Retinoic Acid Receptors Recognize the Mouse Genome through Binding Elements with Diverse Spacing and Topology

Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA

(2011) Igor Orlov et al.   EMBO JOURNAL

Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings

(2011) Natacha Rochel et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Inferring transcription factor complexes from ChIP-seq data

(2011) Tom Whitington et al.   NUCLEIC ACIDS RESEARCH

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

(2011) Shaun Mahony et al.   GENOME BIOLOGY

Cell-specific occupancy of an extended repertoire of CREM and CREB binding loci in male germ cells

(2010) Igor Martianov et al.   BMC GENOMICS

Activation of retinoic acid receptor signaling coordinates lineage commitment of spontaneously differentiating mouse embryonic stem cells in embryoid bodies

(2010) Zoltan Simandi et al.   FEBS LETTERS

A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution

(2010) S. V. Ramagopalan et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis of POU3F2/BRN2 promoter occupancy in human melanoma cells reveals Kitl as a novel regulated target gene

(2010) Dominique Kobi et al.   Pigment Cell & Melanoma Research

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

GPAT: Retrieval of genomic annotation from large genomic position datasets

(2009) Arnaud Krebs et al.   BMC BIOINFORMATICS

Genomic Antagonism between Retinoic Acid and Estrogen Signaling in Breast Cancer

(2009) Sujun Hua et al.   CELL

ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

(2009) Willem-Jan Welboren et al.   EMBO JOURNAL

Cell-Specific Interaction of Retinoic Acid Receptors with Target Genes in Mouse Embryonic Fibroblasts and Embryonic Stem Cells

(2009) L. Delacroix et al.   MOLECULAR AND CELLULAR BIOLOGY

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

(2009) S. H. Meijsing et al.   SCIENCE

Genome-wide profiling of PPAR :RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis

(2008) R. Nielsen et al.   GENES & DEVELOPMENT

Retinoic acid in development: towards an integrated view

(2008) Karen Niederreither et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY