Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

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

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

(2012) E. Z. Kvon et al.   GENES & DEVELOPMENT

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

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

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

(2012) R. Satija et al.   GENOME RESEARCH

A Functional Evolutionary Approach to Identify Determinants of Nucleosome Positioning: A Unifying Model for Establishing the Genome-wide Pattern

(2012) Amanda L. Hughes et al.   MOLECULAR CELL

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos

(2012) Per-Henrik Holmqvist et al.   PLoS Genetics

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

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

(2011) Matthew Slattery et al.   CELL

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL 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

Integrated Approaches Reveal Determinants of Genome-wide Binding and Function of the Transcription Factor Pho4

(2011) Xu Zhou et al.   MOLECULAR CELL

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS 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

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

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

Nucleosome-mediated cooperativity between transcription factors

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

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

The homeobox gene Mohawk represses transcription by recruiting the sin3A/HDAC co-repressor complex

(2009) Douglas M. Anderson et al.   DEVELOPMENTAL DYNAMICS

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

(2009) T. Wasson et al.   GENOME RESEARCH

Distinguishing direct versus indirect transcription factor-DNA interactions

(2009) R. Gordan et al.   GENOME RESEARCH

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

A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data

(2009) Xin He et al.   PLoS One

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

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

Predicting the binding preference of transcription factors to individual DNA k-mers

(2008) T. M. Alleyne et al.   BIOINFORMATICS

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

(2008) Michael F. Berger et al.   CELL

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

(2008) Marcus B. Noyes et al.   CELL

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

(2008) Hsiao-Lan Liang et al.   NATURE