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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: albu m. bioRxiv [Preprint]. 2024 Nov 13:2024.11.11.619379. doi: 10.1101/2024.11.11.619379. bioRxiv. 2024. PMID: 39605530 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: albu m. bioRxiv [Preprint]. 2024 Oct 18:2024.10.15.618476. doi: 10.1101/2024.10.15.618476. bioRxiv. 2024. PMID: 39464061 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: albu m. bioRxiv [Preprint]. 2024 Nov 12:2024.11.11.622123. doi: 10.1101/2024.11.11.622123. bioRxiv. 2024. PMID: 39605320 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: albu m. bioRxiv [Preprint]. 2024 Nov 12:2024.11.11.618478. doi: 10.1101/2024.11.11.618478. bioRxiv. 2024. PMID: 39605368 Free PMC article. Preprint.
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: albu m. bioRxiv [Preprint]. 2024 Nov 12:2024.11.11.622097. doi: 10.1101/2024.11.11.622097. bioRxiv. 2024. PMID: 39605729 Free PMC article. Preprint.
The Human Transcription Factors.
Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. Lambert SA, et al. Among authors: albu m. Cell. 2018 Feb 8;172(4):650-665. doi: 10.1016/j.cell.2018.01.029. Cell. 2018. PMID: 29425488 Free article. Review.
The Human Transcription Factors.
Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. Lambert SA, et al. Among authors: albu m. Cell. 2018 Oct 4;175(2):598-599. doi: 10.1016/j.cell.2018.09.045. Cell. 2018. PMID: 30290144 Free article. No abstract available.
Motif comparison based on similarity of binding affinity profiles.
Lambert SA, Albu M, Hughes TR, Najafabadi HS. Lambert SA, et al. Among authors: albu m. Bioinformatics. 2016 Nov 15;32(22):3504-3506. doi: 10.1093/bioinformatics/btw489. Epub 2016 Jul 27. Bioinformatics. 2016. PMID: 27466627 Free PMC article.
83 results