DNAcycP: a deep learning tool for DNA cyclizability prediction

iDHS-Deep: an integrated tool for predicting DNase I hypersensitive sites by deep neural network

(2021) Fu-Ying Dao et al.   BRIEFINGS IN BIOINFORMATICS

DNA mechanics and its biological impact

(2021) Aakash Basu et al.   JOURNAL OF MOLECULAR BIOLOGY

Genome folding through loop extrusion by SMC complexes

(2021) Iain F. Davidson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles

(2021) Jejoong Yoo et al.   NUCLEIC ACIDS RESEARCH

Pioneer Transcription Factors Initiating Gene Network Changes

(2020) Kenneth S. Zaret   Annual Review of Genetics

What do we know about DNA mechanics so far?

(2020) Abhishek Aggarwal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics

(2020) Etienne Routhier et al.   GENOME RESEARCH

Measuring DNA mechanics on the genome scale

(2020) Aakash Basu et al.   NATURE

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

(2020) Runjhun Saran et al.   SENSORS

FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data

(2019) Daniel Quang et al.   METHODS

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking

(2019) Jiyoun Jeong et al.   PHYSICAL REVIEW LETTERS

DNA Sequence Is a Major Determinant of Tetrasome Dynamics

(2019) Orkide Ordu et al.   BIOPHYSICAL JOURNAL

Building machines with DNA molecules

(2019) Hamid Ramezani et al.   NATURE REVIEWS GENETICS

LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks

(2018) Juhua Zhang et al.   BIOINFORMATICS

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants

(2018) Meng Wang et al.   NUCLEIC ACIDS RESEARCH

Deep learning architectures for prediction of nucleosome positioning from sequences data

(2018) Mattia Di Gangi et al.   BMC BIOINFORMATICS

Deep learning for DNase I hypersensitive sites identification

(2018) Chuqiao Lyu et al.   BMC GENOMICS

Sequence-Dependent Persistence Lengths of DNA

(2017) Jonathan S. Mitchell et al.   Journal of Chemical Theory and Computation

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

(2016) Lilien N. Voong et al.   CELL

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Gabriel Rosanio et al.   BIOPOLYMERS

Probing the elastic limit of DNA bending

(2014) Tung T. Le et al.   NUCLEIC ACIDS RESEARCH

Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs

(2013) Narasimharao Nalabothula et al.   BMC GENOMICS

Impact of Methylation on the Physical Properties of DNA

(2012) Alberto Pérez et al.   BIOPHYSICAL JOURNAL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

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

(2012) Kristin Brogaard et al.   NATURE

Sequence dependence of transcription factor-mediated DNA looping

(2012) Stephanie Johnson et al.   NUCLEIC ACIDS RESEARCH

Extreme Bendability of DNA Less than 100 Base Pairs Long Revealed by Single-Molecule Cyclization

(2012) R. Vafabakhsh et al.   SCIENCE

Cooperative kinking at distant sites in mechanically stressed DNA

(2011) Troy A. Lionberger et al.   NUCLEIC ACIDS RESEARCH

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures

(2011) Do-Nyun Kim et al.   NUCLEIC ACIDS RESEARCH

Cytosine methylation alters DNA mechanical properties

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

Sequence dependence of DNA bending rigidity

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

The flexibility of locally melted DNA

(2009) Robert A. Forties et al.   NUCLEIC ACIDS RESEARCH

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

(2009) Davide Demurtas et al.   NUCLEIC ACIDS RESEARCH

Concentration and Length Dependence of DNA Looping in Transcriptional Regulation

(2009) Lin Han et al.   PLoS One

What controls nucleosome positions?

(2009) Eran Segal et al.   TRENDS IN GENETICS

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

(2008) Xi Chen et al.   CELL