Jaime Abraham Castro-Mondragon

COBIND identifies TF co-binding patterns using NMF on TFBS data, revealing both known and novel co-binding configurations across species.

The paper updates RhizoBindingSites with S-matrices derived from O-matrices, showing improved gene detection and TF coverage compared to the original database.

The paper identifies cis-regulatory mutations in cancer that disrupt gene regulatory programs by affecting both transcriptional and post-transcriptional regulation.

The paper identifies genetic networks and regulatory elements associated with cardiac performance variation in Drosophila and finds conserved genetic architecture between flies and humans.

UniBind compiles high-confidence TF-DNA interactions from ChIP-seq data across nine species, predicting 56 million TFBSs and cis-regulatory modules.

The paper identifies regulatory motifs in peach using co-expression networks and RSAT::Plants, finding that small promoter regions are optimal for motif discovery.

The paper introduces matrix-clustering, a tool that reduces redundancy and clusters transcription factor binding motifs from multiple sources, improving interpretation of motif collections.