Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells

Regularization Paths for Generalized Linear Models via Coordinate Descent

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ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs

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UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

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DNA-Binding Specificities of Human Transcription Factors

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Transcriptome and genome sequencing uncovers functional variation in humans

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The Cancer Genome Atlas Pan-Cancer analysis project

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

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oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

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MotifSuite: workflow for probabilistic motif detection and assessment

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Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma

(2012) Manu Setty et al.   Molecular Systems Biology

MotifMap: integrative genome-wide maps of regulatory motif sites for model species

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Evolution of Promoter Affinity for Transcription Factors in the Human Lineage

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Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

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Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

(2011) Chao Cheng et al.   NUCLEIC ACIDS RESEARCH

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

hPDI: a database of experimental human protein-DNA interactions

(2009) Z. Xie et al.   BIOINFORMATICS

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

(2008) Lucas D. Ward et al.   BIOINFORMATICS

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE