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Page 1
Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors.
Jolma A, Laverty KU, Fathi A, Yang AWH, Yellan I, Vorontsov IE, Inukai S, Kribelbauer-Swietek JF, Gralak AJ, Razavi R, Albu M, Brechalov A, Patel ZM, Nozdrin V, Meshcheryakov G, Kozin I, Abramov S, Boytsov A; Codebook Consortium; Fornes O, Makeev VJ, Grau J, Grosse I, Bucher P, Deplancke B, Kulakovskiy IV, Hughes TR. Jolma A, et al. Among authors: laverty ku. bioRxiv [Preprint]. 2024 Nov 12:2024.11.11.622097. doi: 10.1101/2024.11.11.622097. bioRxiv. 2024. PMID: 39605729 Free PMC article. Preprint.
Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.
Vorontsov IE, Kozin I, Abramov S, Boytsov A, Jolma A, Albu M, Ambrosini G, Faltejskova K, Gralak AJ, Gryzunov N, Inukai S, Kolmykov S, Kravchenko P, Kribelbauer-Swietek JF, Laverty KU, Nozdrin V, Patel ZM, Penzar D, Plescher ML, Pour SE, Razavi R, Yang AWH, Yevshin I, Zinkevich A, Weirauch MT, Bucher P, Deplancke B, Fornes O, Grau J, Grosse I, Kolpakov FA; Codebook/GRECO-BIT Consortium; Makeev VJ, Hughes TR, Kulakovskiy IV. Vorontsov IE, et al. Among authors: laverty ku. bioRxiv [Preprint]. 2024 Nov 13:2024.11.11.619379. doi: 10.1101/2024.11.11.619379. bioRxiv. 2024. PMID: 39605530 Free PMC article. Preprint.
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors.
Jolma A, Hernandez-Corchado A, Yang AWH, Fathi A, Laverty KU, Brechalov A, Razavi R, Albu M, Zheng H; Codebook Consortium; Kulakovskiy IV, Najafabadi HS, Hughes TR. Jolma A, et al. Among authors: laverty ku. bioRxiv [Preprint]. 2024 Nov 12:2024.11.11.618478. doi: 10.1101/2024.11.11.618478. bioRxiv. 2024. PMID: 39605368 Free PMC article. Preprint.
Extensive binding of uncharacterized human transcription factors to genomic dark matter.
Razavi R, Fathi A, Yellan I, Brechalov A, Laverty KU, Jolma A, Hernandez-Corchado A, Zheng H, Yang AWH, Albu M, Barazandeh M, Hu C, Vorontsov IE, Patel ZM; Codebook Consortium; Kulakovskiy IV, Bucher P, Morris Q, Najafabadi HS, Hughes TR. Razavi R, et al. Among authors: laverty ku. bioRxiv [Preprint]. 2024 Nov 12:2024.11.11.622123. doi: 10.1101/2024.11.11.622123. bioRxiv. 2024. PMID: 39605320 Free PMC article. Preprint.
Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes.
Sasse A, Ray D, Laverty KU, Tam CL, Albu M, Zheng H, Lyudovyk O, Dalal T, Nie K, Magis C, Notredame C, Weirauch MT, Hughes TR, Morris Q. Sasse A, et al. Among authors: laverty ku. bioRxiv [Preprint]. 2024 Oct 18:2024.10.15.618476. doi: 10.1101/2024.10.15.618476. bioRxiv. 2024. PMID: 39464061 Free PMC article. Preprint.
RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific.
Ray D, Laverty KU, Jolma A, Nie K, Samson R, Pour SE, Tam CL, von Krosigk N, Nabeel-Shah S, Albu M, Zheng H, Perron G, Lee H, Najafabadi H, Blencowe B, Greenblatt J, Morris Q, Hughes TR. Ray D, et al. Among authors: laverty ku. Sci Rep. 2023 Mar 31;13(1):5238. doi: 10.1038/s41598-023-32245-9. Sci Rep. 2023. PMID: 37002329 Free PMC article.
Motif models for RNA-binding proteins.
Sasse A, Laverty KU, Hughes TR, Morris QD. Sasse A, et al. Among authors: laverty ku. Curr Opin Struct Biol. 2018 Dec;53:115-123. doi: 10.1016/j.sbi.2018.08.001. Epub 2018 Aug 29. Curr Opin Struct Biol. 2018. PMID: 30172081 Review.
11 results