DNA-dependent formation of transcription factor pairs alters their binding specificity

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

(2015) Kazuhiro R Nitta et al.   eLife

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding

(2014) Qilai Huang et al.   NATURE GENETICS

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

The Mediator complex and transcription regulation

(2013) Zachary C. Poss et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

cis -Regulatory Requirements for Tissue-Specific Programs of the Circadian Clock

(2013) Antonio C.A. Meireles-Filho et al.   CURRENT BIOLOGY

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

(2013) H. Guturu et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

Analysis of the DNA-Binding Profile and Function of TALE Homeoproteins Reveals Their Specialization and Specific Interactions with Hox Genes/Proteins

(2013) Dmitry Penkov et al.   Cell Reports

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

(2012) Tali Raveh-Sadka et al.   NATURE GENETICS

The ETS Transcription Factors ELK1 and GABPA Regulate Different Gene Networks to Control MCF10A Breast Epithelial Cell Migration

(2012) Zaneta Odrowaz et al.   PLoS One

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Identification and characterization of Hoxa9 binding sites in hematopoietic cells

(2011) Y. Huang et al.   BLOOD

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

High-throughput protein expression screening and purification in Escherichia coli

(2011) Renaud Vincentelli et al.   METHODS

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Discovering homotypic binding events at high spatial resolution

(2010) Yuchun Guo et al.   BIOINFORMATICS

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

High-throughput production of human proteins for crystallization: The SGC experience

(2010) Pavel Savitsky et al.   JOURNAL OF STRUCTURAL BIOLOGY

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

(2009) Christian A. Grove et al.   CELL

An ensemble model of competitive multi-factor binding of the genome

(2009) T. Wasson et al.   GENOME RESEARCH

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

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

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

(2008) Rocco Moretti et al.   ACS Chemical Biology

Natural similarity measures between position frequency matrices with an application to clustering

(2008) Utz J. Pape et al.   BIOINFORMATICS

Combinatorial Regulation of Endothelial Gene Expression by Ets and Forkhead Transcription Factors

(2008) Sarah De Val et al.   CELL

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH