 10.1016/j.ygyno.2017.01.015 16 view
Guillaumet-Adkins Genome Biol. Single-cell transcriptome conservation in cryopreserved cells and tissues. 2017-03-01 10.1186/s13059-017-1171-9 31 view
Salehi Genome Biol. ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data. 2017-03-01 10.1186/s13059-017-1169-3 16 view
Perraudeau F1000Res Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference. 2017-03-01 10.12688/f1000research.12122.1 6 view
Pavličev Genome Res. Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface. 2017-03-01 10.1101/gr.207597.116 27 view
Carmona Genome Res. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. 2017-03-01 10.1101/gr.207704.116 22 view
Smith Genome Res. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. 2017-03-01 10.1101/gr.209601.116 44 view
Gao Cereb. Cortex Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation During Postnatal Neurogenesis. 2017-03-01 10.1093/cercor/bhw040 18 view
Zhu Cell. Mol. Life Sci. Next-generation molecular diagnosis: single-cell sequencing from bench to bedside. 2017-03-01 10.1007/s00018-016-2368-x 11 view
Wang Biotechnol. Lett. Single-cell RNA-seq reveals lincRNA expression differences in Hela-S3 cells. 2017-03-01 10.1007/s10529-016-2260-7 2 view
Datlinger Nat. Methods Pooled CRISPR screening with single-cell transcriptome readout. 2017-03-01 10.1038/nmeth.4177 98 view
Lee Wiley Interdiscip Rev Syst Biol Med Quantitative approaches for investigating the spatial context of gene expression. 2017-03-01 10.1002/wsbm.1369 16 view
Romanov J. Endocrinol. Molecular diversity of corticotropin-releasing hormone mRNA-containing neurons in the hypothalamus. 2017-03-01 10.1530/JOE-16-0256 7 view
Martelotto Nat. Med. Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. 2017-03-01 10.1038/nm.4279 32 view
Specht Bioinformatics LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering. 2017-03-01 10.1093/bioinformatics/btw729 10 view
Yang Bioinformatics Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud. 2017-03-01 10.1093/bioinformatics/btw732 9 view
Chen Nat Protoc Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq. 2017-03-01 10.1038/nprot.2017.003 31 view
Posfai Elife Position- and Hippo signaling-dependent plasticity during lineage segregation in the early mouse embryo. 2017-02-22 10.7554/eLife.22906 26 view
Knouse J Vis Exp Detection of Copy Number Alterations Using Single Cell Sequencing. 2017-02-17 10.3791/55143 1 view
Yang Nucleic Acids Res. Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. 2017-02-17 10.1093/nar/gkw1214 15 view
Ziegenhain Mol. Cell Comparative Analysis of Single-Cell RNA Sequencing Methods. 2017-02-16 10.1016/j.molcel.2017.01.023 176 view
Henley J Vis Exp Reliable Identification of Living Dopaminergic Neurons in Midbrain Cultures Using RNA Sequencing and TH-promoter-driven eGFP Expression. 2017-02-10 10.3791/54981 view
Gong Nat Commun Dpath software reveals hierarchical haemato-endothelial lineages of Etv2 progenitors based on single-cell transcriptome analysis. 2017-02-09 10.1038/ncomms14362 11 view
Zheng Nat Commun Expression of β-globin by cancer cells promotes cell survival during blood-borne dissemination. 2017-02-09 10.1038/ncomms14344 13 view
Wang Brief. Bioinformatics DNA copy number profiling using single-cell sequencing. 2017-02-04 10.1093/bib/bbx004 view
Stanescu Physiol. Genomics Single cell transcriptomic profiling of mouse pancreatic progenitors. 2017-02-01 10.1152/physiolgenomics.00114.2016 9 view
Neu Trends Immunol. Single-Cell Genomics: Approaches and Utility in Immunology. 2017-02-01 10.1016/ 14 view
Romanov Nat. Neurosci. Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. 2017-02-01 10.1038/nn.4462 82 view
Johnson Curr. Opin. Neurobiol. Cerebral cortical neuron diversity and development at single-cell resolution. 2017-02-01 10.1016/j.conb.2016.11.001 20 view
Tsoucas Curr. Opin. Genet. Dev. Recent progress in single-cell cancer genomics. 2017-02-01 10.1016/j.gde.2017.01.002 20 view
Saliba Curr. Opin. Microbiol. New RNA-seq approaches for the study of bacterial pathogens. 2017-02-01 10.1016/j.mib.2017.01.001 25 view
Macaulay Trends Genet. Single-Cell Multiomics: Multiple Measurements from Single Cells. 2017-02-01 10.1016/j.tig.2016.12.003 103 view
Canzar Bioinformatics BASIC: BCR assembly from single cells. 2017-02-01 10.1093/bioinformatics/btw631 22 view
Frazer Nat Commun Transcriptomic and anatomic parcellation of 5-HT3AR expressing cortical interneuron subtypes revealed by single-cell RNA sequencing. 2017-01-30 10.1038/ncomms14219 view
Ji Nat Commun MetaSort untangles metagenome assembly by reducing microbial community complexity. 2017-01-23 10.1038/ncomms14306 19 view
Zhang Sci Rep Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms. 2017-01-23 10.1038/srep41192 24 view
Gambardella Nat Commun The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cells. 2017-01-19 10.1038/ncomms14126 6 view
Hsueh Elife Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey. 2017-01-18 10.7554/eLife.20023 11 view
Sasagawa Genome Biol. Erratum to: Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. 2017-01-18 10.1186/s13059-017-1154-x 2 view
Dulken Cell Rep Single-Cell Transcriptomic Analysis Defines Heterogeneity and Transcriptional Dynamics in the Adult Neural Stem Cell Lineage. 2017-01-17 10.1016/j.celrep.2016.12.060 51 view
Wang BMC Genomics Random X-chromosome inactivation dynamics in vivo by single-cell RNA sequencing. 2017-01-17 10.1186/s12864-016-3466-8 3 view
Spaethling Cell Rep Primary Cell Culture of Live Neurosurgically Resected Aged Adult Human Brain Cells and Single Cell Transcriptomics. 2017-01-17 10.1016/j.celrep.2016.12.066 23 view
Zhu Acc. Chem. Res. Hydrogel Droplet Microfluidics for High-Throughput Single Molecule/Cell Analysis. 2017-01-17 10.1021/acs.accounts.6b00370 30 view
Shao Bioinformatics Robust classification of single-cell transcriptome data by nonnegative matrix factorization. 2017-01-15 10.1093/bioinformatics/btw607 13 view
Cho Cell Rep Neonatal Transplantation Confers Maturation of PSC-Derived Cardiomyocytes Conducive to Modeling Cardiomyopathy. 2017-01-10 10.1016/j.celrep.2016.12.040 21 view
Wills BMC Genomics The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq. 2017-01-07 10.1186/s12864-016-3445-0 8 view
Guthals J. Proteome Res. De Novo MS/MS Sequencing of Native Human Antibodies. 2017-01-06 10.1021/acs.jproteome.6b00608 9 view
Vallot Cell Stem Cell XACT Noncoding RNA Competes with XIST in the Control of X Chromosome Activity during Human Early Development. 2017-01-05 10.1016/j.stem.2016.10.014 52 view
Yao Cell Stem Cell A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development. 2017-01-05 10.1016/j.stem.2016.09.011 36 view
Kee Cell Stem Cell Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages. 2017-01-05 10.1016/j.stem.2016.10.003 29 view
Tung Sci Rep Batch effects and the effective design of single-cell gene expression studies. 2017-01-03 10.1038/srep39921 87 view
Gerber Oncotarget Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq. 2017-01-03 10.18632/oncotarget.13666 17 view
Kumar Development Understanding development and stem cells using single cell-based analyses of gene expression. 2017-01-01 10.1242/dev.133058 35 view
Yang Eur. Urol. Single-cell Sequencing Reveals Variants in ARID1A, GPRC5A and MLL2 Driving Self-renewal of Human Bladder Cancer Stem Cells. 2017-01-01 10.1016/j.eururo.2016.06.025 31 view
Casasent J. Pathol. Genome evolution in ductal carcinoma in situ: invasion of the clones. 2017-01-01 10.1002/path.4840 16 view
Wu Eur. Urol. Attention to Detail by Single-cell Sequencing. 2017-01-01 10.1016/j.eururo.2016.09.005 2 view
Yang Eur. Urol. Reply from Authors re: Xue-Ru Wu. Attention to Detail by Single-cell sequencing. Eur Urol 2017;71:13-4. 2017-01-01 10.1016/j.eururo.2016.11.003 view
Cloney Nat. Rev. Genet. Cancer genomics: Single-cell RNA-seq to decipher tumour architecture. 2017-01-01 10.1038/nrg.2016.151 4 view
Zilionis Nat Protoc Single-cell barcoding and sequencing using droplet microfluidics. 2017-01-01 10.1038/nprot.2016.154 137 view
Wu J. Exp. Med. Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE. 2017-01-01 10.1084/jem.20161056 12 view
Lee PLoS Comput. Biol. Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing. 2017-01-01 10.1371/journal.pcbi.1005313 9 view
Hu BMC Genomics A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data. 2016-12-22 10.1186/s12864-016-3317-7 4 view
Liu Sci Rep Single-cell analysis of differences in transcriptomic profiles of oocytes and cumulus cells at GV, MI, MII stages from PCOS patients. 2016-12-22 10.1038/srep39638 9 view
Lux BMC Bioinformatics acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data. 2016-12-20 10.1186/s12859-016-1397-7 10 view
Zhao Nat Commun Evolution of multiple cell clones over a 29-year period of a CLL patient. 2016-12-16 10.1038/ncomms13765 7 view
Dixit Cell Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. 2016-12-15 10.1016/j.cell.2016.11.038 228 view
Adamson Cell A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. 2016-12-15 10.1016/j.cell.2016.11.048 194 view
Jaitin Cell Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. 2016-12-15 10.1016/j.cell.2016.11.039 153 view
Ghazanfar BMC Syst Biol Integrated single cell data analysis reveals cell specific networks and novel coactivation markers. 2016-12-05 10.1186/s12918-016-0370-4 11 view
Zeng Nucleic Acids Res. Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity. 2016-12-01 15 view
Faridani Nat. Biotechnol. Single-cell sequencing of the small-RNA transcriptome. 2016-12-01 10.1038/nbt.3701 58 view
Klimovskaia PLoS Comput. Biol. Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series. 2016-12-01 10.1371/journal.pcbi.1005234 6 view
Fontana PLoS Pathog. Macrophage Colony Stimulating Factor Derived from CD4+ T Cells Contributes to Control of a Blood-Borne Infection. 2016-12-01 10.1371/journal.ppat.1006046 view
Hart Int. J. Dev. Neurosci. Long noncoding RNAs: Central to nervous system development. 2016-12-01 10.1016/j.ijdevneu.2016.06.001 12 view
Bian Trends Biotechnol. Computational Tools for Stem Cell Biology. 2016-12-01 10.1016/j.tibtech.2016.05.010 24 view
Erwin Nat. Neurosci. L1-associated genomic regions are deleted in somatic cells of the healthy human brain. 2016-12-01 10.1038/nn.4388 54 view
Müller Mol. Syst. Biol. Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. 2016-11-25 10.15252/msb.20166969 30 view
Park Sci Rep Measuring intratumor heterogeneity by network entropy using RNA-seq data. 2016-11-24 10.1038/srep37767 4 view
McConnell Cell Rep p53 Regulates Progenitor Cell Quiescence and Differentiation in the Airway. 2016-11-22 10.1016/j.celrep.2016.11.007 13 view
DeLaughter Dev. Cell Single-Cell Resolution of Temporal Gene Expression during Heart Development. 2016-11-21 10.1016/j.devcel.2016.10.001 86 view
Saliba Nat Microbiol Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella. 2016-11-14 10.1038/nmicrobiol.2016.206 34 view
Butcher Circ. Res. Atherosclerosis-Driven Treg Plasticity Results in Formation of a Dysfunctional Subset of Plastic IFNγ+ Th1/Tregs. 2016-11-11 10.1161/CIRCRESAHA.116.309764 24 view
Tirosh Nature Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. 2016-11-10 10.1038/nature20123 177 view
Wagner Nat. Biotechnol. Revealing the vectors of cellular identity with single-cell genomics. 2016-11-08 10.1038/nbt.3711 151 view
Yu Nature Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway. 2016-11-03 10.1038/nature20105 view
Ohta Sci Rep Laminin-guided highly efficient endothelial commitment from human pluripotent stem cells. 2016-11-02 10.1038/srep35680 10 view
Perié FEBS Lett. Retracing the in vivo haematopoietic tree using single-cell methods. 2016-11-01 10.1002/1873-3468.12299 5 view
Moris Nat. Rev. Genet. Transition states and cell fate decisions in epigenetic landscapes. 2016-11-01 10.1038/nrg.2016.98 85 view
Bardy Mol. Psychiatry Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology. 2016-11-01 10.1038/mp.2016.158 33 view
Sanchez-Delgado PLoS Genet. Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting. 2016-11-01 10.1371/journal.pgen.1006427 24 view
Reinius Nat. Genet. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq. 2016-11-01 10.1038/ng.3678 33 view
Cannoodt Eur. J. Immunol. Computational methods for trajectory inference from single-cell transcriptomics. 2016-11-01 10.1002/eji.201646347 38 view
Baron Cell Syst A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. 2016-10-26 10.1016/j.cels.2016.08.011 147 view
Vickovic Nat Commun Massive and parallel expression profiling using microarrayed single-cell sequencing. 2016-10-14 10.1038/ncomms13182 19 view
Xin Cell Metab. RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes. 2016-10-11 10.1016/j.cmet.2016.08.018 89 view
Prasad Cell Metab. Single-Cell Sequencing of Human Pancreatic Islets-New Kids on the Block. 2016-10-11 10.1016/j.cmet.2016.09.012 view
Glinsky Cancer Lett. Single cell genomics reveals activation signatures of endogenous SCAR's networks in aneuploid human embryos and clinically intractable malignant tumors. 2016-10-10 10.1016/j.canlet.2016.08.001 view
Chen Cell Stem Cell Out of Many, One: Computational Reconstruction of Mouse Skin using Single-Cell Transcriptomics. 2016-10-06 10.1016/j.stem.2016.09.009 view
La Manno Cell Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. 2016-10-06 10.1016/j.cell.2016.09.027 view
Zhang Oncotarget Single-cell analyses of transcriptional heterogeneity in squamous cell carcinoma of urinary bladder. 2016-10-04 10.18632/oncotarget.11803 12 view
Kwan Curr Pharmacol Rep Single-Cell Transcriptome Analysis of Developing and Regenerating Spiral Ganglion Neurons. 2016-10-01 10.1007/s40495-016-0064-z 2 view
Zhao Reprod. Domest. Anim. Transcriptome analyses of inner cell mass and trophectoderm cells isolated by magnetic-activated cell sorting from bovine blastocysts using single cell RNA-seq. 2016-10-01 10.1111/rda.12737 7 view
Wang Diabetes Single-Cell Transcriptomics of the Human Endocrine Pancreas. 2016-10-01 10.2337/db16-0405 82 view
Edsgärd Bioinformatics scphaser: haplotype inference using single-cell RNA-seq data. 2016-10-01 10.1093/bioinformatics/btw484 4 view
Welch Nucleic Acids Res. Selective single cell isolation for genomics using microraft arrays. 2016-09-30 10.1093/nar/gkw700 12 view
Olsson Nature Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. 2016-09-29 10.1038/nature19348 138 view
Joost Cell Syst Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity. 2016-09-28 10.1016/j.cels.2016.08.010 52 view
Chen Sci Rep Single-cell SNP analyses and interpretations based on RNA-Seq data for colon cancer research. 2016-09-28 10.1038/srep34420 5 view
Song Cell Rep The Homeobox Transcription Factor RHOX10 Drives Mouse Spermatogonial Stem Cell Establishment. 2016-09-27 10.1016/j.celrep.2016.08.090 15 view
Moffitt Proc. Natl. Acad. Sci. U.S.A. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. 2016-09-27 10.1073/pnas.1612826113 80 view
Eckersley-Maslin Cell Rep MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs. 2016-09-27 10.1016/j.celrep.2016.08.087 37 view
Yuan Sci Rep An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq. 2016-09-27 10.1038/srep33883 44 view
Barron Sci Rep Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. 2016-09-27 10.1038/srep33892 17 view
Nath Curr. Biol. C. elegans Stress-Induced Sleep Emerges from the Collective Action of Multiple Neuropeptides. 2016-09-26 10.1016/j.cub.2016.07.048 26 view
Mora-Bermúdez Elife Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development. 2016-09-26 10.7554/eLife.18683 36 view
Qiu Oncotarget Identification and functional analysis of long non-coding RNAs in human and mouse early embryos based on single-cell transcriptome data. 2016-09-20 10.18632/oncotarget.11304 15 view
Zhang BMC Bioinformatics nbCNV: a multi-constrained optimization model for discovering copy number variants in single-cell sequencing data. 2016-09-17 10.1186/s12859-016-1239-7 4 view
duVerle BMC Bioinformatics CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. 2016-09-13 10.1186/s12859-016-1175-6 view
Onorati Cell Rep Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia. 2016-09-06 10.1016/j.celrep.2016.08.038 106 view
Xin Endocrinology Single-Cell RNAseq Reveals That Pancreatic β-Cells From Very Old Male Mice Have a Young Gene Signature. 2016-09-01 10.1210/en.2016-1235 8 view
Liu F1000Res Single-cell transcriptome sequencing: recent advances and remaining challenges. 2016-09-01 10.12688/f1000research.7223.1 84 view
Petropoulos J. Intern. Med. Single-cell RNA sequencing: revealing human pre-implantation development, pluripotency and germline development. 2016-09-01 10.1111/joim.12493 5 view
Stumpf Proteomics Single-cell pluripotency regulatory networks. 2016-09-01 10.1002/pmic.201500528 6 view
Qian Sci China Life Sci Single-cell RNA-seq technology lends a hand into HSC ontogeny. 2016-09-01 10.1007/s11427-016-5092-8 view
Nakamura Nature A developmental coordinate of pluripotency among mice, monkeys and humans. 2016-09-01 10.1038/nature19096 88 view
Zhou Cell Stem Cell Advanced Technologies Lead iNto New Reprogramming Routes. 2016-09-01 10.1016/j.stem.2016.08.014 view
Mato Prado Expert Rev. Mol. Diagn. Single-cell sequencing in cancer research. 2016-09-01 10.1586/14737159.2016.1115345 view
Xu Nat. Methods Virtual microfluidics for digital quantification and single-cell sequencing. 2016-09-01 10.1038/nmeth.3955 26 view
Földy Proc. Natl. Acad. Sci. U.S.A. Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons. 2016-08-30 10.1073/pnas.1610155113 48 view
Habib Science Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. 2016-08-26 10.1126/science.aad7038 134 view
Poulin Nat. Neurosci. Disentangling neural cell diversity using single-cell transcriptomics. 2016-08-26 10.1038/nn.4366 113 view
Hu Sci Rep Single-cell RNA-seq reveals distinct injury responses in different types of DRG sensory neurons. 2016-08-25 10.1038/srep31851 32 view
Shekhar Cell Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics. 2016-08-25 10.1016/j.cell.2016.07.054 233 view
Nestorowa Blood A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation. 2016-08-25 10.1182/blood-2016-05-716480 104 view
Gury-BenAri Cell The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome. 2016-08-25 10.1016/j.cell.2016.07.043 129 view
DeTomaso BMC Bioinformatics FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data. 2016-08-23 10.1186/s12859-016-1176-5 25 view
Chen BMC Genomics Detection of high variability in gene expression from single-cell RNA-seq profiling. 2016-08-22 10.1186/s12864-016-2897-6 7 view
Chu Genome Biol. Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm. 2016-08-17 10.1186/s13059-016-1033-x 71 view
Jiang Bioinformatics Quality control of single-cell RNA-seq by SinQC. 2016-08-15 10.1093/bioinformatics/btw176 15 view
Mantsoki Comput Biol Chem Gene expression variability in mammalian embryonic stem cells using single cell RNA-seq data. 2016-08-01 10.1016/j.compbiolchem.2016.02.004 7 view
Zhou J. Physiol. (Lond.) Single cell transcriptome analysis of mouse carotid body glomus cells. 2016-08-01 10.1113/JP271936 30 view
Wucherpfennig Curr. Opin. Immunol. Genetic screens to study the immune system in cancer. 2016-08-01 10.1016/j.coi.2016.05.007 3 view
Venteicher Neurosurgery 142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis. 2016-08-01 10.1227/01.neu.0000489712.44702.0d 3 view
Duscher Gerontology Stem Cells in Wound Healing: The Future of Regenerative Medicine? A Mini-Review. 2016-08-01 10.1159/000381877 79 view
Niemöller Leuk. Res. Single cell genotyping of exome sequencing-identified mutations to characterize the clonal composition and evolution of inv(16) AML in a CBL mutated clonal hematopoiesis. 2016-08-01 10.1016/j.leukres.2016.05.008 4 view
Xu Comput Biol Chem Copy number variants calling for single cell sequencing data by multi-constrained optimization. 2016-08-01 10.1016/j.compbiolchem.2016.02.007 5 view
Ji Nucleic Acids Res. TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis. 2016-07-27 10.1093/nar/gkw430 113 view
Redmond Genome Med Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq. 2016-07-27 10.1186/s13073-016-0335-7 37 view
Gokce Cell Rep Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq. 2016-07-26 10.1016/j.celrep.2016.06.059 83 view
Diaz Bioinformatics SCell: integrated analysis of single-cell RNA-seq data. 2016-07-15 10.1093/bioinformatics/btw201 23 view
Vu Bioinformatics Beta-Poisson model for single-cell RNA-seq data analyses. 2016-07-15 10.1093/bioinformatics/btw202 38 view
Bremges Bioinformatics MeCorS: Metagenome-enabled error correction of single cell sequencing reads. 2016-07-15 10.1093/bioinformatics/btw144 4 view
Scialdone Nature Resolving early mesoderm diversification through single-cell expression profiling. 2016-07-14 10.1038/nature18633 124 view
Nichterwitz Nat Commun Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling. 2016-07-08 10.1038/ncomms12139 38 view
Eltahla Immunol. Cell Biol. Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells. 2016-07-01 10.1038/icb.2016.16 40 view
Fang Curr Protoc Mol Biol Depletion of Ribosomal RNA Sequences from Single-Cell RNA-Sequencing Library. 2016-07-01 10.1002/cpmb.11 2 view
Jiang Genome Biol. GiniClust: detecting rare cell types from single-cell gene expression data with Gini index. 2016-07-01 10.1186/s13059-016-1010-4 58 view
Liu PLoS ONE Nonlinear Network Reconstruction from Gene Expression Data Using Marginal Dependencies Measured by DCOL. 2016-07-01 10.1371/journal.pone.0158247 1 view
Anchang Nat Protoc Visualization and cellular hierarchy inference of single-cell data using SPADE. 2016-07-01 10.1038/nprot.2016.066 40 view
Morris Trends Biotechnol. Single-Cell RNA-Seq Steps Up to the Growth Plate. 2016-07-01 10.1016/j.tibtech.2016.05.007 2 view
Chen Nat Commun Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development. 2016-06-30 10.1038/ncomms11988 32 view
Zhang Oncotarget Tumor-selective replication herpes simplex virus-based technology significantly improves clinical detection and prognostication of viable circulating tumor cells. 2016-06-28 10.18632/oncotarget.9465 9 view
Schmidt Pharmaceuticals (Basel) Tumor Heterogeneity, Single-Cell Sequencing, and Drug Resistance. 2016-06-16 10.3390/ph9020033 34 view
Treutlein Nature Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. 2016-06-16 10.1038/nature18323 137 view
Schissler Bioinformatics Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells. 2016-06-15 10.1093/bioinformatics/btw248 8 view
De Sano Bioinformatics TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. 2016-06-15 10.1093/bioinformatics/btw035 view
Marques Science Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. 2016-06-10 10.1126/science.aaf6463 154 view
McDavid Nat. Biotechnol. The contribution of cell cycle to heterogeneity in single-cell RNA-seq data. 2016-06-09 10.1038/nbt.3498 29 view
Matsumoto BMC Bioinformatics SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation. 2016-06-08 10.1186/s12859-016-1109-3 18 view
Chan Biochem. Biophys. Res. Commun. Heterogeneity of Mesp1+ mesoderm revealed by single-cell RNA-seq. 2016-06-03 10.1016/j.bbrc.2016.04.139 5 view
Krzywinski Mol. Cell Visualizing Clonal Evolution in Cancer. 2016-06-02 10.1016/j.molcel.2016.05.025 4 view
Caiado FEBS J. Intra-tumour heterogeneity - going beyond genetics. 2016-06-01 10.1111/febs.13705 31 view
Engel Nat. Immunol. Innate-like functions of natural killer T cell subsets result from highly divergent gene programs. 2016-06-01 10.1038/ni.3437 79 view
Drissen Nat. Immunol. Distinct myeloid progenitor-differentiation pathways identified through single-cell RNA sequencing. 2016-06-01 10.1038/ni.3412 80 view
Ryu Hum. Genet. Deciphering intratumor heterogeneity using cancer genome analysis. 2016-06-01 10.1007/s00439-016-1670-x 13 view
Marr Curr. Opin. Biotechnol. Single-cell gene expression profiling and cell state dynamics: collecting data, correlating data points and connecting the dots. 2016-06-01 10.1016/j.copbio.2016.04.015 22 view
Bakker Genome Biol. Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies. 2016-05-31 10.1186/s13059-016-0971-7 37 view
Ntranos Genome Biol. Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts. 2016-05-26 10.1186/s13059-016-0970-8 47 view
Zhou Nature Tracing haematopoietic stem cell formation at single-cell resolution. 2016-05-26 10.1038/nature17997 83 view
Kim J Neuroinflammation Brain trauma elicits non-canonical macrophage activation states. 2016-05-24 10.1186/s12974-016-0581-z 48 view
Welch Genome Biol. SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. 2016-05-23 10.1186/s13059-016-0975-3 59 view
Li Cell Rep Systematic Reconstruction of Molecular Cascades Regulating GP Development Using Single-Cell RNA-Seq. 2016-05-17 10.1016/j.celrep.2016.04.043 20 view
Lutas Elife The leak channel NALCN controls tonic firing and glycolytic sensitivity of substantia nigra pars reticulata neurons. 2016-05-13 10.7554/eLife.15271 14 view
Proserpio Genome Biol. Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. 2016-05-12 10.1186/s13059-016-0957-5 view
Crow Genome Biol. Exploiting single-cell expression to characterize co-expression replicability. 2016-05-06 10.1186/s13059-016-0964-6 19 view
Welch Nucleic Acids Res. Robust detection of alternative splicing in a population of single cells. 2016-05-05 10.1093/nar/gkv1525 22 view
Jahn Genome Biol. Tree inference for single-cell data. 2016-05-05 10.1186/s13059-016-0936-x 58 view
Petropoulos Cell Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos. 2016-05-05 10.1016/j.cell.2016.03.023 view
Nowakowski Cell Stem Cell Expression Analysis Highlights AXL as a Candidate Zika Virus Entry Receptor in Neural Stem Cells. 2016-05-05 10.1016/j.stem.2016.03.012 293 view
Miner Cell Stem Cell Understanding How Zika Virus Enters and Infects Neural Target Cells. 2016-05-05 10.1016/j.stem.2016.04.009 33 view
Ciuffi Viruses Single-Cell Genomics for Virology. 2016-05-04 10.3390/v8050123 22 view
Nguyen Nat Commun Highly variable cancer subpopulations that exhibit enhanced transcriptome variability and metastatic fitness. 2016-05-03 10.1038/ncomms11246 23 view
Rossjohn Mucosal Immunol A biased view toward celiac disease. 2016-05-01 10.1038/mi.2016.17 1 view
Scholz Chem. Senses Transcriptome Analysis of Murine Olfactory Sensory Neurons during Development Using Single Cell RNA-Seq. 2016-05-01 10.1093/chemse/bjw003 21 view
Smith Cytometry A Cytometric routes to single cell transcriptomics. 2016-05-01 10.1002/cyto.a.22869 2 view
Meyer Cancer Discov DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia. 2016-05-01 10.1158/2159-8290.CD-16-0008 6 view
Koh PLoS ONE Dynamic ASXL1 Exon Skipping and Alternative Circular Splicing in Single Human Cells. 2016-05-01 10.1371/journal.pone.0164085 5 view
Leng Bioinformatics OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data. 2016-05-01 10.1093/bioinformatics/btw004 11 view
Kim Genome Biol. Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma. 2016-04-29 10.1186/s13059-016-0945-9 38 view
Hashimshony Genome Biol. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. 2016-04-28 10.1186/s13059-016-0938-8 195 view
Lun Genome Biol. Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. 2016-04-27 10.1186/s13059-016-0947-7 160 view
Molinaro Genome Biol. In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians. 2016-04-27 10.1186/s13059-016-0937-9 33 view
Nelson Nat Commun Single-cell RNA-seq reveals cell type-specific transcriptional signatures at the maternal-foetal interface during pregnancy. 2016-04-25 10.1038/ncomms11414 14 view
Lacar Nat Commun Nuclear RNA-seq of single neurons reveals molecular signatures of activation. 2016-04-19 10.1038/ncomms11022 97 view
Ross Genome Biol. OncoNEM: inferring tumor evolution from single-cell sequencing data. 2016-04-15 10.1186/s13059-016-0929-9 65 view
Wen Genome Biol. Single-cell sequencing in stem cell biology. 2016-04-15 10.1186/s13059-016-0941-0 48 view
Ma Genome Biol. Single-cell profiling of lncRNAs in the developing human brain. 2016-04-14 10.1186/s13059-016-0933-0 9 view
Liu Genome Biol. Single-cell analysis of long non-coding RNAs in the developing human neocortex. 2016-04-14 10.1186/s13059-016-0932-1 118 view
Scimone Elife Two FGFRL-Wnt circuits organize the planarian anteroposterior axis. 2016-04-11 10.7554/eLife.12845 41 view
Tirosh Science Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. 2016-04-08 10.1126/science.aad0501 558 view
Bacher Genome Biol. Design and computational analysis of single-cell RNA-sequencing experiments. 2016-04-07 10.1186/s13059-016-0927-y 162 view
Lv Oncotarget Systematic characterization of lncRNAs' cell-to-cell expression heterogeneity in glioblastoma cells. 2016-04-05 10.18632/oncotarget.7580 view
Efroni Genome Biol. The potential of single-cell profiling in plants. 2016-04-05 10.1186/s13059-016-0931-2 29 view
Krjutškov Hum. Reprod. Single-cell transcriptome analysis of endometrial tissue. 2016-04-01 10.1093/humrep/dew008 27 view
Björklund Nat. Immunol. The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing. 2016-04-01 10.1038/ni.3368 view
Stubbington Nat. Methods T cell fate and clonality inference from single-cell transcriptomes. 2016-04-01 10.1038/nmeth.3800 133 view
Bai PLoS ONE RNA-Seq Profiling of Intact and Enucleated Oocyte SCNT Embryos Reveals the Role of Pig Oocyte Nucleus in Somatic Reprogramming. 2016-04-01 10.1371/journal.pone.0153093 3 view
Telley Science Sequential transcriptional waves direct the differentiation of newborn neurons in the mouse neocortex. 2016-03-25 10.1126/science.aad8361 75 view
Grover Nat Commun Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells. 2016-03-24 10.1038/ncomms11075 53 view
Xin Proc. Natl. Acad. Sci. U.S.A. Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells. 2016-03-22 10.1073/pnas.1602306113 62 view
Freeman Sci Rep Single-cell RNA-seq reveals activation of unique gene groups as a consequence of stem cell-parenchymal cell fusion. 2016-03-21 10.1038/srep23270 10 view
Zhang Cancer Res. Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects. 2016-03-15 10.1158/0008-5472.CAN-15-1907 52 view
Handel Hum. Mol. Genet. Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics. 2016-03-01 10.1093/hmg/ddv637 38 view
Fan Nat. Methods Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. 2016-03-01 10.1038/nmeth.3734 132 view
Angermueller Nat. Methods Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. 2016-03-01 10.1038/nmeth.3728 199 view
Gerovska Mol. Hum. Reprod. Does mouse embryo primordial germ cell activation start before implantation as suggested by single-cell transcriptomics dynamics? 2016-03-01 10.1093/molehr/gav072 7 view
Knouse Genome Res. Assessment of megabase-scale somatic copy number variation using single-cell sequencing. 2016-03-01 10.1101/gr.198937.115 30 view
Koch Nat. Rev. Genet. Epigenomics: Parallel single-cell sequencing. 2016-03-01 10.1038/nrg.2016.5 view
Delmans BMC Bioinformatics Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data. 2016-02-29 10.1186/s12859-016-0944-6 view
Nakamura Sci Rep Culture-independent method for identification of microbial enzyme-encoding genes by activity-based single-cell sequencing using a water-in-oil microdroplet platform. 2016-02-26 10.1038/srep22259 9 view
Evrony Elife Resolving rates of mutation in the brain using single-neuron genomics. 2016-02-22 10.7554/eLife.12966 45 view
Ilicic Genome Biol. Classification of low quality cells from single-cell RNA-seq data. 2016-02-17 10.1186/s13059-016-0888-1 96 view
Chea Cell Rep Single-Cell Gene Expression Analyses Reveal Heterogeneous Responsiveness of Fetal Innate Lymphoid Progenitors to Notch Signaling. 2016-02-16 10.1016/j.celrep.2016.01.015 30 view
Macaulay Cell Rep Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells. 2016-02-02 10.1016/j.celrep.2015.12.082 62 view
Cadwell Nat. Biotechnol. Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq. 2016-02-01 10.1038/nbt.3445 97 view
Fuzik Nat. Biotechnol. Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes. 2016-02-01 10.1038/nbt.3443 101 view
Li EMBO Rep. Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types. 2016-02-01 10.15252/embr.201540946 91 view
Tasic Nat. Neurosci. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. 2016-02-01 10.1038/nn.4216 407 view
Yu Genomics Proteomics Bioinformatics Single-cell Transcriptome Study as Big Data. 2016-02-01 10.1016/j.gpb.2016.01.005 11 view
