Published in Nature on May 19, 2013
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods (2013) 7.06
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell (2015) 6.38
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science (2014) 6.09
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature (2014) 5.47
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science (2014) 4.91
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol (2015) 4.09
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol (2014) 4.06
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature (2014) 3.86
CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell (2014) 3.68
Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods (2013) 3.61
Regulation of type I interferon responses. Nat Rev Immunol (2014) 3.60
Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods (2013) 3.59
Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods (2013) 3.52
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol (2014) 3.43
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol (2014) 2.75
Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses. Nat Immunol (2014) 2.52
Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments. Nat Biotechnol (2013) 2.33
Spatial reconstruction of single-cell gene expression data. Nat Biotechnol (2015) 2.31
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity. Cell (2015) 2.30
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res (2013) 2.23
Single cell genomics: advances and future perspectives. PLoS Genet (2014) 2.16
Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res (2014) 2.06
Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens. Science (2015) 2.06
Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol (2015) 2.03
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science (2016) 1.95
Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature (2014) 1.91
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses. Cell (2015) 1.87
Dynamic heterogeneity and DNA methylation in embryonic stem cells. Mol Cell (2014) 1.80
Epigenetics. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science (2015) 1.78
Single-cell technologies for monitoring immune systems. Nat Immunol (2014) 1.78
Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science (2015) 1.75
The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing. Nat Immunol (2016) 1.74
Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol (2015) 1.66
A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. Cell (2016) 1.61
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol (2015) 1.56
A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians. Dev Cell (2015) 1.54
Clonal evolution in hematological malignancies and therapeutic implications. Leukemia (2013) 1.50
Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. Mol Cell (2015) 1.48
Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell (2014) 1.47
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc Natl Acad Sci U S A (2014) 1.42
Image-based transcriptomics in thousands of single human cells at single-molecule resolution. Nat Methods (2013) 1.41
IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system. Science (2015) 1.32
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell (2016) 1.28
Advances and applications of single-cell sequencing technologies. Mol Cell (2015) 1.28
Defining cell types and states with single-cell genomics. Genome Res (2015) 1.27
Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow. Nat Immunol (2015) 1.23
Single-cell analysis tools for drug discovery and development. Nat Rev Drug Discov (2015) 1.23
Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells. Nat Biotechnol (2014) 1.22
Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat Methods (2016) 1.20
Unifying immunology with informatics and multiscale biology. Nat Immunol (2014) 1.15
SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis. PLoS Comput Biol (2015) 1.14
Biased allelic expression in human primary fibroblast single cells. Am J Hum Genet (2014) 1.13
Modeling bi-modality improves characterization of cell cycle on gene expression in single cells. PLoS Comput Biol (2014) 1.13
Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun (2015) 1.07
Understanding HIV latency: the road to an HIV cure. Annu Rev Med (2015) 1.07
Microglial diversity by responses and responders. Front Cell Neurosci (2014) 1.07
Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Nature (2016) 1.06
Massively parallel digital transcriptional profiling of single cells. Nat Commun (2017) 1.05
Single-cell transcriptome analyses reveal signals to activate dormant neural stem cells. Cell (2015) 1.05
Single-Cell Analysis in Cancer Genomics. Trends Genet (2015) 1.05
Pseudotime estimation: deconfounding single cell time series. Bioinformatics (2016) 1.04
A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Mol Cell (2015) 1.04
Single-cell analysis of G-protein signal transduction. J Biol Chem (2015) 1.04
Multi-Scale Molecular Deconstruction of the Serotonin Neuron System. Neuron (2015) 1.04
Technical variations in low-input RNA-seq methodologies. Sci Rep (2014) 1.03
Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. Genome Res (2014) 1.03
Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear. Nat Commun (2015) 1.03
Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium. J Extracell Vesicles (2015) 1.02
Design and computational analysis of single-cell RNA-sequencing experiments. Genome Biol (2016) 1.01
Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles. Proc Natl Acad Sci U S A (2014) 1.01
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells. Genome Res (2015) 1.01
Single-cell epigenomics: techniques and emerging applications. Nat Rev Genet (2015) 1.00
High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics. PLoS One (2015) 1.00
Single-Cell Transcriptomics of the Human Endocrine Pancreas. Diabetes (2016) 0.99
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing. Curr Protoc Mol Biol (2014) 0.99
Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands. Proc Natl Acad Sci U S A (2015) 0.99
The Many Alternative Faces of Macrophage Activation. Front Immunol (2015) 0.98
Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. Nat Commun (2015) 0.98
Heterogeneity in immune responses: from populations to single cells. Trends Immunol (2014) 0.98
Spatiotemporal transcriptomics reveals the evolutionary history of the endoderm germ layer. Nature (2014) 0.98
Calibrating genomic and allelic coverage bias in single-cell sequencing. Nat Commun (2015) 0.98
Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biol (2014) 0.97
Revealing the vectors of cellular identity with single-cell genomics. Nat Biotechnol (2016) 0.97
A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data. Genome Biol (2014) 0.96
A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae). PLoS One (2016) 0.96
Diffusion pseudotime robustly reconstructs lineage branching. Nat Methods (2016) 0.95
Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs. Nucleic Acids Res (2014) 0.95
Multiplex parenting: IVG and the generations to come. J Med Ethics (2014) 0.95
Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol (2015) 0.95
