Development and applications of single-cell transcriptome analysis

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

Circadian Rhythms and Metabolic Syndrome

(2010) Eleonore Maury et al.   CIRCULATION RESEARCH

Recent advances in single-molecule sequencing

(2010) Regina Treffer et al.   CURRENT OPINION IN BIOTECHNOLOGY

Single-cell cDNA microarray profiling of complex biological processes of differentiation

(2010) Kazuki Kurimoto et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

(2010) D. Xie et al.   GENOME RESEARCH

The therapeutic promise of the cancer stem cell concept

(2010) Natasha Y. Frank et al.   JOURNAL OF CLINICAL INVESTIGATION

Single-cell gene expression profiling using reverse transcription quantitative real-time PCR

(2010) Anders Ståhlberg et al.   METHODS

Regulation of Protein Levels in Subcellular Domains through mRNA Transport and Localized Translation

(2010) Dianna E. Willis et al.   MOLECULAR & CELLULAR PROTEOMICS

Measurement of single-cell dynamics

(2010) David G. Spiller et al.   NATURE

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Dynamic single-cell imaging of direct reprogramming reveals an early specifying event

(2010) Zachary D Smith et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Grand Challenge Commentary: RNA epigenetics?

(2010) Chuan He   Nature Chemical Biology

Amplification-free digital gene expression profiling from minute cell quantities

(2010) Fatih Ozsolak et al.   NATURE METHODS

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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

(2010) Fuchou Tang et al.   Nature Protocols

Accurate quantification of transcriptome from RNA-Seq data by effective length normalization

(2010) Soohyun Lee et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Y. Taniguchi et al.   SCIENCE

Coexistence of Quiescent and Active Adult Stem Cells in Mammals

(2010) L. Li et al.   SCIENCE

Heterogeneity in Cancer: Cancer Stem Cells versus Clonal Evolution

(2009) Mark Shackleton et al.   CELL

Non-genetic heterogeneity of cells in development: more than just noise

(2009) S. Huang   DEVELOPMENT

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human

(2009) Kun Zhang et al.   NATURE METHODS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Quantitative analysis of gene expression in a single cell by qPCR

(2009) Kiyomi Taniguchi et al.   NATURE METHODS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Transcriptome transfer produces a predictable cellular phenotype

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

Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis

(2009) A. Mustroph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

(2009) E. Sanz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Application of a Translational Profiling Approach for the Comparative Analysis of CNS Cell Types

(2008) Joseph P. Doyle et al.   CELL

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

(2008) Myriam Heiman et al.   CELL

Dynamic Equilibrium and Heterogeneity of Mouse Pluripotent Stem Cells with Distinct Functional and Epigenetic States

(2008) Katsuhiko Hayashi et al.   Cell Stem Cell

The stochastic nature of biochemical networks

(2008) Vahid Shahrezaei et al.   CURRENT OPINION IN BIOTECHNOLOGY

Identification and characterization of subpopulations in undifferentiated ES cell culture

(2008) Y. Toyooka et al.   DEVELOPMENT

Complex genome-wide transcription dynamics orchestrated by Blimp1 for the specification of the germ cell lineage in mice

(2008) K. Kurimoto et al.   GENES & DEVELOPMENT

Integrating whole transcriptome assays on a lab-on-a-chip for single cell gene profiling

(2008) N. Bontoux et al.   LAB ON A CHIP

Imaging stem-cell-driven regeneration in mammals

(2008) Timm Schroeder   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Global Characterization of Cell-Specific Gene Expression through Fluorescence-Activated Sorting of Nuclei

(2008) C. Zhang et al.   PLANT PHYSIOLOGY

Stochasticity and Cell Fate

(2008) R. Losick et al.   SCIENCE

A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell

(2008) P. J. Choi et al.   SCIENCE

Transcriptome content and dynamics at single-nucleotide resolution

(2008) Nicole Cloonan et al.   GENOME BIOLOGY