The Next Generation of Transcription Factor Binding Site Prediction

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions

(2012) Yue Zhao et al.   GENETICS

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

Variable structure motifs for transcription factor binding sites

(2010) John E Reid et al.   BMC GENOMICS

Improved detection of motifs with preferential location in promoters

(2010) Virginie Bernard et al.   GENOME

Discrete Roles of STAT4 and STAT6 Transcription Factors in Tuning Epigenetic Modifications and Transcription during T Helper Cell Differentiation

(2010) Lai Wei et al.   IMMUNITY

Statistical Mechanics of Transcription-Factor Binding Site Discovery Using Hidden Markov Models

(2010) Pankaj Mehta et al.   JOURNAL OF STATISTICAL PHYSICS

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

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

Dinucleotide Weight Matrices for Predicting Transcription Factor Binding Sites: Generalizing the Position Weight Matrix

(2010) Rahul Siddharthan   PLoS One

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

A Novel HMM-Based Method for Detecting Enriched Transcription Factor Binding Sites Reveals RUNX3 as a Potential Target in Pancreatic Cancer Biology

(2010) Liron Levkovitz et al.   PLoS One

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif

(2009) Amar Drawid et al.   BMC BIOINFORMATICS

The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes

(2009) Todd Riley et al.   BMC BIOINFORMATICS

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

(2009) T. Wasson et al.   GENOME RESEARCH

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

Transcription Factor Binding Sites Are Genetic Determinants of Retroviral Integration in the Human Genome

(2009) Barbara Felice et al.   PLoS One

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Discovery of novel tumor suppressor p53 response elements using information theory

(2008) Ilya G. Lyakhov et al.   NUCLEIC ACIDS RESEARCH

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

(2008) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology