Inherent limitations of probabilistic models for protein-DNA binding specificity

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

(2017) Lin Yang et al.   Molecular Systems Biology

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

(2017) Alina Isakova et al.   NATURE METHODS

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo

(2016) Anthony Mathelier et al.   Cell Systems

Recent progress in understanding transcription factor binding specificity

(2015) H. J. Bussemaker   Briefings in Functional Genomics

A Biophysical Approach to Predicting Protein–DNA Binding Energetics

(2015) George Locke et al.   GENETICS

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE

(2015) Todd R Riley et al.   eLife

A Biophysical Approach to Predicting Protein–DNA Binding Energetics

(2015) George Locke et al.   GENETICS

Spec-seq: determining protein-DNA-binding specificity by sequencing

(2014) G. D. Stormo et al.   Briefings in Functional Genomics

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

High-Resolution Specificity from DNA Sequencing Highlights Alternative Modes of Lac Repressor Binding

(2014) Z. Zuo et al.   GENETICS

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

(2014) Yaron Orenstein et al.   NUCLEIC ACIDS RESEARCH

Protein−DNA binding in the absence of specific base-pair recognition

(2014) Ariel Afek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

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

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

(2011) Matthew Slattery et al.   CELL

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

(2011) Razvan Nutiu et al.   NATURE BIOTECHNOLOGY

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

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

(2011) Morgane Thomas-Chollier et al.   Nature Protocols

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

(2010) A. Jolma et al.   GENOME RESEARCH

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

(2010) Polly M Fordyce et al.   NATURE BIOTECHNOLOGY

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An ensemble model of competitive multi-factor binding of the genome

(2009) T. Wasson et al.   GENOME RESEARCH

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

Bind-n-Seq: high-throughput analysis of in vitro protein–DNA interactions using massively parallel sequencing

(2009) Artem Zykovich et al.   NUCLEIC ACIDS RESEARCH

Modeling the Quantitative Specificity of DNA-Binding Proteins from Example Binding Sites

(2009) Dana S. F. Homsi et al.   PLoS One

Inferring Binding Energies from Selected Binding Sites

(2009) Yue Zhao et al.   PLoS Computational Biology

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE