Transcription factors (TFs) are key players in eukaryotic gene regulation, but the DNA binding specificity of many TFs remains unknown. Here, we assay 284 mostly uncharacterized putative human TFs using selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq), revealing 74 new DNA binding moti...
Antoni J. Gralak, Kateřina Faltejsková, Ally W. H. Yang et al.· Nature Communications· 2 citations
Gene expression is regulated by transcription factors (TFs), which recognize specific DNA sequence motifs. Several hundred putative human TFs, identified mainly by an apparent DNA-binding domain, lack known binding motifs1. Furthermore, even for well-characterized TFs, it remains controversial the degree to which motif...
A. Jolma, Kaitlin U. Laverty, Ali Fathi et al.· Nature· 3 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
The exact marginalization of the mixture weight is studied, and it is shown that the exact posterior of the weight is a finite mixture of Beta distributions, delivering closed-form posterior summaries, credible intervals and per-observation local false-discovery rates without any sampling.
G. Meshcheryakov· 0 citations
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