MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

(2017) Jeanne Chèneby et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Sunil Kumar et al.   NUCLEIC ACIDS RESEARCH

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

Identification of altered cis-regulatory elements in human disease

(2015) Anthony Mathelier et al.   TRENDS IN GENETICS

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas

(2015) Anthony Mathelier et al.   GENOME BIOLOGY

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Dynamic DNA methylation across diverse human cell lines and tissues

(2013) K. E. Varley et al.   GENOME RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY