Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

(2017) Judith F. Kribelbauer et al.   Cell Reports

Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds

(2017) Luca Mariani et al.   Cell Systems

Prospective functional classification of all possible missense variants in PPARG

(2016) Amit R Majithia et al.   NATURE GENETICS

Survey of variation in human transcription factors reveals prevalent DNA binding changes

(2016) L. A. Barrera et al.   SCIENCE

A Simple Grammar Defines Activating and Repressing cis -Regulatory Elements in Photoreceptors

(2016) Michael A. White et al.   Cell Reports

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

(2015) Justin Crocker et al.   CELL

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the earlyDrosophilaembryo

(2015) Katharine N. Schulz et al.   GENOME RESEARCH

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

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

(2015) Arttu Jolma et al.   NATURE

Affinity regression predicts the recognition code of nucleic acid–binding proteins

(2015) Raphael Pelossof et al.   NATURE BIOTECHNOLOGY

A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity

(2015) Michael Garton et al.   NUCLEIC ACIDS RESEARCH

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

(2015) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Quantitative modeling of transcription factor binding specificities using DNA shape

(2015) Tianyin Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers

(2015) Zeba Wunderlich et al.   Cell Reports

Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites

(2015) Dave W Anderson et al.   eLife

Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE

(2015) Todd R Riley et al.   eLife

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Diversification of Transcription Factor Paralogs via Noncanonical Modularity in C2H2 Zinc Finger DNA Binding

(2014) Trevor Siggers et al.   MOLECULAR CELL

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding Specificity

(2014) C. Sayou et al.   SCIENCE

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

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

(2013) M. A. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA-binding specificity changes in the evolution of forkhead transcription factors

(2013) S. Nakagawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

(2013) Raluca Gordân et al.   Cell Reports

Recognition models to predict DNA-binding specificities of homeodomain proteins

(2012) R. G. Christensen et al.   BIOINFORMATICS

Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification

(2012) Christopher R. Baker et al.   CELL

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

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

(2011) Matthew Slattery et al.   CELL

Jury remains out on simple models of transcription factor specificity

(2011) Quaid Morris et al.   NATURE BIOTECHNOLOGY

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding

(2011) Trevor Siggers et al.   NATURE IMMUNOLOGY

Extensive DNA-binding specificity divergence of a conserved transcription regulator

(2011) C. R. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

(2011) D. S. Parker et al.   Science Signaling

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

(2011) Raluca Gordân et al.   GENOME BIOLOGY

Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity

(2010) S. Rowan et al.   GENES & DEVELOPMENT

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions

(2010) Phaedra Agius et al.   PLoS Computational Biology

Evolution of transcriptional control in mammals

(2009) Michael D Wilson et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

High-resolution DNA-binding specificity analysis of yeast transcription factors

(2009) C. Zhu et al.   GENOME RESEARCH

Developmental and species-divergent globin switching are driven by BCL11A

(2009) Vijay G. Sankaran et al.   NATURE

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

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

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

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

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

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

The gene regulatory logic of transcription factor evolution

(2008) Günter P. Wagner et al.   TRENDS IN ECOLOGY & EVOLUTION