Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regions

(2014) Yahli Lorch et al.   GENES & DEVELOPMENT

A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress

(2014) Nils Elfving et al.   NUCLEIC ACIDS RESEARCH

Protein−DNA binding in the absence of specific base-pair recognition

(2014) Ariel Afek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression

(2014) Daphne Ezer et al.   Computational and Structural Biotechnology Journal

Genome-Wide Organization of Eukaryotic Preinitiation Complex Is Influenced by Nonconsensus Protein-DNA Binding

(2013) Ariel Afek et al.   BIOPHYSICAL JOURNAL

High-resolution mapping of transcription factor binding sites on native chromatin

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

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

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

(2013) Timothy Bailey et al.   PLoS Computational Biology

The Effect of Nonspecific Binding of Lambda Repressor on DNA Looping Dynamics

(2012) Carlo Manzo et al.   BIOPHYSICAL JOURNAL

Nonspecific Protein-DNA Binding Is Widespread in the Yeast Genome

(2012) Ariel Afek et al.   BIOPHYSICAL JOURNAL

Energy Fluctuations Shape Free Energy of Nonspecific Biomolecular Interactions

(2012) Michael Elkin et al.   JOURNAL OF STATISTICAL PHYSICS

A transcription factor–based mechanism for mouse heterochromatin formation

(2012) Aydan Bulut-Karslioglu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

DNA Sequence Correlations Shape Nonspecific Transcription Factor-DNA Binding Affinity

(2011) Itamar Sela et al.   BIOPHYSICAL JOURNAL

Nonspecific Transcription-Factor-DNA Binding Influences Nucleosome Occupancy in Yeast

(2011) Ariel Afek et al.   BIOPHYSICAL JOURNAL

Sequence correlations shape protein promiscuity

(2011) David B. Lukatsky et al.   JOURNAL OF CHEMICAL PHYSICS

Multi-Scale Sequence Correlations Increase Proteome Structural Disorder and Promiscuity

(2011) Ariel Afek et al.   JOURNAL OF MOLECULAR BIOLOGY

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

WormBase 2012: more genomes, more data, new website

(2011) K. Yook et al.   NUCLEIC ACIDS RESEARCH

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

A spatial and temporal map of C. elegans gene expression

(2010) W. C. Spencer et al.   GENOME RESEARCH

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

(2010) W. Niu et al.   GENOME RESEARCH

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans

(2010) S. Ercan et al.   GENOME RESEARCH

Broad chromosomal domains of histone modification patterns in C. elegans

(2010) T. Liu et al.   GENOME RESEARCH

Determination of the number of proteins bound non-specifically to DNA

(2010) Paul Liebesny et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Physics of protein–DNA interactions: mechanisms of facilitated target search

(2010) Anatoly B. Kolomeisky   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

An end to 40 years of mistakes in DNA–protein association kinetics?

(2009) Stephen E. Halford   BIOCHEMICAL SOCIETY TRANSACTIONS

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

(2009) Christian A. Grove et al.   CELL

How a protein searches for its site on DNA: the mechanism of facilitated diffusion

(2009) Leonid Mirny et al.   Journal of Physics A-Mathematical and Theoretical

Modeling promoter search by E. coli RNA polymerase: One-dimensional diffusion in a sequence-dependent energy landscape

(2009) Johanna Weindl et al.   JOURNAL OF THEORETICAL BIOLOGY

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

Nonspecifically bound proteins spin while diffusing along DNA

(2009) Paul C Blainey et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

(2009) Yong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Direct demonstration and quantification of long-range DNA looping by the λ bacteriophage repressor

(2009) Chiara Zurla et al.   NUCLEIC ACIDS RESEARCH

WormBase: a comprehensive resource for nematode research

(2009) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

Structure of an RNA Polymerase II-TFIIB Complex and the Transcription Initiation Mechanism

(2009) X. Liu et al.   SCIENCE

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability

(2008) Anahita Tafvizi et al.   BIOPHYSICAL JOURNAL

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

(2008) Michael F. Berger et al.   CELL

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA

(2008) Isabelle Bonnet et al.   NUCLEIC ACIDS RESEARCH