Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

Associating cellular epigenetic models with human phenotypes

(2017) Tuuli Lappalainen et al.   NATURE REVIEWS GENETICS

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

(2017) Judith F. Kribelbauer et al.   Cell Reports

Measuring quantitative effects of methylation on transcription factor–DNA binding affinity

(2017) Zheng Zuo et al.   Science Advances

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

(2015) Tsu-Pei Chiu et al.   BIOINFORMATICS

Deconvolving the Recognition of DNA Shape from Sequence

(2015) Namiko Abe et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Evolving insights on how cytosine methylation affects protein-DNA binding

(2014) A. C. Dantas Machado et al.   Briefings in Functional Genomics

DNA methylation: old dog, new tricks?

(2014) Cornelia G Spruijt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GBshape: a genome browser database for DNA shape annotations

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

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

CG methylated microarrays identify a novel methylated sequence bound by the CEBPB ATF4 heterodimer that is active in vivo

(2013) I. K. Mann et al.   GENOME RESEARCH

Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling

(2013) Xiaojun Zhang et al.   NUCLEIC ACIDS RESEARCH

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

(2013) Tianyin Zhou et al.   NUCLEIC ACIDS RESEARCH

TFBSshape: a motif database for DNA shape features of transcription factor binding sites

(2013) Lin Yang et al.   NUCLEIC ACIDS RESEARCH

Probing DNA shape and methylation state on a genomic scale with DNase I

(2013) A. Lazarovici et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A common mode of recognition for methylated CpG

(2013) Yiwei Liu et al.   TRENDS IN BIOCHEMICAL SCIENCES

Impact of Methylation on the Physical Properties of DNA

(2012) Alberto Pérez et al.   BIOPHYSICAL JOURNAL

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso

(2012) B. A. Buck-Koehntop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

Loops MC: an all-atom Monte Carlo simulation program for RNAs based on inverse kinematic loop closure

(2011) C. H. Mak   MOLECULAR SIMULATION

ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species

(2011) Aaron T. Spivak et al.   NUCLEIC ACIDS RESEARCH

Origins of Specificity in Protein-DNA Recognition

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

CpG methylation of half-CRE sequences creates C/EBP  binding sites that activate some tissue-specific genes

(2010) V. Rishi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

The unique structure of A-tracts and intrinsic DNA bending

(2009) Tali E. Haran et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis — A personal account

(2008) Hikoya HAYATSU   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES