Deciphering the mechanical code of the genome and epigenome

A high-resolution protein architecture of the budding yeast genome

(2021) Matthew J. Rossi et al.   NATURE

Genome information processing by the INO80 chromatin remodeler positions nucleosomes

(2021) Elisa Oberbeckmann et al.   Nature Communications

A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level

(2020) Jürgen Walther et al.   NUCLEIC ACIDS RESEARCH

Measuring DNA mechanics on the genome scale

(2020) Aakash Basu et al.   NATURE

Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs

(2019) Masae Ohno et al.   CELL

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

CTCF: a Swiss-army knife for genome organization and transcription regulation

(2019) Luca Braccioli et al.   Essays in Biochemistry

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

(2019) Christopher T Clarkson et al.   NUCLEIC ACIDS RESEARCH

The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules

(2019) Pablo D Dans et al.   NUCLEIC ACIDS RESEARCH

Dynamic coupling between conformations and nucleotide states in DNA gyrase

(2018) Aakash Basu et al.   Nature Chemical Biology

DNA sequence encodes the position of DNA supercoils

(2018) Sung Hyun Kim et al.   eLife

Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding

(2017) Jinsen Li et al.   NUCLEIC ACIDS RESEARCH

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

(2016) Lilien N. Voong et al.   CELL

Genomic Nucleosome Organization Reconstituted with Pure Proteins

(2016) Nils Krietenstein et al.   CELL

Genomic Organization of Human Transcription Initiation Complexes

(2016) B. Franklin Pugh et al.   PLoS One

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

(2016) Thuy T. M. Ngo et al.   Nature Communications

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

(2016) Jejoong Yoo et al.   Nature Communications

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

(2016) Nicola Wiechens et al.   PLoS Genetics

In vitro selection of DNAs with an increased propensity to form small circles

(2015) Gabriel Rosanio et al.   BIOPOLYMERS

Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility

(2015) Thuy T.M. Ngo et al.   CELL

Quantitative modeling of transcription factor binding specificities using DNA shape

(2015) Tianyin Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

(2014) Maureen K. Thomason et al.   JOURNAL OF BACTERIOLOGY

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

GBshape: a genome browser database for DNA shape annotations

(2014) Tsu-Pei Chiu et al.   NUCLEIC ACIDS RESEARCH

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA

(2014) Pablo Daniel Dans et al.   NUCLEIC ACIDS RESEARCH

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

(2014) Marco Pasi et al.   NUCLEIC ACIDS RESEARCH

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

(2013) G. Moyle-Heyrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Under Torsion

(2013) J. Ma et al.   SCIENCE

Impact of Methylation on the Physical Properties of DNA

(2012) Alberto Pérez et al.   BIOPHYSICAL JOURNAL

A map of nucleosome positions in yeast at base-pair resolution

(2012) Kristin Brogaard et al.   NATURE

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Exploring polymorphisms in B-DNA helical conformations

(2012) Pablo D. Dans et al.   NUCLEIC ACIDS RESEARCH

Effects of DNA Methylation on the Structure of Nucleosomes

(2011) Ju Yeon Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cytosine methylation alters DNA mechanical properties

(2011) Philip M. D. Severin et al.   NUCLEIC ACIDS RESEARCH

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Sequence dependence of DNA bending rigidity

(2010) S. Geggier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

IHF-binding sites inhibit DNA loop formation and transcription initiation

(2009) Yi-Xin Huo 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

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

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

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL