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

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

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

(2013) Tianyin Zhou 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

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

Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes

(2012) Ana Carolina Dantas Machado et al.   BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION

Recognition models to predict DNA-binding specificities of homeodomain proteins

(2012) R. G. Christensen et al.   BIOINFORMATICS

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

Exploring the DNA-recognition potential of homeodomains

(2012) S. W. Chu et al.   GENOME RESEARCH

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

(2012) Yongheng Chen et al.   Cell Reports

Correlated evolution of transcription factors and their binding sites

(2011) Shu Yang et al.   BIOINFORMATICS

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

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

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

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

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

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

A Feature-Based Approach to Modeling Protein–DNA Interactions

(2008) Eilon Sharon et al.   PLoS Computational Biology