Genome-wide mutation avalanches induced in diploid yeast cells by a base analog or an APOBEC deaminase. PLoS Genet (2013) 0.94
Dissecting the causal genetic mechanisms of coronary heart disease. Curr Atheroscler Rep (2014) 0.93
Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol (2016) 0.92
Single cell transcriptome analysis of mouse carotid body glomus cells. J Physiol (2016) 0.92
Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data. BMC Genomics (2014) 0.92
Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells. Proc Natl Acad Sci U S A (2016) 0.91
A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types. Mol Cell (2014) 0.91
Investigating Evolutionary Conservation of Dendritic Cell Subset Identity and Functions. Front Immunol (2015) 0.91
Transcriptional control of inflammatory responses. Cold Spring Harb Perspect Biol (2014) 0.91
A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Syst (2016) 0.90
Transcriptional and translational heterogeneity among neonatal mouse spermatogonia. Biol Reprod (2015) 0.90
Causal protein-signaling networks derived from multiparameter single-cell data. Science (2005) 34.28
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics (2011) 25.76
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science (2011) 15.45
mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods (2009) 11.71
Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods (2010) 10.13
Inferring cellular networks using probabilistic graphical models. Science (2004) 9.91
Noise in protein expression scales with natural protein abundance. Nat Genet (2006) 8.03
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol (2012) 7.37
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res (2011) 6.90
Variability and memory of protein levels in human cells. Nature (2006) 6.15
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07
Dynamic proteomics of individual cancer cells in response to a drug. Science (2008) 5.43
Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature (2010) 5.27
CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep (2012) 5.17
Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res (2005) 4.98
Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature (2008) 4.63
Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods (2011) 4.18
Disruption of E-cadherin-mediated adhesion induces a functionally distinct pathway of dendritic cell maturation. Immunity (2007) 3.58
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell (2012) 3.04
Central dogma at the single-molecule level in living cells. Nature (2011) 3.00
Single-molecule approaches to stochastic gene expression. Annu Rev Biophys (2009) 2.75
Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response. Mol Syst Biol (2010) 2.21
Genomic analysis at the single-cell level. Annu Rev Genet (2011) 1.96
The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biol (2012) 1.82
Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response. Mol Syst Biol (2012) 1.48
Stochastic expression of the interferon-β gene. PLoS Biol (2012) 1.47
Regulation of the transcriptional activity of the IRF7 promoter by a pathway independent of interferon signaling. J Biol Chem (2005) 1.45
Cell-to-cell variability of alternative RNA splicing. Mol Syst Biol (2011) 1.38
Analysis of alternative splicing of cassette exons at single-cell level using two fluorescent proteins. Nucleic Acids Res (2012) 0.99
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet (2008) 17.67
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell (2013) 9.24
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol (2011) 9.18
Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods (2010) 9.09
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69
A module map showing conditional activity of expression modules in cancer. Nat Genet (2004) 8.57
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell (2011) 8.21
SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet (2009) 7.48
Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A (2008) 7.45
Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet (2010) 7.39
Natural history and evolutionary principles of gene duplication in fungi. Nature (2007) 7.26
Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell (2011) 7.03
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature (2012) 7.00
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol (2009) 6.76
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
The genome of the sea urchin Strongylocentrotus purpuratus. Science (2006) 6.41
A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature (2012) 6.34
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A (2009) 6.01
Comparative functional genomics of the fission yeasts. Science (2011) 6.00
Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol (2010) 5.96
Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods (2006) 5.96
Charting a dynamic DNA methylation landscape of the human genome. Nature (2013) 5.80
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature (2010) 5.79
Medical sequencing at the extremes of human body mass. Am J Hum Genet (2007) 5.61
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature (2006) 5.52
Rab27a and Rab27b control different steps of the exosome secretion pathway. Nat Cell Biol (2009) 5.44
Peroxisomes are signaling platforms for antiviral innate immunity. Cell (2010) 5.24
A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell (2009) 4.98
Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci U S A (2007) 4.91
Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1. Nature (2013) 4.74
Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells. Nature (2013) 4.57
Induction and molecular signature of pathogenic TH17 cells. Nat Immunol (2012) 4.43
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods (2010) 4.30
From signatures to models: understanding cancer using microarrays. Nat Genet (2005) 4.29
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc (2011) 4.18
Genome-scale loss-of-function screening with a lentiviral RNAi library. Nat Methods (2006) 4.12
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science (2013) 4.12
Dynamic single-cell imaging of direct reprogramming reveals an early specifying event. Nat Biotechnol (2010) 3.98
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol (2011) 3.81
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res (2011) 3.81
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci U S A (2005) 3.58
High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science (2011) 3.53
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol (2012) 3.52
Proto-genes and de novo gene birth. Nature (2012) 3.43
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog (2012) 3.35
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell (2011) 3.20
Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL. Science (2008) 3.17
Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell (2011) 3.16
High-throughput bisulfite sequencing in mammalian genomes. Methods (2009) 3.14
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol (2002) 3.09
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol (2010) 3.09