SNP2TFBS – a database of regulatory SNPs affecting predicted transcription factor binding site affinity

atSNP: transcription factor binding affinity testing for regulatory SNP detection

(2015) Chandler Zuo et al.   BIOINFORMATICS

motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites: Fig. 1.

(2015) Simon G. Coetzee et al.   BIOINFORMATICS

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

(2015) Lucas D. Ward et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

The Genetic and Mechanistic Basis for Variation in Gene Regulation

(2015) Athma A. Pai et al.   PLoS Genetics

Genetic variation in the non-coding genome: Involvement of micro-RNAs and long non-coding RNAs in disease

(2014) Barbara Hrdlickova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Increased SRF transcriptional activity in human and mouse skeletal muscle is a signature of insulin resistance

(2011) Wanzhu Jin et al.   JOURNAL OF CLINICAL INVESTIGATION

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

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

(2011) Morgane Thomas-Chollier et al.   Nature Protocols

is-rSNP: a novel technique for in silico regulatory SNP detection

(2010) Geoff Macintyre et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

In Silico Detection of Sequence Variations Modifying Transcriptional Regulation

(2008) Malin C. Andersen et al.   PLoS Computational Biology