Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites

Gene regulatory network inference resources: A practical overview

(2019) Daniele Mercatelli et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A novel method for improved accuracy of transcription factor binding site prediction

(2018) Abdullah M Khamis et al.   NUCLEIC ACIDS RESEARCH

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

(2018) Stephen K Burley et al.   NUCLEIC ACIDS RESEARCH

An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes

(2016) Bingqiang Liu et al.   BMC GENOMICS

The identification of cis-regulatory elements: A review from a machine learning perspective

(2015) Yifeng Li et al.   BIOSYSTEMS

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

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

Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes

(2014) Mario Pujato et al.   NUCLEIC ACIDS RESEARCH

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces

(2013) Alvaro Sebastian et al.   BIOINFORMATICS

The TetR Family of Regulators

(2013) L. Cuthbertson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins

(2013) Anton V. Persikov et al.   NUCLEIC ACIDS RESEARCH

Atomistic modeling of protein–DNA interaction specificity: progress and applications

(2012) Limin Angela Liu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Genome Context as a Predictive Tool for Identifying Regulatory Targets of the TetR Family Transcriptional Regulators

(2012) Sang Kyun Ahn et al.   PLoS One

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

(2011) Matthew Slattery et al.   CELL

Discovery of DNA operators for TetR and MarR family transcription factors from Burkholderia xenovorans

(2011) T. S. Maity et al.   MICROBIOLOGY-SGM

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic footprinting: a boost for microbial regulatory genomics

(2011) Pramod Katara et al.   PROTOPLASMA

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

(2010) A. Jolma et al.   GENOME RESEARCH

A Comprehensive Analysis of Structural and Sequence Conservation in the TetR Family Transcriptional Regulators

(2010) Zhou Yu et al.   JOURNAL OF MOLECULAR BIOLOGY

Determining the specificity of protein–DNA interactions

(2010) Gary D. Stormo et al.   NATURE REVIEWS GENETICS

A new framework for identifying cis-regulatory motifs in prokaryotes

(2010) Guojun Li et al.   NUCLEIC ACIDS RESEARCH

Using protein design algorithms to understand the molecular basis of disease caused by protein–DNA interactions: the Pax6 example

(2010) Andreu Alibés et al.   NUCLEIC ACIDS RESEARCH

Accurate recognition of cis -regulatory motifs with the correct lengths in prokaryotic genomes

(2009) Guojun Li et al.   NUCLEIC ACIDS RESEARCH

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

(2009) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

Predicting DNA recognition by Cys2His2 zinc finger proteins

(2008) Anton V. Persikov et al.   BIOINFORMATICS

Predicted transcription factor binding sites as predictors of operons in Escherichia coli and Streptomyces coelicolor

(2008) Emma Laing et al.   BMC GENOMICS

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1

(2008) Christof Francke et al.   BMC GENOMICS

Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach

(2008) Zhijie Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS