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

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

(2013) F. Mordelet et al.   BIOINFORMATICS

Lineages, cell types and functional states: a genomic view

(2013) Renato Ostuni et al.   CURRENT OPINION IN CELL BIOLOGY

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals

(2013) Lisa C Watson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Covariation between homeodomain transcription factors and the shape of their DNA binding sites

(2013) Iris Dror et al.   NUCLEIC ACIDS RESEARCH

Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion

(2013) Yongheng Chen et al.   NUCLEIC ACIDS RESEARCH

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

Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions

(2013) A. Eldar 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

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier 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

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

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

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

A flexible integrative approach based on random forest improves prediction of transcription factor binding sites

(2012) Bart Hooghe et al.   NUCLEIC ACIDS RESEARCH

Improved predictions of transcription factor binding sites using physicochemical features of DNA

(2012) Mark Maienschein-Cline et al.   NUCLEIC ACIDS RESEARCH

DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation

(2012) Yongheng Chen et al.   Cell Reports

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

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

(2011) Matthew Slattery et al.   CELL

DNA shape, genetic codes, and evolution

(2011) Stephen CJ Parker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

Origins of Specificity in Protein-DNA Recognition

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

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

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

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

(2010) K. Robasky et al.   NUCLEIC ACIDS RESEARCH

Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli

(2010) Pieter Meysman et al.   NUCLEIC ACIDS RESEARCH

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Michael F. Berger et al.   CELL

A Feature-Based Approach to Modeling Protein–DNA Interactions

(2008) Eilon Sharon et al.   PLoS Computational Biology