Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

(2013) M. S. Enuameh et al.   GENOME RESEARCH

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS

(2013) Markku Varjosalo et al.   NATURE METHODS

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

(2012) Katherine M. Lelli et al.   Annual Review of Genetics

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

(2012) J. O. Yanez-Cuna et al.   GENOME RESEARCH

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements

(2012) Calista K. L. Ng et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Repression by a bZIP Protein Regulates Dictyostelium Prespore Differentiation

(2012) Beatriz Nuñez-Corcuera et al.   PLoS One

Genomic and Biochemical Insights into the Specificity of ETS Transcription Factors

(2011) Peter C. Hollenhorst et al.   Annual Review of Biochemistry

A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites

(2011) I. V. Kulakovskiy et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

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

(2011) Matthew Slattery et al.   CELL

Pioneer transcription factors: establishing competence for gene expression

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

Structural Constraints in Collaborative Competition of Transcription Factors against the Nucleosome

(2011) Georgette Moyle-Heyrman et al.   JOURNAL OF MOLECULAR BIOLOGY

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Inferring transcription factor complexes from ChIP-seq data

(2011) Tom Whitington et al.   NUCLEIC ACIDS RESEARCH

Pioneer factors: directing transcriptional regulators within the chromatin environment

(2011) Luca Magnani et al.   TRENDS IN GENETICS

Formation of Regulatory Modules by Local Sequence Duplication

(2011) Armita Nourmohammad et al.   PLoS Computational Biology

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

(2011) Chung-Yi Nien et al.   PLoS Genetics

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

(2011) Xiao-Yong Li et al.   GENOME BIOLOGY

Origins of Specificity in Protein-DNA Recognition

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

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo

(2010) Walid D Fakhouri et al.   Molecular Systems Biology

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

The BioGRID Interaction Database: 2011 update

(2010) C. Stark et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Nucleosome-mediated cooperativity between transcription factors

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

Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

(2010) Majid Kazemian et al.   PLOS BIOLOGY

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

(2010) Xin He et al.   PLoS Computational Biology

SOX–partner code for cell specification: Regulatory target selection and underlying molecular mechanisms

(2009) Hisato Kondoh et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Organization of developmental enhancers in the Drosophila embryo

(2009) Dmitri Papatsenko et al.   NUCLEIC ACIDS RESEARCH

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships

(2009) Ken Daigoro Yokoyama et al.   NUCLEIC ACIDS RESEARCH

LuMPIS – A modified luminescence-based mammalian interactome mapping pull-down assay for the investigation of protein–protein interactions encoded by GC-low ORFs

(2009) Maria Guadalupe Vizoso Pinto et al.   PROTEOMICS

Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos

(2009) Bernd Schuettengruber et al.   PLOS BIOLOGY

Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View

(2009) Yongping Pan et al.   PLoS Computational Biology

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

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

An experimentally derived confidence score for binary protein-protein interactions

(2008) Pascal Braun et al.   NATURE METHODS

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

(2008) Marcus B. Noyes et al.   NUCLEIC ACIDS RESEARCH

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts

(2008) Justin Crocker et al.   PLOS BIOLOGY

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

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