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

Molecular cell, 2014-06, Vol.54 (5), p.844-857

2014

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DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes

Nucleic acids research, 2020-01, Vol.48 (D1), p.D277

2020

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ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Nature communications, 2015-10, Vol.6 (1), p.8733-8733, Article 8733

2015

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Predicting DNA structure using a deep learning method

Nature communications, 2024-02, Vol.15 (1), p.1243-1243, Article 1243

2024

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The role of DNA shape in protein-DNA recognition

Nature (London), 2009-10, Vol.461 (7268), p.1248-1253

2009

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Genome information processing by the INO80 chromatin remodeler positions nucleosomes

Nature communications, 2021-05, Vol.12 (1), p.3231-3231, Article 3231

2021

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Origins of specificity in protein-DNA recognition

Annual review of biochemistry, 2010-01, Vol.79 (1), p.233-269

2010

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A widespread role of the motif environment in transcription factor binding across diverse protein families

Genome research, 2015-09, Vol.25 (9), p.1268

2015

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Quantum annealing versus classical machine learning applied to a simplified computational biology problem

npj quantum information, 2018-02, Vol.4 (1), p.1-10, Article 14

2018

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

Bioinformatics, 2016-04, Vol.32 (8), p.1211-1213

2016

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Humanizing the yeast origin recognition complex

Nature communications, 2021-01, Vol.12 (1), p.33-33, Article 33

2021

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DNAproDB: an interactive tool for structural analysis of DNA-protein complexes

Nucleic acids research, 2017-07, Vol.45 (W1), p.W89

2017

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

Nucleic acids research, 2020-01, Vol.48 (D1), p.D246

2020

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Quantitative modeling of transcription factor binding specificities using DNA shape

Proceedings of the National Academy of Sciences - PNAS, 2015-04, Vol.112 (15), p.4654-4659

2015

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

Nucleic acids research, 2013-07, Vol.41 (Web Server issue), p.W56

2013

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Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

Cell reports (Cambridge), 2013-04, Vol.3 (4), p.1093-1104

2013

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Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models

Molecular systems biology, 2017-02, Vol.13 (2), p.910-n/a

2017

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

Cell, 2011-12, Vol.147 (6), p.1270-1282

2011

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How motif environment influences transcription factor search dynamics: Finding a needle in a haystack

BioEssays, 2016-07, Vol.38 (7), p.605-612

2016

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Unraveling determinants of transcription factor binding outside the core binding site

Genome research, 2015-07, Vol.25 (7), p.1018

2015

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

Nucleic acids research, 2014-01, Vol.42 (Database issue), p.D148

2014

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High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

Cell reports (Cambridge), 2015-05, Vol.11 (5), p.821-834

2015

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

Proceedings of the National Academy of Sciences - PNAS, 2013-04, Vol.110 (16), p.6376-6381

2013

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Control of DNA minor groove width and Fis protein binding by the purine 2-amino group

Nucleic acids research, 2013-07, Vol.41 (13), p.6750

2013

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Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

Nature communications, 2016-09, Vol.7 (1), p.12621-12621, Article 12621

2016

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

DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes

ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Predicting DNA structure using a deep learning method

The role of DNA shape in protein-DNA recognition

Genome information processing by the INO80 chromatin remodeler positions nucleosomes

Origins of specificity in protein-DNA recognition

A widespread role of the motif environment in transcription factor binding across diverse protein families

Quantum annealing versus classical machine learning applied to a simplified computational biology problem

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

Humanizing the yeast origin recognition complex

DNAproDB: an interactive tool for structural analysis of DNA-protein complexes

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

Quantitative modeling of transcription factor binding specificities using DNA shape

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

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

Transcription factor family‐specific DNA shape readout revealed by quantitative specificity models

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

How motif environment influences transcription factor search dynamics: Finding a needle in a haystack

Unraveling determinants of transcription factor binding outside the core binding site

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

High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins

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

Control of DNA minor groove width and Fis protein binding by the purine 2-amino group

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

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