CiiiDER: A tool for predicting and analysing transcription factor binding sites

A novel method for improved accuracy of transcription factor binding site prediction

(2018) Abdullah M Khamis 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

Regulation of H3K4me3 at Transcriptional Enhancers Characterizes Acquisition of Virus-Specific CD8 + T Cell-Lineage-Specific Function

(2017) Brendan E. Russ et al.   Cell Reports

Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells

(2016) Valentina Boeva   Frontiers in Genetics

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The MEME Suite

(2015) Timothy L. Bailey 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

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

(2013) Andrew T. Kwon et al.   G3-Genes Genomes Genetics

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape

(2012) Bradley N Bidwell et al.   NATURE MEDICINE

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

(2010) A. Jolma et al.   GENOME RESEARCH

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

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

(2009) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

Evolutionary conservation of zinc finger transcription factor binding sites in promoters of genes co-expressed with WT1 in prostate cancer

(2008) Kurtis Eisermann et al.   BMC GENOMICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

INTERFEROME: the database of interferon regulated genes

(2008) Shamith A. Samarajiwa et al.   NUCLEIC ACIDS RESEARCH