HSA21 Single-Minded 2 (Sim2) Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells

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

(2013) Warren A. Whyte et al.   CELL

The homeobox gene Otx2 in development and disease

(2013) Francis Beby et al.   EXPERIMENTAL EYE RESEARCH

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

Haploinsufficiency of ARID1B , a Member of the SWI/SNF-A Chromatin-Remodeling Complex, Is a Frequent Cause of Intellectual Disability

(2012) Juliane Hoyer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

OTX2mutations contribute to the otocephaly-dysgnathia complex

(2012) Nicolas Chassaing et al.   JOURNAL OF MEDICAL GENETICS

Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome

(2012) Gijs W E Santen et al.   NATURE GENETICS

Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome

(2012) Yoshinori Tsurusaki et al.   NATURE GENETICS

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Sequentially acting Sox transcription factors in neural lineage development

(2011) M. Bergsland et al.   GENES & DEVELOPMENT

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

(2011) A. A. Serandour et al.   GENOME RESEARCH

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

(2011) Mingyan Lin et al.   PLoS One

The Role of the Transcription Factor SIM2 in Prostate Cancer

(2011) Bin Lu et al.   PLoS One

Pioneer factors: directing transcriptional regulators within the chromatin environment

(2011) Luca Magnani et al.   TRENDS IN GENETICS

Single minded 2-s (SIM2-s) gene is expressed in human GBM Cells and involved in GBM invasion

(2010) Qiaowei He et al.   CANCER BIOLOGY & THERAPY

Epigenetic Priming of a Pre-B Cell-Specific Enhancer through Binding of Sox2 and Foxd3 at the ESC Stage

(2010) Daniel Liber et al.   Cell Stem Cell

OTX2 microphthalmia syndrome: four novel mutations and delineation of a phenotype

(2010) KF Schilter et al.   CLINICAL GENETICS

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

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

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

Deciphering the Code for Retroviral Integration Target Site Selection

(2010) Federico Andrea Santoni et al.   PLoS Computational Biology

A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes

(2010) Rossella De Cegli et al.   GENOME BIOLOGY

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Uncovering Early Response of Gene Regulatory Networks in ESCs by Systematic Induction of Transcription Factors

(2009) Akira Nishiyama et al.   Cell Stem Cell

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

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

(2008) Xi Chen et al.   CELL

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH