Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

Control of ground-state pluripotency by allelic regulation of Nanog

(2012) Yusuke Miyanari 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

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Signals and Combinatorial Functions of Histone Modifications

(2011) Tamaki Suganuma et al.   Annual Review of Biochemistry

Chromosomal Position Effects Are Linked to Sir2-Mediated Variation in Transcriptional Burst Size

(2011) Cory Batenchuk et al.   BIOPHYSICAL JOURNAL

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

What do expression dynamics tell us about the mechanism of transcription?

(2011) Daniel R Larson   CURRENT OPINION IN GENETICS & DEVELOPMENT

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

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

(2011) S. Islam et al.   GENOME RESEARCH

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Microbial environments confound antibiotic efficacy

(2011) Henry H Lee et al.   Nature Chemical Biology

Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Blastomeres

(2011) Fuchou Tang et al.   PLoS One

Varying virulence: epigenetic control of expression noise and disease processes

(2011) Kathryn Miller-Jensen et al.   TRENDS IN BIOTECHNOLOGY

Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads

(2011) Ernest Turro et al.   GENOME BIOLOGY

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

Cell structure and dynamics

(2010) Anne Ridley et al.   CURRENT OPINION IN CELL BIOLOGY

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Global Expression of Cell Surface Proteins in Embryonic Stem Cells

(2010) Bin Gu et al.   PLoS One

Functional Heterogeneity of Embryonic Stem Cells Revealed through Translational Amplification of an Early Endodermal Transcript

(2010) Maurice A. Canham et al.   PLOS BIOLOGY

Cell Lineage Determination in State Space: A Systems View Brings Flexibility to Dogmatic Canonical Rules

(2010) Sui Huang   PLOS BIOLOGY

HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency

(2010) Ron Skupsky et al.   PLoS Computational Biology

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

Gene expression dynamics in randomly varying environments

(2009) Michael W. Smiley et al.   JOURNAL OF MATHEMATICAL BIOLOGY

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

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

(2008) Arjun Raj et al.   CELL

Capturing Pluripotency

(2008) Jose Silva et al.   CELL

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

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

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics