DREME: motif discovery in transcription factor ChIP-seq data

Evolution of the interaction between Runx2 and VDR, two transcription factors involved in osteoblastogenesis

(2012) Sylvain Marcellini et al.   BMC EVOLUTIONARY BIOLOGY

Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data

(2010) Mike J. Mason et al.   BIOINFORMATICS

Macrophage-specific gene functions in Spi1-directed innate immunity

(2010) A. Zakrzewska et al.   BLOOD

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

A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells

(2010) M. R. Tallack et al.   GENOME RESEARCH

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells

(2010) M. T. Kassouf et al.   GENOME RESEARCH

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

The Pluripotency Regulator Zic3 Is a Direct Activator of the Nanog Promoter in ESCs

(2010) Linda Shushan Lim et al.   STEM CELLS

Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

(2009) A. A. Sharov et al.   DNA RESEARCH

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

(2009) Y. Cheng et al.   GENOME RESEARCH

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Gene Expression Atlas at the European Bioinformatics Institute

(2009) Misha Kapushesky et al.   NUCLEIC ACIDS RESEARCH

Runx1 is involved in primitive erythropoiesis in the mouse

(2008) T. Yokomizo et al.   BLOOD

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

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

(2008) C. Linhart et al.   GENOME RESEARCH

Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog

(2007) Ralf Jauch et al.   JOURNAL OF MOLECULAR BIOLOGY