Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Serotonergic neuron regulation informed by in vivo single-cell transcriptomics

(2013) Jennifer M. Spaethling et al.   FASEB JOURNAL

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

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 sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Molecular Roadblocks for Cellular Reprogramming

(2012) Thomas Vierbuchen et al.   MOLECULAR CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

IUPHAR-DB: updated database content and new features

(2012) J. L. Sharman et al.   NUCLEIC ACIDS RESEARCH

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

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

(2011) S. Islam et al.   GENOME RESEARCH

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Cytoplasmic Intron Sequence-Retaining Transcripts Can Be Dendritically Targeted via ID Element Retrotransposons

(2011) Peter T. Buckley et al.   NEURON

The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

(2011) J. T. Eppig et al.   NUCLEIC ACIDS RESEARCH

Variability, compensation, and modulation in neurons and circuits

(2011) E. Marder   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparison of scores for bimodality of gene expression distributions and genome-wide evaluation of the prognostic relevance of high-scoring genes

(2010) Birte Hellwig et al.   BMC BIOINFORMATICS

Transcriptional Control of Brown Fat Development

(2010) Shingo Kajimura et al.   Cell Metabolism

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

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Variability in gene expression underlies incomplete penetrance

(2010) Arjun Raj et al.   NATURE

Single-cell NF-κB dynamics reveal digital activation and analogue information processing

(2010) Savaş Tay et al.   NATURE

Pet-1 is required across different stages of life to regulate serotonergic function

(2010) Chen Liu et al.   NATURE NEUROSCIENCE

RNA: state memory and mediator of cellular phenotype

(2010) Junhyong Kim et al.   TRENDS IN CELL BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Myocardin is required for cardiomyocyte survival and maintenance of heart function

(2009) J. Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The mammalian phenotype ontology: enabling robust annotation and comparative analysis

(2009) Cynthia L. Smith et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Simultaneous Inference in General Parametric Models

(2008) Torsten Hothorn et al.   BIOMETRICAL JOURNAL

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL

Interferon Regulatory Factors Are Transcriptional Regulators of Adipogenesis

(2008) Jun Eguchi et al.   Cell Metabolism

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

(2008) J. D. Cahoy et al.   JOURNAL OF NEUROSCIENCE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH