Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

(2014) Bidesh Mahata et al.   Cell Reports

Posttranscriptional Control of T Cell Effector Function by Aerobic Glycolysis

(2013) Chih-Hao Chang et al.   CELL

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-Cell Profiling of Epigenetic Modifiers Identifies PRDM14 as an Inducer of Cell Fate in the Mammalian Embryo

(2013) Adam Burton et al.   Cell Reports

Cell-Cycle Control of Developmentally Regulated Transcription Factors Accounts for Heterogeneity in Human Pluripotent Cells

(2013) Amar M. Singh et al.   Stem Cell Reports

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst

(2012) F. Buettner et al.   BIOINFORMATICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies

(2012) Nicoló Fusi et al.   PLoS Computational Biology

Using control genes to correct for unwanted variation in microarray data

(2011) J. A. Gagnon-Bartsch et al.   BIOSTATISTICS

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

The Transcription Factor STAT3 Is Required for T Helper 2 Cell Development

(2011) Gretta L. Stritesky et al.   IMMUNITY

Stat6 and c-Jun Mediate Th2 Cell-Specific IL-24 Gene Expression

(2011) Anupama Sahoo et al.   JOURNAL OF IMMUNOLOGY

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

Comprehensive qPCR profiling of gene expression in single neuronal cells

(2011) Ami Citri et al.   Nature Protocols

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Batf coordinates multiple aspects of B and T cell function required for normal antibody responses

(2010) Briana C. Betz et al.   JOURNAL OF EXPERIMENTAL MEDICINE

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Real-Time Gene Expression: Statistical Challenges in Design and Inference

(2008) David Gold et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH