BACKGROUND: The chromosome 9p21.3 locus is among the strongest genetic risk loci for cardiovascular disease (CVD), yet the regulatory mechanisms underlying this association remain poorly understood. Previous vascular disease studies focused predominantly on the role of this locus in smooth muscle cell (SMC) dysfunction...
A. Zhigulev, F. Poujade, N. Gryzunov et al.· medRxiv· 0 citations
DNA motif discovery and, particularly, computational modeling of transcription factor binding motifs, has been a mecca of algorithmic bioinformatics for several decades. Here, we report the results of the largest open community challenge in Inferring BInding Specificities (IBIS), where participants all over the world w...
Nikita Gryzunov, Dmitry D. Penzar, V. Kamenets et al.· Cell Reports· 0 citations
This study profiles 284 largely uncharacterized human transcription factors with a microfluidic methylation-sensitive DNA-binding assay, uncovering 74 new motifs and showing how DNA methylation shapes TF binding.
Antoni J. Gralak, Kateřina Faltejsková, Ally W. H. Yang et al.· Nature Communications· 2 citations
EPIC, the Eukaryotic Promoter and transcription Initiation prediction Challenge, relies on understudied animals spanning three phyla: octopus, oyster, milkweed bug, Indian meal moth, and shark and is open to everyone.
Ilya E. Vorontsov, N. Gryzunov, Bayley R. McDonald et al.· bioRxiv· 0 citations
It is found that induction of TPRX1, a known regulator of zygotic preimplantation, leads to chromatin opening at many of its binding sites in the dark matter genome, suggesting that the genome encodes many putative transcription factors.
Rozita Razavi, Ali Fathi, Isaac Yellan et al.· Nature Communications· 3 citations
There is ongoing debate regarding the degree to which transcription factors (TFs) independently specify genomic binding: TF binding motifs are typically short and degenerate, yielding many more binding site predictions than observed in cells. Here we present genomic high-throughput SELEX (GHT-SELEX)—a scalable method t...
A. Jolma, A. Hernandez-Corchado, A. Yang et al.· Nature Methods· 3 citations
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