KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation

Extended Self-Renewal and Accelerated Reprogramming in the Absence of Kdm5b

(2013) B. L. Kidder et al.   MOLECULAR AND CELLULAR BIOLOGY

The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3

(2013) Mareike Albert et al.   PLoS Genetics

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network

(2011) Yen-Sin Ang et al.   CELL

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

(2011) Oren Ram et al.   CELL

Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency

(2011) R David Hawkins et al.   CELL RESEARCH

Jarid1b targets genes regulating development and is involved in neural differentiation

(2011) Sandra U Schmitz et al.   EMBO JOURNAL

KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription

(2011) Liangqi Xie et al.   EMBO JOURNAL

LSD1 regulates the balance between self-renewal and differentiation in human embryonic stem cells

(2011) Antonio Adamo et al.   NATURE CELL BIOLOGY

HDAC1 regulates pluripotency and lineage specific transcriptional networks in embryonic and trophoblast stem cells

(2011) Benjamin L. Kidder et al.   NUCLEIC ACIDS RESEARCH

Reversal of Histone Methylation: Biochemical and Molecular Mechanisms of Histone Demethylases

(2010) Nima Mosammaparast et al.   Annual Review of Biochemistry

AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

(2010) Aaron M Newman et al.   BMC BIOINFORMATICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Examination of transcriptional networks reveals an important role for TCFAP2C, SMARCA4, and EOMES in trophoblast stem cell maintenance

(2010) B. L. Kidder et al.   GENOME RESEARCH

Lysine-Specific Demethylase 1 Regulates the Embryonic Transcriptome and CoREST Stability

(2010) C. T. Foster et al.   MOLECULAR AND CELLULAR BIOLOGY

JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells

(2010) Diego Pasini et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

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

(2008) Xi Chen et al.   CELL

The Histone Demethylase KDM5b/JARID1b Plays a Role in Cell Fate Decisions by Blocking Terminal Differentiation

(2008) B. K. Dey et al.   MOLECULAR AND CELLULAR BIOLOGY

The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation

(2008) Jing Wang et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

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

(2008) Manching Ku et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY