We are sad to report that the one the principal contributors to the HOCOMOCO projeсt, the founding Director of CBRC KAUST, Professor Vladimir Bajic passed away on 31st October, 2019 at the age of 67.

“Vlad was a world-class researcher in our relatively new field,” said Professor Takashi Gojobori, Acting Director, CBRC. “More important to all of us in CBRC, he was a world-class leader and human. [...] We will all double our efforts to conduct leading-edge research as we keep Vlad in our memories” (full text)

Please cite:

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

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Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Ruslan N. Sharipov; Alla D. Fedorova; Eugene I. Rumynskiy; Yulia A. Medvedeva; Arturo Magana-Mora; Vladimir B. Bajic; Dmitry A. Papatsenko; Fedor A. Kolpakov; Vsevolod J. Makeev

Nucl. Acids Res., Database issue, gkx1106 (11 November 2017)

doi: 10.1093/nar/gkx1106

HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v11 provides transcription factor (TF) binding models for 680 human and 453 mouse TFs.

Since v11, HOCOMOCO is complemented by MoLoTool, an interactive web tool to mark motif occurrences in a given set of DNA sequences.

In addition to basic mononucleotide position weight matrices (PWMs), HOCOMOCO provides dinucleotide position weight matrices based on ChIP-Seq data.

All the models were produced by the ChIPMunk motif discovery tool. Model quality ratings are results of a comprehensive cross-validation benchmark.

ChIP-Seq data for motif discovery was extracted from GTRD database of BioUML platform, that also provides an interface for motif finding (sequence scanning) with HOCOMOCO models.