Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

Reprogramming the Methylome: Erasing Memory and Creating Diversity

(2014) Heather J. Lee et al.   Cell Stem Cell

Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage

(2014) M.-E. Torres-Padilla et al.   DEVELOPMENT

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency

(2013) Gabriella Ficz et al.   Cell Stem Cell

Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells

(2013) Ehsan Habibi et al.   Cell Stem Cell

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

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

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

Pluripotency re-centered around Esrrb

(2012) Bernadett Papp et al.   EMBO JOURNAL

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells

(2009) Tibor Kalmar et al.   PLOS BIOLOGY