The Robustness and Evolvability of Transcription Factor Binding Sites

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm

(2013) Irene Aksoy et al.   EMBO JOURNAL

Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes

(2013) Alexander E. Lobkovsky et al.   Molecular BioSystems

Building synthetic gene circuits from combinatorial libraries: screening and selection strategies

(2013) Yolanda Schaerli et al.   Molecular BioSystems

Mapping the fine structure of a eukaryotic promoter input-output function

(2013) Arun S Rajkumar et al.   NATURE GENETICS

Endogenous retroviruses function as species-specific enhancer elements in the placenta

(2013) Edward B Chuong et al.   NATURE GENETICS

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

Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine

(2013) I. Guerreiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide analysis reveals that Smad3 and JMJD3 HDM co-activate the neural developmental program

(2012) C. Estaras et al.   DEVELOPMENT

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

(2012) A. J. Stewart et al.   GENETICS

Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding

(2012) M. P. Verzi et al.   MOLECULAR AND CELLULAR BIOLOGY

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

Insights into Negative Regulation by the Glucocorticoid Receptor from Genome-wide Profiling of Inflammatory Cistromes

(2012) N. Henriette Uhlenhaut et al.   MOLECULAR CELL

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan 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

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of robustness in phenotypic adaptation and innovation

(2012) A. Wagner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Tcf7 Is an Important Regulator of the Switch of Self-Renewal and Differentiation in a Multipotential Hematopoietic Cell Line

(2012) Jia Qian Wu et al.   PLoS Genetics

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

The SNF2-like helicase HELLS mediates E2F3-dependent transcription and cellular transformation

(2011) Björn von Eyss et al.   EMBO JOURNAL

Pioneer transcription factors: establishing competence for gene expression

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

Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types

(2011) Gang Wei et al.   IMMUNITY

Multiple Sequence-Specific DNA-Binding Proteins Mediate Estrogen Receptor Signaling through a Tethering Pathway

(2011) Nina Heldring et al.   MOLECULAR ENDOCRINOLOGY

The nucleosome map of the mammalian liver

(2011) Zhaoyu Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients

(2010) James Cotterell et al.   Molecular Systems Biology

Mutational robustness can facilitate adaptation

(2010) Jeremy A. Draghi et al.   NATURE

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

(2010) Polly M Fordyce et al.   NATURE BIOTECHNOLOGY

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

(2010) D. Schmidt et al.   SCIENCE

The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts

(2010) Ryan K. Shultzaberger et al.   PLoS Genetics

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

(2009) Christian A. Grove et al.   CELL

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

(2009) C. Zhu et al.   GENOME RESEARCH

Distinguishing direct versus indirect transcription factor-DNA interactions

(2009) R. Gordan et al.   GENOME RESEARCH

Analysis of a complete DNA-protein affinity landscape

(2009) W. Rowe et al.   Journal of the Royal Society Interface

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Experimental determination of the evolvability of a transcription factor

(2009) S. J. Maerkl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

(2008) Gwenael Badis et al.   MOLECULAR CELL

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

The Evolution of Combinatorial Gene Regulation in Fungi

(2008) Brian B Tuch 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

Robustness and evolvability: a paradox resolved

(2007) A. Wagner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES