Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Genenames.org: the HGNC resources in 2013

(2012) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

Analysis of variation at transcription factor binding sites in Drosophila and humans

(2012) Mikhail Spivakov et al.   GENOME BIOLOGY

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

The opposing transcriptional functions of Sin3a and c-Myc are required to maintain tissue homeostasis

(2011) Elisabete M. Nascimento et al.   NATURE CELL BIOLOGY

Developmental function of HMGN proteins

(2010) Takashi Furusawa et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Discovering homotypic binding events at high spatial resolution

(2010) Yuchun Guo et al.   BIOINFORMATICS

Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes

(2010) Henriette O'Geen et al.   BMC GENOMICS

The THAP-Zinc Finger Protein THAP1 Associates with Coactivator HCF-1 andO-GlcNAc Transferase

(2010) Raoul Mazars et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Ubiquitin Carboxyl Hydrolase BAP1 Forms a Ternary Complex with YY1 and HCF-1 and Is a Critical Regulator of Gene Expression

(2010) H. Yu et al.   MOLECULAR AND CELLULAR BIOLOGY

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Tmod: toolbox of motif discovery

(2009) H. Sun et al.   BIOINFORMATICS

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Genomic Targets of the KRAB and SCAN Domain-containing Zinc Finger Protein 263

(2009) Seth Frietze et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

Role of chromodomain helicase DNA-binding protein 2 in DNA damage response signaling and tumorigenesis

(2009) P Nagarajan et al.   ONCOGENE

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Interferon Regulatory Factor 4 Is Involved in Epstein-Barr Virus-Mediated Transformation of Human B Lymphocytes

(2008) D. Xu et al.   JOURNAL OF VIROLOGY

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

CTCF physically links cohesin to chromatin

(2008) E. D. Rubio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY