Quantitative single-cell RNA-seq with unique molecular identifiers

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

(2013) Alex K. Shalek et al.   NATURE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

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

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

(2012) Saiful Islam et al.   Nature Protocols

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Transcriptional burst frequency and burst size are equally modulated across the human genome

(2012) R. D. Dar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

(2012) K. Shiroguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TGF-β-Superfamily Signaling Regulates Embryonic Stem Cell Heterogeneity: Self-Renewal as a Dynamic and Regulated Equilibrium

(2012) Katherine E. Galvin-Burgess et al.   STEM CELLS

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

(2012) Tamar Hashimshony et al.   Cell Reports

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

(2011) S. Islam et al.   GENOME RESEARCH

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Counting individual DNA molecules by the stochastic attachment of diverse labels

(2011) G. K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cyclic gene Hes1 contributes to diverse differentiation responses of embryonic stem cells

(2009) T. Kobayashi et al.   GENES & DEVELOPMENT

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells

(2008) Mark G. Carter et al.   GENE EXPRESSION PATTERNS

Embryonic stem cell–specific microRNAs regulate the G1-S transition and promote rapid proliferation

(2008) Yangming Wang et al.   NATURE GENETICS

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Contrasting Expression of Keratins in Mouse and Human Embryonic Stem Cells

(2008) Jochen Maurer et al.   PLoS One