Movahedi Front Bioeng Biotechnol Efficient Synergistic Single-Cell Genome Assembly. 2016-02-01 10.3389/fbioe.2016.00042 3 view
Ford Am. J. Transplant. Single-Cell Transcriptomics Comes of Age. 2016-02-01 10.1111/ajt.13719 view
Ye Anal Cell Pathol (Amst) Single-Cell Sequencing Technology in Oncology: Applications for Clinical Therapies and Research. 2016-02-01 10.1155/2016/9369240 4 view
Winkel Front Microbiol Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions. 2016-02-01 10.3389/fmicb.2016.00964 13 view
Liu Cell Discov Identification of key factors conquering developmental arrest of somatic cell cloned embryos by combining embryo biopsy and single-cell sequencing. 2016-02-01 10.1038/celldisc.2016.10 40 view
Harbom Bioessays Single neuron transcriptome analysis can reveal more than cell type classification: Does it matter if every neuron is unique? 2016-02-01 10.1002/bies.201500097 7 view
Martignetti Front Genet ROMA: Representation and Quantification of Module Activity from Target Expression Data. 2016-02-01 10.3389/fgene.2016.00018 15 view
Schultze Immunity Myelopoiesis Reloaded: Single-Cell Transcriptomics Leads the Way. 2016-01-19 10.1016/j.immuni.2015.12.019 5 view
Kim Nat Commun Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. 2016-01-11 10.1038/ncomms10415 4 view
Kimmerling Nat Commun A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages. 2016-01-06 10.1038/ncomms10220 60 view
Spaethling FASEB J. Single-cell transcriptomics and functional target validation of brown adipocytes show their complex roles in metabolic homeostasis. 2016-01-01 10.1096/fj.15-273797 10 view
Li Cell Res. Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity. 2016-01-01 10.1038/cr.2015.149 129 view
Camp Proc. Natl. Acad. Sci. U.S.A. Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. 2015-12-22 10.1073/pnas.1520760112 232 view
Saraiva Sci Rep Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq. 2015-12-16 10.1038/srep18178 49 view
Finak Genome Biol. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. 2015-12-10 10.1186/s13059-015-0844-5 223 view
Hanchate Science Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. 2015-12-04 10.1126/science.aad2456 85 view
Wang Cell CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity. 2015-12-03 10.1016/j.cell.2015.10.068 120 view
Gaublomme Cell Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity. 2015-12-03 10.1016/j.cell.2015.11.009 205 view
Kebschull Nucleic Acids Res. Sources of PCR-induced distortions in high-throughput sequencing data sets. 2015-12-02 10.1093/nar/gkv717 54 view
Kowalczyk Genome Res. Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. 2015-12-01 10.1101/gr.192237.115 134 view
Grün Cell Design and Analysis of Single-Cell Sequencing Experiments. 2015-11-05 10.1016/j.cell.2015.10.039 177 view
Pierson Genome Biol. ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis. 2015-11-02 10.1186/s13059-015-0805-z 189 view
Guo PLoS Comput. Biol. SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis. 2015-11-01 10.1371/journal.pcbi.1004575 87 view
Martijn ISME J Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution. 2015-11-01 10.1038/ismej.2015.46 20 view
Labonté ISME J Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. 2015-11-01 10.1038/ismej.2015.48 75 view
Urbieta Biotechnol. Adv. Thermophiles in the genomic era: Biodiversity, science, and applications. 2015-11-01 10.1016/j.biotechadv.2015.04.007 46 view
Osborne Cytometry A Development of a novel cell sorting method that samples population diversity in flow cytometry. 2015-11-01 10.1002/cyto.a.22678 3 view
Choubey PLoS Comput. Biol. Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules. 2015-11-01 10.1371/journal.pcbi.1004345 21 view
Wang Integr Biol (Camb) RNA-seq based transcriptomic analysis of single bacterial cells. 2015-11-01 10.1039/c5ib00191a 27 view
Kim Nat Commun Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. 2015-10-22 10.1038/ncomms9687 90 view
Burns Nat Commun Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear. 2015-10-15 10.1038/ncomms9557 73 view
Blakeley Development Defining the three cell lineages of the human blastocyst by single-cell RNA-seq. 2015-10-15 10.1242/dev.131235 172 view
Juliá Bioinformatics Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq. 2015-10-15 10.1093/bioinformatics/btv368 31 view
Shi Development Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq. 2015-10-15 10.1242/dev.123950 42 view
Dulin J. Neurosci. Transcriptomic Approaches to Neural Repair. 2015-10-14 10.1523/JNEUROSCI.2599-15.2015 13 view
Barry Roche Sci Rep An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life. 2015-10-05 10.1038/srep14717 view
Lodato Science Somatic mutation in single human neurons tracks developmental and transcriptional history. 2015-10-02 10.1126/science.aab1785 207 view
Kolodziejczyk Cell Stem Cell Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation. 2015-10-01 10.1016/j.stem.2015.09.011 161 view
Navin Genome Res. The first five years of single-cell cancer genomics and beyond. 2015-10-01 10.1101/gr.191098.115 157 view
Leng Nat. Methods Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. 2015-10-01 10.1038/nmeth.3549 61 view
Freeman PLoS ONE Single-Cell RNA-Seq of Bone Marrow-Derived Mesenchymal Stem Cells Reveals Unique Profiles of Lineage Priming. 2015-10-01 10.1371/journal.pone.0136199 18 view
Fu Proc. Natl. Acad. Sci. U.S.A. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. 2015-09-22 10.1073/pnas.1513988112 90 view
Tsang Genome Biol. Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells. 2015-09-21 10.1186/s13059-015-0739-5 60 view
Miyamoto Science RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance. 2015-09-18 10.1126/science.aab0917 291 view
Töhönen Nat Commun Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development. 2015-09-11 10.1038/ncomms9207 40 view
Avraham Cell Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses. 2015-09-10 10.1016/j.cell.2015.08.027 105 view
Tay Cell Single-Cell Analysis: The Differences That Kill. 2015-09-10 10.1016/j.cell.2015.08.053 3 view
Llorens-Bobadilla Cell Stem Cell Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury. 2015-09-03 10.1016/j.stem.2015.07.002 205 view
Shin Cell Stem Cell Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. 2015-09-03 10.1016/j.stem.2015.07.013 285 view
Martinez J. Immunol. Methods Identification of T cell clones without the need for sequencing. 2015-09-01 10.1016/j.jim.2015.04.018 3 view
Stoeger Methods Computer vision for image-based transcriptomics. 2015-09-01 10.1016/j.ymeth.2015.05.016 17 view
Scialdone Methods Computational assignment of cell-cycle stage from single-cell transcriptome data. 2015-09-01 10.1016/j.ymeth.2015.06.021 106 view
Meredith Nat. Immunol. Aire controls gene expression in the thymic epithelium with ordered stochasticity. 2015-09-01 10.1038/ni.3247 87 view
Brennecke Nat. Immunol. Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells. 2015-09-01 10.1038/ni.3246 58 view
Okawa Stem Cell Res A computational strategy for predicting lineage specifiers in stem cell subpopulations. 2015-09-01 10.1016/j.scr.2015.08.006 6 view
Sun Cancer Lett. Recent advances and current issues in single-cell sequencing of tumors. 2015-08-28 10.1016/j.canlet.2015.04.022 16 view
de Vargas Roditi Curr. Opin. Biotechnol. Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics. 2015-08-01 10.1016/j.copbio.2014.10.010 view
Hasegawa PLoS Genet. Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development. 2015-08-01 10.1371/journal.pgen.1005428 32 view
Zoller Mol. Syst. Biol. Structure of silent transcription intervals and noise characteristics of mammalian genes. 2015-07-27 10.15252/msb.20156257 36 view
Fan Genome Biol. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. 2015-07-23 10.1186/s13059-015-0706-1 113 view
Gavelis BMC Genomics Single-cell transcriptomics using spliced leader PCR: Evidence for multiple losses of photosynthesis in polykrikoid dinoflagellates. 2015-07-17 10.1186/s12864-015-1636-8 11 view
Navin Sci Transl Med Delineating cancer evolution with single-cell sequencing. 2015-07-15 10.1126/scitranslmed.aac8319 27 view
Ding Bioinformatics Normalization and noise reduction for single cell RNA-seq experiments. 2015-07-01 10.1093/bioinformatics/btv122 50 view
Herderschee J. Leukoc. Biol. Emerging single-cell technologies in immunology. 2015-07-01 10.1189/jlb.6RU0115-020R 14 view
Wadsworth Genome Biol. Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics. 2015-06-20 10.1186/s13059-015-0695-0 1 view
Ning Sci Rep Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons. 2015-06-19 10.1038/srep11415 33 view
Kim Genome Biol. Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. 2015-06-19 10.1186/s13059-015-0692-3 125 view
Hatch Cell Linking Micronuclei to Chromosome Fragmentation. 2015-06-18 10.1016/j.cell.2015.06.005 15 view
Darmanis Proc. Natl. Acad. Sci. U.S.A. A survey of human brain transcriptome diversity at the single cell level. 2015-06-09 10.1073/pnas.1507125112 366 view
Dueck Genome Biol. Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. 2015-06-09 10.1186/s13059-015-0683-4 48 view
Bose Genome Biol. Scalable microfluidics for single-cell RNA printing and sequencing. 2015-06-06 10.1186/s13059-015-0684-3 65 view
Sun Clin Rev Allergy Immunol The coexistence of Sjögren's syndrome and primary biliary cirrhosis: a comprehensive review. 2015-06-01 10.1007/s12016-015-8471-1 view
Chen PLoS ONE Correction: comparison of multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) in single-cell sequencing. 2015-06-01 10.1371/journal.pone.0124990 5 view
Vallejos PLoS Comput. Biol. BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. 2015-06-01 10.1371/journal.pcbi.1004333 107 view
Klein Cell Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. 2015-05-21 10.1016/j.cell.2015.04.044 895 view
Junker Mol. Cell Single-cell transcriptomics enters the age of mass production. 2015-05-21 10.1016/j.molcel.2015.05.019 15 view
Wang Mol. Cell Advances and applications of single-cell sequencing technologies. 2015-05-21 10.1016/j.molcel.2015.05.005 212 view
Kolodziejczyk Mol. Cell The technology and biology of single-cell RNA sequencing. 2015-05-21 10.1016/j.molcel.2015.04.005 305 view
Nakamura Nucleic Acids Res. SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression. 2015-05-19 10.1093/nar/gkv134 49 view
Achim Nat. Biotechnol. High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. 2015-05-01 10.1038/nbt.3209 164 view
Satija Nat. Biotechnol. Spatial reconstruction of single-cell gene expression data. 2015-05-01 10.1038/nbt.3192 583 view
Voet Genome Biol. SNES makes sense? Single-cell exome sequencing evolves. 2015-04-29 10.1186/s13059-015-0650-0 4 view
Zhang Nat Commun Calibrating genomic and allelic coverage bias in single-cell sequencing. 2015-04-16 10.1038/ncomms7822 42 view
Suzuki Genome Biol. Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment. 2015-04-03 10.1186/s13059-015-0636-y 35 view
Burgess Nat. Rev. Genet. Technology: Bead capture for single-cell transcriptomics. 2015-04-01 10.1038/nrg3919 1 view
Xu Clin. Chem. Embryo genome profiling by single-cell sequencing for preimplantation genetic diagnosis in a β-thalassemia family. 2015-04-01 10.1373/clinchem.2014.228569 15 view
Ji PLoS ONE A simple strategy for reducing false negatives in calling variants from single-cell sequencing data. 2015-04-01 10.1371/journal.pone.0123789 1 view
Lv Mol. Genet. Genomics Identification of 4438 novel lincRNAs involved in mouse pre-implantation embryonic development. 2015-04-01 10.1007/s00438-014-0952-z 14 view
Junankar Nat Commun ID4 controls mammary stem cells and marks breast cancers with a stem cell-like phenotype. 2015-03-27 10.1038/ncomms7548 25 view
Lindeman Curr. Biol. Sexual cell-fate reprogramming in the ovary by DMRT1. 2015-03-16 10.1016/j.cub.2015.01.034 58 view
Castelle Curr. Biol. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. 2015-03-16 10.1016/j.cub.2015.01.014 193 view
Zhang Bioinformatics WemIQ: an accurate and robust isoform quantification method for RNA-seq data. 2015-03-15 10.1093/bioinformatics/btu757 20 view
Olarerin-George Nucleic Acids Res. Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive. 2015-03-11 10.1093/nar/gkv136 view
Zeisel Science Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. 2015-03-06 10.1126/science.aaa1934 4 view
Dey Nat. Biotechnol. Integrated genome and transcriptome sequencing of the same cell. 2015-03-01 10.1038/nbt.3129 206 view
Stegle Nat. Rev. Genet. Computational and analytical challenges in single-cell transcriptomics. 2015-03-01 10.1038/nrg3833 439 view
Oka Sci Rep Whole-mount single molecule FISH method for zebrafish embryo. 2015-02-25 10.1038/srep08571 14 view
Eirew Nature Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. 2015-02-19 10.1038/nature13952 340 view
Wu Gigascience Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells. 2015-02-01 10.1186/s13742-015-0091-4 24 view
Barber Curr. Opin. Genet. Dev. Dissecting cancer evolution at the macro-heterogeneity and micro-heterogeneity scale. 2015-02-01 10.1016/j.gde.2014.12.001 47 view
Buettner Nat. Biotechnol. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. 2015-02-01 10.1038/nbt.3102 487 view
Taher Mol. Hum. Reprod. Bioinformatics approaches to single-blastomere transcriptomics. 2015-02-01 10.1093/molehr/gau083 4 view
Luo Front Microbiol The use of evolutionary approaches to understand single cell genomes. 2015-02-01 10.3389/fmicb.2015.00191 4 view
Kanter Front Oncol Single cell transcriptomics: methods and applications. 2015-02-01 10.3389/fonc.2015.00053 28 view
Kumar Genome Med Whole genome prediction for preimplantation genetic diagnosis. 2015-02-01 10.1186/s13073-015-0160-4 13 view
Nelson Front Microbiol The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. 2015-02-01 10.3389/fmicb.2015.00713 95 view
Subramanian BMC Genomics Reference-free inference of tumor phylogenies from single-cell sequencing data. 2015-02-01 10.1186/1471-2164-16-S11-S7 3 view
Liu Biomed Res Int Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos. 2015-02-01 10.1155/2015/316735 5 view
Min PLoS ONE Identification of Distinct Tumor Subpopulations in Lung Adenocarcinoma via Single-Cell RNA-seq. 2015-02-01 10.1371/journal.pone.0135817 34 view
Vaughan Nature Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury. 2015-01-29 10.1038/nature14112 202 view
Efroni Genome Biol. Quantification of cell identity from single-cell gene expression profiles. 2015-01-22 10.1186/s13059-015-0580-x 41 view
Borel Am. J. Hum. Genet. Biased allelic expression in human primary fibroblast single cells. 2015-01-08 10.1016/j.ajhg.2014.12.001 65 view
Kim Cell Stem Cell Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. 2015-01-08 10.1016/j.stem.2014.11.005 87 view
Wei Biol. Reprod. Polar bodies in assisted reproductive technology: current progress and future perspectives. 2015-01-01 10.1095/biolreprod.114.125575 19 view
Usoskin Nat. Neurosci. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. 2015-01-01 10.1038/nn.3881 509 view
Luo Genome Biol. The importance of study design for detecting differentially abundant features in high-throughput experiments. 2014-12-03 10.1186/s13059-014-0527-7 12 view
Yao J. Thorac. Cardiovasc. Surg. Tumor cells are dislodged into the pulmonary vein during lobectomy. 2014-12-01 10.1016/j.jtcvs.2014.06.074 12 view
Chen PLoS ONE Comparison of multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) in single-cell sequencing. 2014-12-01 10.1371/journal.pone.0114520 30 view
Picelli Genome Res. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. 2014-12-01 10.1101/gr.177881.114 150 view
Abelin BMC Bioinformatics A ratiometric-based measure of gene co-expression. 2014-11-20 10.1186/1471-2105-15-331 3 view
McCorrison BMC Bioinformatics NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly. 2014-11-19 10.1186/s12859-014-0357-3 7 view
Kolisko Curr. Biol. Single-cell transcriptomics for microbial eukaryotes. 2014-11-17 10.1016/j.cub.2014.10.026 32 view
Daley Bioinformatics Modeling genome coverage in single-cell sequencing. 2014-11-15 10.1093/bioinformatics/btu540 18 view
Khera J Transl Med Single-cell transcriptomics: an emerging tool in the study of cardiometabolic disease. 2014-11-06 10.1186/s12967-014-0312-0 2 view
Huang Proc. Natl. Acad. Sci. U.S.A. Time-variant clustering model for understanding cell fate decisions. 2014-11-04 10.1073/pnas.1407388111 15 view
Ha Genome Res. TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. 2014-11-01 10.1101/gr.180281.114 130 view
Biase Genome Res. Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. 2014-11-01 10.1101/gr.177725.114 90 view
Morgan Cold Spring Harb Perspect Med Differential Gene Expression in Age-Related Macular Degeneration. 2014-10-23 10.1101/cshperspect.a017210 7 view
Liang J Genet Genomics Single-cell sequencing technologies: current and future. 2014-10-20 10.1016/j.jgg.2014.09.005 33 view
Yang Stem Cell Reports Generation of haploid spermatids with fertilization and development capacity from human spermatogonial stem cells of cryptorchid patients. 2014-10-14 10.1016/j.stemcr.2014.08.004 54 view
Yu Anal. Chem. Microfluidic whole genome amplification device for single cell sequencing. 2014-10-07 10.1021/ac5032176 43 view
Zhang BMC Genomics Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data. 2014-10-03 10.1186/1471-2164-15-845 45 view
Bar-Haim PLoS ONE CD8+ TCR transgenic strains expressing public versus private TCR targeting the respiratory syncytial virus K(d)M2(82-90) epitope demonstrate similar functional profiles. 2014-10-01 10.1371/journal.pone.0099249 view
Streets Nat. Biotechnol. How deep is enough in single-cell RNA-seq? 2014-10-01 10.1038/nbt.3039 18 view
Ting Cell Rep Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells. 2014-09-25 10.1016/j.celrep.2014.08.029 199 view
Knouse Proc. Natl. Acad. Sci. U.S.A. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. 2014-09-16 10.1073/pnas.1415287111 126 view
Lasken Nat. Rev. Genet. Recent advances in genomic DNA sequencing of microbial species from single cells. 2014-09-01 10.1038/nrg3785 110 view
Pettit PLoS Comput. Biol. Identifying cell types from spatially referenced single-cell expression datasets. 2014-09-01 10.1371/journal.pcbi.1003824 19 view
Navin Genome Biol. Cancer genomics: one cell at a time. 2014-08-30 10.1186/s13059-014-0452-9 161 view
Wang Nature Clonal evolution in breast cancer revealed by single nucleus genome sequencing. 2014-08-14 10.1038/nature13600 559 view
Zhu J Transl Med Single-cell transcriptome in the identification of disease biomarkers: opportunities and challenges. 2014-08-12 10.1186/s12967-014-0212-3 12 view
Francis Cancer Discov EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing. 2014-08-01 10.1158/2159-8290.CD-13-0879 139 view
Becker BMC Plant Biol. Transcriptional profiling of Arabidopsis root hairs and pollen defines an apical cell growth signature. 2014-08-01 10.1186/s12870-014-0197-3 35 view
Gini Cancer Discov Greater than the sum of its parts: single-nucleus sequencing identifies convergent evolution of independent EGFR mutants in GBM. 2014-08-01 10.1158/2159-8290.CD-14-0635 6 view
Brunskill Development Single cell dissection of early kidney development: multilineage priming. 2014-08-01 10.1242/dev.110601 63 view
Saliba Nucleic Acids Res. Single-cell RNA-seq: advances and future challenges. 2014-08-01 10.1093/nar/gku555 321 view
Dayarian Genetics How to infer relative fitness from a sample of genomic sequences. 2014-07-01 10.1534/genetics.113.160986 5 view
Hughes PLoS Genet. Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing. 2014-07-01 10.1371/journal.pgen.1004462 76 view
Kharchenko Nat. Methods Bayesian approach to single-cell differential expression analysis. 2014-07-01 10.1038/nmeth.2967 406 view
Trombetta Curr Protoc Mol Biol Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing. 2014-07-01 10.1002/0471142727.mb0422s107 84 view
Patel Science Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. 2014-06-20 10.1126/science.1254257 1199 view
Shalek Nature Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. 2014-06-19 10.1038/nature13437 498 view
Prjibelski Bioinformatics ExSPAnder: a universal repeat resolver for DNA fragment assembly. 2014-06-15 10.1093/bioinformatics/btu266 51 view
Yu Cell Res. Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing. 2014-06-01 10.1038/cr.2014.43 69 view
Grün Nat. Methods Validation of noise models for single-cell transcriptomics. 2014-06-01 10.1038/nmeth.2930 295 view
Baslan Curr. Opin. Genet. Dev. Single cell sequencing approaches for complex biological systems. 2014-06-01 10.1016/j.gde.2014.06.004 26 view
Portmann Cell Rep Behavioral abnormalities and circuit defects in the basal ganglia of a mouse model of 16p11.2 deletion syndrome. 2014-05-22 10.1016/j.celrep.2014.03.036 90 view
Mahata Cell Rep Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis. 2014-05-22 10.1016/j.celrep.2014.04.011 93 view
Treutlein Nature Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. 2014-05-15 10.1038/nature13173 606 view
Streets Proc. Natl. Acad. Sci. U.S.A. Microfluidic single-cell whole-transcriptome sequencing. 2014-05-13 10.1073/pnas.1402030111 163 view
Robson Dev. Cell Deciphering developmental processes from single-cell transcriptomes. 2014-05-12 10.1016/j.devcel.2014.04.032 view
Roth Nat. Methods PyClone: statistical inference of clonal population structure in cancer. 2014-04-01 10.1038/nmeth.2883 313 view
Voo Methods Mol. Biol. Sample preparation for single cell transcriptomics: essential oil glands in Citrus fruit peel as an example. 2014-04-01 10.1007/978-1-4939-0606-2_14 4 view
Trapnell Nat. Biotechnol. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. 2014-04-01 10.1038/nbt.2859 736 view
Avital Genome Biol. Seeing is believing: new methods for in situ single-cell transcriptomics. 2014-03-31 10.1186/gb4169 13 view
Marinov Genome Res. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. 2014-03-01 10.1101/gr.161034.113 275 view
Jaitin Science Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. 2014-02-14 10.1126/science.1247651 707 view
Ning Front Oncol Current challenges in the bioinformatics of single cell genomics. 2014-02-01 10.3389/fonc.2014.00007 38 view
de Bourcy PLoS ONE A quantitative comparison of single-cell whole genome amplification methods. 2014-02-01 10.1371/journal.pone.0105585 view
Lusk PLoS ONE Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data. 2014-02-01 10.1371/journal.pone.0110808 83 view
Clingenpeel Front Microbiol Reconstructing each cell's genome within complex microbial communities-dream or reality? 2014-02-01 10.3389/fmicb.2014.00771 view
Spaethling FASEB J. Serotonergic neuron regulation informed by in vivo single-cell transcriptomics. 2014-02-01 10.1096/fj.13-240267 34 view
Islam Nat. Methods Quantitative single-cell RNA-seq with unique molecular identifiers. 2014-02-01 10.1038/nmeth.2772 480 view
Kim BMC Bioinformatics Using single cell sequencing data to model the evolutionary history of a tumor. 2014-01-24 10.1186/1471-2105-15-27 38 view
Deng Science Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. 2014-01-10 10.1126/science.1245316 490 view
Wu Nat. Methods Quantitative assessment of single-cell RNA-sequencing methods. 2014-01-01 10.1038/nmeth.2694 423 view
Picelli Nat Protoc Full-length RNA-seq from single cells using Smart-seq2. 2014-01-01 10.1038/nprot.2014.006 605 view
Wong Semin. Cancer Biol. Genome-wide association and sequencing studies on colorectal cancer. 2013-12-01 10.1016/j.semcancer.2013.09.005 16 view
Close BMC Microbiol. Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. 2013-11-27 10.1186/1471-2180-13-270 6 view
Milot Front Genet The National DNA Data Bank of Canada: a Quebecer perspective. 2013-11-20 10.3389/fgene.2013.00249 8 view
Katayama Bioinformatics SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization. 2013-11-15 10.1093/bioinformatics/btt511 59 view
Patel Cancer Lett. Cancer genome sequencing: understanding malignancy as a disease of the genome, its conformation, and its evolution. 2013-11-01 10.1016/j.canlet.2012.10.018 24 view
Ding Cancer Lett. Advances for studying clonal evolution in cancer. 2013-11-01 10.1016/j.canlet.2012.12.028 54 view
Ren Asian J. Androl. Investigating intratumour heterogeneity by single-cell sequencing. 2013-11-01 10.1038/aja.2013.106 16 view
McConnell Science Mosaic copy number variation in human neurons. 2013-11-01 10.1126/science.1243472 347 view
Brennecke Nat. Methods Accounting for technical noise in single-cell RNA-seq experiments. 2013-11-01 10.1038/nmeth.2645 403 view
Spaethling Curr Opin Pharmacol Single-cell transcriptomics for drug target discovery. 2013-10-01 10.1016/j.coph.2013.04.011 9 view
Josefsson PLoS Pathog. Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule. 2013-10-01 10.1371/journal.ppat.1003432 view
Taghavi Bioinformatics Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities. 2013-10-01 10.1093/bioinformatics/btt420 6 view
Adalsteinsson Integr Biol (Camb) Single cells from human primary colorectal tumors exhibit polyfunctional heterogeneity in secretions of ELR+ CXC chemokines. 2013-10-01 10.1039/c3ib40059j view
Nurk J. Comput. Biol. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. 2013-10-01 10.1089/cmb.2013.0084 499 view
Bertelli Clin. Microbiol. Infect. Rapid bacterial genome sequencing: methods and applications in clinical microbiology. 2013-09-01 10.1111/1469-0691.12217 141 view
Shapiro Nat. Rev. Genet. Single-cell sequencing-based technologies will revolutionize whole-organism science. 2013-09-01 10.1038/nrg3542 610 view
Yan Nat. Struct. Mol. Biol. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. 2013-09-01 10.1038/nsmb.2660 622 view
Xue Nature Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. 2013-08-29 10.1038/nature12364 476 view
Shalek Nature Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. 2013-06-13 10.1038/nature12172 701 view
Fitzsimons Genome Res. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. 2013-05-01 10.1101/gr.142208.112 49 view
Sasagawa Genome Biol. Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. 2013-04-17 10.1186/gb-2013-14-4-r31 210 view
Lasken Nat. Biotechnol. Single-cell sequencing in its prime. 2013-03-01 10.1038/nbt.2523 54 view
McGettigan Curr Opin Chem Biol Transcriptomics in the RNA-seq era. 2013-02-01 10.1016/j.cbpa.2012.12.008 206 view
Soon Mol. Syst. Biol. High-throughput sequencing for biology and medicine. 2013-02-01 10.1038/msb.2012.61 230 view
Nikolenko BMC Genomics BayesHammer: Bayesian clustering for error correction in single-cell sequencing. 2013-02-01 10.1186/1471-2164-14-S1-S7 171 view
Hills Genome Med BAIT: Organizing genomes and mapping rearrangements in single cells. 2013-02-01 10.1186/gm486 18 view
Grad J Micromech Microeng A simple add-on microfluidic appliance for accurately sorting small populations of cells with high fidelity. 2013-02-01 10.1088/0960-1317/23/11/117003 5 view
Moroz Methods Mol. Biol. Single-neuron transcriptome and methylome sequencing for epigenomic analysis of aging. 2013-02-01 10.1007/978-1-62703-556-9_21 19 view
Zajac PLoS ONE Base preferences in non-templated nucleotide incorporation by MMLV-derived reverse transcriptases. 2013-02-01 10.1371/journal.pone.0085270 21 view
Xu Genet Res Int Feasibility of whole RNA sequencing from single-cell mRNA amplification. 2013-02-01 10.1155/2013/724124 3 view
Kim Genome Biol. Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data. 2013-01-28 10.1186/gb-2013-14-1-r7 83 view
Zong Science Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. 2012-12-21 10.1126/science.1229164 617 view
Hebenstreit Biology (Basel) Methods, Challenges and Potentials of Single Cell RNA-seq. 2012-11-16 10.3390/biology1030658 40 view
Falconer Nat. Methods DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. 2012-11-01 10.1038/nmeth.2206 65 view
Hartmaier Breast Cancer Res. Who's driving anyway? Herculean efforts to identify the drivers of breast cancer. 2012-10-31 10.1186/bcr3325 view
Hashimshony Cell Rep CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. 2012-09-27 10.1016/j.celrep.2012.08.003 554 view
Mason ISME J Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. 2012-09-01 10.1038/ismej.2012.59 349 view
Lasken Nat. Rev. Microbiol. Genomic sequencing of uncultured microorganisms from single cells. 2012-09-01 10.1038/nrmicro2857 178 view
Li Gigascience Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer. 2012-08-14 10.1186/2047-217X-1-12 66 view
Saunders EMBO Mol Med Role of intratumoural heterogeneity in cancer drug resistance: molecular and clinical perspectives. 2012-08-01 10.1002/emmm.201101131 149 view
Yilmaz Curr. Opin. Biotechnol. Single cell genome sequencing. 2012-06-01 10.1016/j.copbio.2011.11.018 75 view
Dupont ISME J Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. 2012-06-01 10.1038/ismej.2011.189 294 view
Pamp Genome Res. Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). 2012-06-01 10.1101/gr.131482.111 92 view
Peng Bioinformatics IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. 2012-06-01 10.1093/bioinformatics/bts174 1156 view
Bankevich J. Comput. Biol. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. 2012-05-01 10.1089/cmb.2012.0021 4902 view
Hou Cell Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. 2012-03-02 10.1016/j.cell.2012.02.028 438 view
Martinez-Garcia ISME J Unveiling in situ interactions between marine protists and bacteria through single cell sequencing. 2012-03-01 10.1038/ismej.2011.126 57 view
Ma Curr. Opin. Genet. Dev. Opening Pandora's Box--the new biology of driver mutations and clonal evolution in cancer as revealed by next generation sequencing. 2012-02-01 10.1016/j.gde.2012.01.008 view
Martinez-Garcia ISME J High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. 2012-01-01 10.1038/ismej.2011.84 132 view
Bartfai Trends Pharmacol. Sci. Drug targets: single-cell transcriptomics hastens unbiased discovery. 2012-01-01 10.1016/ 28 view
de Bekker Genome Biol. Single cell transcriptomics of neighboring hyphae of Aspergillus niger. 2011-08-04 10.1186/gb-2011-12-8-r71 view
Surman J. Immunol. Clonally related CD8+ T cells responsible for rapid population of both diffuse nasal-associated lymphoid tissue and lung after respiratory virus infection. 2011-07-15 10.4049/jimmunol.1100125 view
Islam Genome Res. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. 2011-07-01 10.1101/gr.110882.110 473 view
Medvedev Bioinformatics Error correction of high-throughput sequencing datasets with non-uniform coverage. 2011-07-01 10.1093/bioinformatics/btr208 123 view
Salman Syst. Appl. Microbiol. A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria. 2011-06-01 10.1016/j.syapm.2011.02.001 72 view
Navin Genome Med Future medical applications of single-cell sequencing in cancer. 2011-05-31 10.1186/gm247 170 view
Navin Nature Tumour evolution inferred by single-cell sequencing. 2011-04-07 10.1038/nature09807 1726 view
Heywood ISME J Capturing diversity of marine heterotrophic protists: one cell at a time. 2011-04-01 10.1038/ismej.2010.155 73 view
Eberwine Pharmacol. Ther. Single cell transcriptomics of hypothalamic warm sensitive neurons that control core body temperature and fever response Signaling asymmetry and an extension of chemical neuroanatomy. 2011-03-01 10.1016/j.pharmthera.2010.09.010 72 view
Tang PLoS ONE Deterministic and stochastic allele specific gene expression in single mouse blastomeres. 2011-03-01 10.1371/journal.pone.0021208 113 view
Woyke PLoS ONE Decontamination of MDA reagents for single cell whole genome amplification. 2011-01-01 10.1371/journal.pone.0026161 119 view
Lingner BMC Bioinformatics Predicting phenotypic traits of prokaryotes from protein domain frequencies. 2010-09-24 10.1186/1471-2105-11-481 15 view
Tang Cell Stem Cell Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. 2010-05-07 10.1016/j.stem.2010.03.015 413 view
Liang BMC Bioinformatics JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. 2009-11-29 10.1186/1471-2105-10-391 6 view
Woyke PLoS ONE Assembling the marine metagenome, one cell at a time. 2009-02-01 10.1371/journal.pone.0005299 305 view
Altarescu Prenat. Diagn. PGD on a recombinant allele: crossover between the TSC2 gene and 'linked' markers impairs accurate diagnosis. 2008-10-01 10.1002/pd.2070 25 view
Ishoey Curr. Opin. Microbiol. Genomic sequencing of single microbial cells from environmental samples. 2008-06-01 10.1016/j.mib.2008.05.006 149 view