Calculating transcription factor binding maps for chromatin

Distribution of Unselectively Bound Ligands Along DNA

(2012) Dmitri Y. Lando et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

An effect of DNA sequence on nucleosome occupancy and removal

(2011) Xin Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cracking the chromatin code: Precise rule of nucleosome positioning

(2011) Edward N. Trifonov   Physics of Life Reviews

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

CplexA: a Mathematica package to study macromolecular-assembly control of gene expression

(2010) Jose M.G. Vilar et al.   BIOINFORMATICS

FineStr: a web server for single-base-resolution nucleosome positioning

(2010) I. Gabdank et al.   BIOINFORMATICS

Predicting Gene-Regulation Functions: Lessons from Temperate Bacteriophages

(2010) Vladimir B. Teif   BIOPHYSICAL JOURNAL

A Lattice Model for Transcription Factor Access to Nucleosomal DNA

(2010) Vladimir B. Teif et al.   BIOPHYSICAL JOURNAL

A novel computational approach “BP-STOCH” to study ligand binding to finite lattice

(2010) Daria A. Beshnova et al.   BIOPOLYMERS

Predicting nucleosome positioning using a duration Hidden Markov Model

(2010) Liqun Xi et al.   BMC BIOINFORMATICS

Stochastic and reversible assembly of a multiprotein DNA repair complex ensures accurate target site recognition and efficient repair

(2010) Martijn S. Luijsterburg et al.   JOURNAL OF CELL BIOLOGY

Statistical–mechanical lattice models for protein–DNA binding in chromatin

(2010) Vladimir B Teif et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

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

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

From the editors

(2010)   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Human single-nucleotide polymorphisms alter p53 sequence-specific binding at gene regulatory elements

(2010) Omari J. Bandele et al.   NUCLEIC ACIDS RESEARCH

High-throughput sequencing reveals a simple model of nucleosome energetics

(2010) G. Locke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome-mediated cooperativity between transcription factors

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

Condensed DNA: Condensing the concepts

(2010) Vladimir B. Teif et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Transcription by the numbers redux: experiments and calculations that surprise

(2010) Hernan G. Garcia et al.   TRENDS IN CELL BIOLOGY

Combinatorial Gene Regulation Using Auto-Regulation

(2010) Rutger Hermsen et al.   PLoS Computational 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

spFRET Using Alternating Excitation and FCS Reveals Progressive DNA Unwrapping in Nucleosomes

(2009) W.J.A. Koopmans et al.   BIOPHYSICAL JOURNAL

Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA

(2009) T. Sekiya et al.   GENES & DEVELOPMENT

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

(2009) T. Wasson et al.   GENOME RESEARCH

Incorporating nucleosomes into thermodynamic models of transcription regulation

(2009) T. Raveh-Sadka et al.   GENOME RESEARCH

Dynamics and function of compact nucleosome arrays

(2009) Michael G Poirier et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosomes can invade DNA territories occupied by their neighbors

(2009) Maik Engeholm et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database

(2009) Ulrike Pfreundt et al.   NUCLEIC ACIDS RESEARCH

A protein–protein interaction guided method for competitive transcription factor binding improves target predictions

(2009) Kirsti Laurila et al.   NUCLEIC ACIDS RESEARCH

Using DNA mechanics to predict in vitro nucleosome positions and formation energies

(2009) Alexandre V. Morozov et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities

(2009) Vladimir B. Teif et al.   NUCLEIC ACIDS RESEARCH

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

Nucleosome disassembly intermediates characterized by single-molecule FRET

(2009) A. Gansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Genome organization: Balancing stability and plasticity

(2008) Malte Wachsmuth et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH

Spontaneous Access to DNA Target Sites in Folded Chromatin Fibers

(2008) Michael G. Poirier et al.   JOURNAL OF MOLECULAR BIOLOGY

Semiflexible Oligomer−Polymer Binding: Combinatorial and Conditional Probability Analyses and Stochastic Simulation

(2008) Jiří Horský   MACROMOLECULES

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Analysis of combinatorial cis-regulation in synthetic and genomic promoters

(2008) Jason Gertz et al.   NATURE

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics