Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

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

(2013) Jan Grau et al.   NUCLEIC ACIDS RESEARCH

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

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information

(2012) Xiaotu Ma et al.   NUCLEIC ACIDS RESEARCH

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Novel computational analysis of protein binding array data identifies direct targets of Nkx2.2 in the pancreas

(2011) Jonathon T Hill et al.   BMC BIOINFORMATICS

Development of computational methods to search for FoxA transcription factor binding sites, their experimental verification and application to the analysis of ChIP-seq data

(2011) V. G. Levitsky et al.   Doklady Biochemistry and Biophysics

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles

(2011) Yingtao Bi et al.   PLoS One

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Deep and wide digging for binding motifs in ChIP-Seq data

(2010) I. V. Kulakovskiy et al.   BIOINFORMATICS

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments

(2010) Lakshmi Kuttippurathu et al.   BIOINFORMATICS

The FoxA factors in organogenesis and differentiation

(2010) Klaus H Kaestner   CURRENT OPINION IN GENETICS & DEVELOPMENT

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Identification and characterization of glucocorticoid receptor-binding sites in the human genome

(2010) Keiko Taniguchi-Yanai et al.   JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis

(2010) Valentina Boeva et al.   NUCLEIC ACIDS RESEARCH

Efficient Double Fragmentation ChIP-seq Provides Nucleotide Resolution Protein-DNA Binding Profiles

(2010) Michal Mokry et al.   PLoS One

Structural variants of glucocorticoid receptor binding sites and different versions of positive glucocorticoid responsive elements: Analysis of GR-TRRD database

(2009) Vasily M. Merkulov et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

Extracting transcription factor targets from ChIP-Seq data

(2009) Geetu Tuteja et al.   NUCLEIC ACIDS RESEARCH

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing

(2009) Ola Wallerman et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Genome-wide discovery of functional transcription factor binding sites by comparative genomics: The case of Stat3

(2009) F. Vallania et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

(2008) Elizabeth D. Wederell et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY