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

Mechanisms that Specify Promoter Nucleosome Location and Identity

(2009) Paul D. Hartley et al.   CELL

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

Nucleosomes can invade DNA territories occupied by their neighbors

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

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

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

Stochastic model for nucleosome sliding under an external force

(2009) L. Mollazadeh-Beidokhti et al.   PHYSICAL REVIEW E

Diverse Regulation of SNF2h Chromatin Remodeling by Noncatalytic Subunits

(2008) Xi He et al.   BIOCHEMISTRY

Role of Nucleic Acid Binding in Sir3p-Dependent Interactions with Chromatin Fibers†

(2008) Nicholas L. Adkins et al.   BIOCHEMISTRY

nuScore: a web-interface for nucleosome positioning predictions

(2008) M. Y. Tolstorukov et al.   BIOINFORMATICS

Prediction and analysis of nucleosome exclusion regions in the human genome

(2008) Ahmed Radwan et al.   BMC GENOMICS

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription

(2008) Hinrich Boeger et al.   CELL

Control of Nucleosome Positions by DNA Sequence and Remodeling Machines

(2008) Gavin R. Schnitzler   CELL BIOCHEMISTRY AND BIOPHYSICS

ATP-dependent chromatin remodeling enzymes: two heads are not better, just different

(2008) Lisa R Racki et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Nucleosome positioning in human HOX gene clusters

(2008) P. V. Kharchenko et al.   GENOME RESEARCH

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

(2008) A. Valouev et al.   GENOME RESEARCH

A high-resolution map of nucleosome positioning on a fission yeast centromere

(2008) J. S. Song et al.   GENOME 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

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

Matrix formalism for site-specific binding of unstructured proteins to multicomponent lipid membranes

(2008) Vladimir B. Teif et al.   JOURNAL OF PEPTIDE SCIENCE

Chromatin decouples promoter threshold from dynamic range

(2008) Felix H. Lam et al.   NATURE

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

Structure of a RSC–nucleosome complex and insights into chromatin remodeling

(2008) Yuriy Chaban et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human SWI/SNF directs sequence-specific chromatin changes on promoter polynucleosomes

(2008) Hillel I. Sims et al.   NUCLEIC ACIDS RESEARCH

Nucleosome Switches

(2008) David J. Schwab et al.   PHYSICAL REVIEW LETTERS

Genomic Sequence Is Highly Predictive of Local Nucleosome Depletion

(2008) Guo-Cheng Yuan et al.   PLoS Computational Biology

Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation

(2008) Sushma Shivaswamy et al.   PLOS BIOLOGY

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology

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

(2008) Yutao Fu et al.   PLoS Genetics

Nucleosome destabilization in the epigenetic regulation of gene expression

(2007) Steven Henikoff   NATURE REVIEWS GENETICS