Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions

The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation

(2014) Narasimharao Nalabothula et al.   BMC GENOMICS

The role of chromatin insulators in nuclear architecture and genome function

(2013) Kevin Van Bortle et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Canonical nucleosome organization at promoters forms during genome activation

(2013) Y. Zhang et al.   GENOME RESEARCH

Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging

(2013) A. G. Cherstvy et al.   JOURNAL OF BIOLOGICAL PHYSICS

The roles of the monomer length and nucleotide context of plant tandem repeats in nucleosome positioning

(2013) Victor G. Levitsky et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Taking into account nucleosomes for predicting gene expression

(2013) Vladimir B. Teif et al.   METHODS

Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence

(2013) Jyotsana J. Parmar et al.   NUCLEIC ACIDS RESEARCH

Quantifying the role of steric constraints in nucleosome positioning

(2013) H. Tomas Rube et al.   NUCLEIC ACIDS RESEARCH

H1 histones: current perspectives and challenges

(2013) S. W. Harshman et al.   NUCLEIC ACIDS RESEARCH

Structural insights into the histone H1-nucleosome complex

(2013) B.-R. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toward a unified physical model of nucleosome patterns flanking transcription start sites

(2013) W. Mobius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Active nucleosome positioning beyond intrinsic biophysics is revealed byin vitroreconstitution

(2012) Philipp Korber   BIOCHEMICAL SOCIETY TRANSACTIONS

Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription

(2012) Bianca P Hennig et al.   EMBO REPORTS

Linker Histone Subtypes Differ in Their Effect on Nucleosomal Spacing In Vivo

(2012) Christine Öberg et al.   JOURNAL OF MOLECULAR BIOLOGY

Nucleosome positioning and nucleosome stacking: two faces of the same coin

(2012) Julien Riposo et al.   Molecular BioSystems

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

(2012) Yin Shen et al.   NATURE

Genome-wide nucleosome positioning during embryonic stem cell development

(2012) Vladimir B Teif et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Kinetic Control of Nucleosome Displacement by ISWI/ACF Chromatin Remodelers

(2012) Ana-Maria Florescu et al.   PHYSICAL REVIEW LETTERS

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

(2011) Ariel Afek et al.   BIOPHYSICAL JOURNAL

Calculating transcription factor binding maps for chromatin

(2011) V. B. Teif et al.   BRIEFINGS IN BIOINFORMATICS

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

On the structure and dynamics of the complex of the nucleosome and the linker histone

(2011) Georgi V. Pachov et al.   NUCLEIC ACIDS RESEARCH

Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions

(2011) Răzvan V. Chereji et al.   PHYSICAL REVIEW E

A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome

(2011) Z. Zhang et al.   SCIENCE

Substantial Histone Reduction Modulates Genomewide Nucleosomal Occupancy and Global Transcriptional Output

(2011) Barbara Celona et al.   PLOS BIOLOGY

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

(2010) I. Gabdank et al.   BIOINFORMATICS

A Lattice Model for Transcription Factor Access to Nucleosomal DNA

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

Neuronal MeCP2 Is Expressed at Near Histone-Octamer Levels and Globally Alters the Chromatin State

(2010) Peter J. Skene et al.   MOLECULAR CELL

Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae

(2010) Alexandra B Lantermann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosome-mediated cooperativity between transcription factors

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

Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens

(2010) Sheila M. Reynolds et al.   PLoS Computational Biology

Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites

(2010) Wolfram Möbius et al.   PLoS Computational Biology

The Biology of Chromatin Remodeling Complexes

(2009) Cedric R. Clapier et al.   Annual Review of Biochemistry

Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy

(2009) Shai Lubliner et al.   BIOINFORMATICS

A novel strategy of transcription regulation by intragenic nucleosome ordering

(2009) C. Vaillant et al.   GENOME RESEARCH

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

(2009) Alexandre V. Morozov 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

Thermodynamics of Intragenic Nucleosome Ordering

(2009) G. Chevereau et al.   PHYSICAL REVIEW LETTERS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

nuScore: a web-interface for nucleosome positioning predictions

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

Nucleosome Geometry and Internucleosomal Interactions Control the Chromatin Fiber Conformation

(2008) Nick Kepper et al.   BIOPHYSICAL JOURNAL

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Nucleosome Switches

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

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

(2008) Andrew Routh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae

(2008) Ji-Ping Wang et al.   PLoS Computational Biology