Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding

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

(2017) Lin Yang et al.   Molecular Systems Biology

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

(2017) Jared M. Sagendorf et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Iris Dror et al.   BIOESSAYS

DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis

(2016) Stephen P. Hancock et al.   PLoS One

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

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

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

Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator

(2015) Zengqin Deng et al.   Nature Communications

A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data

(2014) Yaron Orenstein 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

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

Stability selection for regression-based models of transcription factor-DNA binding specificity

(2013) F. Mordelet et al.   BIOINFORMATICS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

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

(2013) Stephen P. Hancock 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

Mechanism of Origin DNA Recognition and Assembly of an Initiator-Helicase Complex by SV40 Large Tumor Antigen

(2013) Y. Paul Chang et al.   Cell Reports

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

(2013) Raluca Gordân et al.   Cell Reports

A Map of Minor Groove Shape and Electrostatic Potential from Hydroxyl Radical Cleavage Patterns of DNA

(2011) Eric P. Bishop et al.   ACS Chemical Biology

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

(2011) Matthew Slattery et al.   CELL

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Origins of Specificity in Protein-DNA Recognition

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

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

(2010) S. Stella et al.   GENES & DEVELOPMENT

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs

(2010) Malka Kitayner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nuance in the double-helix and its role in protein–DNA recognition

(2009) Remo Rohs et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Recognition of AT-Rich DNA Binding Sites by the MogR Repressor

(2009) Aimee Shen et al.   STRUCTURE

Inferring Binding Energies from Selected Binding Sites

(2009) Yue Zhao et al.   PLoS Computational Biology

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL