Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

bwtool: a tool for bigWig files

(2014) Andy Pohl et al.   BIOINFORMATICS

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

(2014) Alexandre Fort et al.   NATURE GENETICS

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

(2014) Xinyi Lu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Derivation of naive human embryonic stem cells

(2014) C. B. Ware et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining an essential transcription factor program for naive pluripotency

(2014) S.- J. Dunn et al.   SCIENCE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Induction of a Human Pluripotent State with Distinct Regulatory Circuitry that Resembles Preimplantation Epiblast

(2013) Yun-Shen Chan et al.   Cell Stem Cell

Identification of the missing pluripotency mediator downstream of leukaemia inhibitory factor

(2013) Graziano Martello et al.   EMBO JOURNAL

Embryonic stem cell self-renewal pathways converge on the transcription factor Tfcp2l1

(2013) Shoudong Ye et al.   EMBO JOURNAL

MYC/MAX control ERK signaling and pluripotency by regulation of dual-specificity phosphatases 2 and 7

(2013) J. Chappell et al.   GENES & DEVELOPMENT

Derivation of novel human ground state naive pluripotent stem cells

(2013) Ohad Gafni et al.   NATURE

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

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

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Uncovering the true identity of naïve pluripotent stem cells

(2013) Maaike Welling et al.   TRENDS IN CELL BIOLOGY

Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells

(2013) Akira Nishiyama et al.   Scientific Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Census of Human Soluble Protein Complexes

(2012) Pierre C. Havugimana et al.   CELL

Distinct Lineage Specification Roles for NANOG, OCT4, and SOX2 in Human Embryonic Stem Cells

(2012) Zheng Wang et al.   Cell Stem Cell

Chromatin-modifying enzymes as modulators of reprogramming

(2012) Tamer T. Onder et al.   NATURE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

(2012) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

Sleeping Beauty transposon-based system for cellular reprogramming and targeted gene insertion in induced pluripotent stem cells

(2012) Ivana Grabundzija et al.   NUCLEIC ACIDS RESEARCH

HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency

(2012) Federico A Santoni et al.   Retrovirology

Transposable elements reveal a stem cell-specific class of long noncoding RNAs

(2012) David Kelley et al.   GENOME BIOLOGY

Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development

(2011) R. Vassena et al.   DEVELOPMENT

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development

(2011) Ikuhiro Okamoto et al.   NATURE

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells

(2010) Debbie L.C. van den Berg et al.   Cell Stem Cell

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Modulation of CP2 Family Transcriptional Activity by CRTR-1 and Sumoylation

(2010) Sarah To et al.   PLoS One

Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs

(2010) J. Hanna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Senescence-Related Mitochondrial/Oxidative Stress Pathway is Repressed in Human Induced Pluripotent Stem Cells

(2010) Alessandro Prigione et al.   STEM CELLS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Generation of Induced Pluripotent Stem Cells from Human Cord Blood

(2009) Alexandra Haase et al.   Cell Stem Cell

Metastable Pluripotent States in NOD-Mouse-Derived ESCs

(2009) Jacob Hanna et al.   Cell Stem Cell

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates

(2009) Lajos Mátés et al.   NATURE GENETICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY