Varying levels of complexity in transcription factor binding motifs

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

On the Value of Intra-Motif Dependencies of Human Insulator Protein CTCF

(2014) Ralf Eggeling et al.   PLoS One

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

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

A general approach for discriminative de novo motif discovery from high-throughput data

(2013) Jan Grau et al.   NUCLEIC ACIDS RESEARCH

c-Jun/c-Fos heterodimers regulate cellular genes via a newly identified class of methylated DNA sequence motifs

(2013) M. Gustems et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Lin Yang et al.   NUCLEIC ACIDS RESEARCH

A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

(2013) Hirotaka Nakahashi 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

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

FROM BINDING MOTIFS IN CHIP-SEQ DATA TO IMPROVED MODELS OF TRANSCRIPTION FACTOR BINDING SITES

(2013) IVAN KULAKOVSKIY et al.   Journal of Bioinformatics and Computational Biology

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

DECOD: fast and accurate discriminative DNA motif finding

(2011) Peter Huggins et al.   BIOINFORMATICS

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells

(2011) Hong-Bing Yu et al.   GENOME RESEARCH

Jury remains out on simple models of transcription factor specificity

(2011) Quaid Morris et al.   NATURE BIOTECHNOLOGY

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

(2011) Yue Zhao et al.   NATURE BIOTECHNOLOGY

Systems Analysis of ATF3 in Stress Response and Cancer Reveals Opposing Effects on Pro-Apoptotic Genes in p53 Pathway

(2011) Yujiro Tanaka et al.   PLoS One

ATF3, an HTLV-1 bZip factor binding protein, promotes proliferation of adult T-cell leukemia cells

(2011) Keita Hagiya et al.   Retrovirology

De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference

(2011) Jens Keilwagen et al.   PLoS Computational Biology

Unifying generative and discriminative learning principles

(2010) Jens Keilwagen et al.   BMC BIOINFORMATICS

Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis

(2010) Jens Keilwagen et al.   BMC BIOINFORMATICS

Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction

(2010) R. A. Salama et al.   NUCLEIC ACIDS RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level

(2009) A. W. Bruce et al.   GENOME RESEARCH

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

A Feature-Based Approach to Modeling Protein–DNA Interactions

(2008) Eilon Sharon et al.   PLoS Computational Biology