HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data

(2015) Michal Dabrowski et al.   BMC BIOINFORMATICS

Recurrent somatic mutations in regulatory regions of human cancer genomes

(2015) Collin Melton et al.   NATURE GENETICS

Varying levels of complexity in transcription factor binding motifs

(2015) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera

(2015) Abdullah M. Khamis et al.   Scientific Reports

Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

(2015) Dmitri Papatsenko et al.   Stem Cell Reports

Effects of cytosine methylation on transcription factor binding sites

(2014) Yulia A Medvedeva et al.   BMC GENOMICS

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

(2014) Victor G Levitsky et al.   BMC GENOMICS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A promoter-level mammalian expression atlas

(2014)   NATURE

TFClass: a classification of human transcription factors and their rodent orthologs

(2014) Edgar Wingender et al.   NUCLEIC ACIDS RESEARCH

Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

(2014) Tanvir Alam et al.   PLoS One

Jaccard index based similarity measure to compare transcription factor binding site models

(2013) Ilya E Vorontsov et al.   Algorithms for Molecular Biology

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

(2013) Alvaro Sebastian et al.   BIOINFORMATICS

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Regional differences in gene expression and promoter usage in aged human brains

(2013) Luba M. Pardo et al.   NEUROBIOLOGY OF AGING

Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development

(2013) Majid Kazemian et al.   NUCLEIC ACIDS RESEARCH

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

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

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse

(2013) Qixuan Wang et al.   NUCLEIC ACIDS RESEARCH

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Large-Scale Quality Analysis of Published ChIP-seq Data

(2013) Georgi K. Marinov et al.   G3-Genes Genomes Genetics

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

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

(2012) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

YB-1 (YBX1) does not bind to Y/CCAAT boxes in vivo

(2012) D Dolfini et al.   ONCOGENE

Mutations and Binding Sites of Human Transcription Factors

(2012) Frederick Kinyua Kamanu et al.   Frontiers in Genetics

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

(2011) Yingtao Bi et al.   PLoS One

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

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

The Oncogenic EWS-FLI1 Protein Binds In Vivo GGAA Microsatellite Sequences with Potential Transcriptional Activation Function

(2009) Noëlle Guillon et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH