Systematic identification of gene family regulators in mouse and human embryonic stem cells

BindDB: An Integrated Database and Webtool Platform for “Reverse-ChIP” Epigenomic Analysis

(2015) Ilana Livyatan et al.   Cell Stem Cell

Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells

(2014) Yu Lu et al.   Cell Stem Cell

MBD3/NuRD Facilitates Induction of Pluripotency in a Context-Dependent Manner

(2014) Rodrigo L. dos Santos et al.   Cell Stem Cell

Epigenetic Regulation of Pluripotency and Differentiation

(2014) Michael J. Boland et al.   CIRCULATION RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities

(2014) Manuel Sánchez-Castillo et al.   NUCLEIC ACIDS RESEARCH

Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease

(2014) Aibin He et al.   Nature Communications

Zfp322a Regulates Mouse ES Cell Pluripotency and Enhances Reprogramming Efficiency

(2014) Hui Ma et al.   PLoS Genetics

Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency

(2014) Yul W Yang et al.   eLife

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Tet Proteins Connect the O-Linked N-acetylglucosamine Transferase Ogt to Chromatin in Embryonic Stem Cells

(2013) Pietro Vella et al.   MOLECULAR CELL

Deterministic direct reprogramming of somatic cells to pluripotency

(2013) Yoach Rais et al.   NATURE

Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency

(2013) Rupa Sridharan et al.   NATURE CELL BIOLOGY

Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation

(2013) Ilana Livyatan et al.   NUCLEIC ACIDS RESEARCH

Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11

(2013) Richard Patryk Ngondo-Mbongo et al.   NUCLEIC ACIDS RESEARCH

Max is a repressor of germ cell-related gene expression in mouse embryonic stem cells

(2013) Ikuma Maeda et al.   Nature Communications

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

(2013) Huilei Xu et al.   Database-The Journal of Biological Databases and Curation

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

(2013) Akira Nishiyama et al.   Scientific Reports

Multiple Structural Maintenance of Chromosome Complexes at Transcriptional Regulatory Elements

(2013) Jill M. Dowen et al.   Stem Cell Reports

H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells

(2012) Krishanpal Karmodiya et al.   BMC GENOMICS

Embryonic stem cell and induced pluripotent stem cell: an epigenetic perspective

(2012) Gaoyang Liang et al.   CELL RESEARCH

Nonoverlapping Functions of the Polycomb Group Cbx Family of Proteins in Embryonic Stem Cells

(2012) Lluis Morey et al.   Cell Stem Cell

The Histone Acetyltransferase MOF Is a Key Regulator of the Embryonic Stem Cell Core Transcriptional Network

(2012) Xiangzhi Li et al.   Cell Stem Cell

Spark: A navigational paradigm for genomic data exploration

(2012) C. B. Nielsen et al.   GENOME RESEARCH

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells

(2012) Mangmang Li et al.   MOLECULAR CELL

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Multilayered chromatin analysis reveals E2f, Smad and Zfx as transcriptional regulators of histones

(2012) David Gokhman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells

(2012) Pietro Vella et al.   NUCLEIC ACIDS RESEARCH

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages

(2012) Xun Lan et al.   NUCLEIC ACIDS RESEARCH

ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data

(2012) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

(2012) J. Wang et al.   NUCLEIC ACIDS RESEARCH

UTX regulates mesoderm differentiation of embryonic stem cells independent of H3K27 demethylase activity

(2012) C. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands

(2012) Anca M Farcas et al.   eLife

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

(2011) Joshua WK Ho et al.   BMC GENOMICS

Jarid1b targets genes regulating development and is involved in neural differentiation

(2011) Sandra U Schmitz et al.   EMBO JOURNAL

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity

(2011) Johannes M. Freudenberg et al.   NUCLEIC ACIDS RESEARCH

RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity

(2011) Anja Nitzsche et al.   PLoS One

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation of mouse ES cell lines engineered for the forced induction of transcription factors

(2011) Lina S. Correa-Cerro et al.   Scientific Reports

Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease

(2011) Alvaro Rada-Iglesias et al.   Genome Medicine

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

The Nuclear Receptor Nr5a2 Can Replace Oct4 in the Reprogramming of Murine Somatic Cells to Pluripotent Cells

(2010) Jian-Chien Dominic Heng et al.   Cell Stem Cell

A genome-wide screen in EpiSCs identifies Nr5a nuclear receptors as potent inducers of ground state pluripotency

(2010) G. Guo et al.   DEVELOPMENT

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Open chromatin in pluripotency and reprogramming

(2010) Alexandre Gaspar-Maia et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell-Specific Gene Expression

(2010) Michael P. Schnetz et al.   PLoS Genetics

An endoderm-specific transcriptional enhancer from the mouseGata4gene requires GATA and homeodomain protein-binding sites for function in vivo

(2009) Anabel Rojas et al.   DEVELOPMENTAL DYNAMICS

Expression of human oocyte-specific linker histone protein and its incorporation into sperm chromatin during fertilization

(2009) Yuri Mizusawa et al.   FERTILITY AND STERILITY

An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity

(2008) Thomas G. Fazzio et al.   CELL

Chromatin Immunoprecipitation on Microarray Analysis of Smad2/3 Binding Sites Reveals Roles of ETS1 and TFAP2A in Transforming Growth Factor   Signaling

(2008) D. Koinuma et al.   MOLECULAR AND CELLULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY