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DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer.
Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert JP, Vaswani A, McLean CY, Nattestad M, Chang PC, Carroll A. Baid G, et al. Among authors: vert jp. Nat Biotechnol. 2023 Feb;41(2):232-238. doi: 10.1038/s41587-022-01435-7. Epub 2022 Sep 1. Nat Biotechnol. 2023. PMID: 36050551
Deep embedding and alignment of protein sequences.
Llinares-López F, Berthet Q, Blondel M, Teboul O, Vert JP. Llinares-López F, et al. Among authors: vert jp. Nat Methods. 2023 Jan;20(1):104-111. doi: 10.1038/s41592-022-01700-2. Epub 2022 Dec 15. Nat Methods. 2023. PMID: 36522501
A community effort to assess and improve drug sensitivity prediction algorithms.
Costello JC, Heiser LM, Georgii E, Gönen M, Menden MP, Wang NJ, Bansal M, Ammad-ud-din M, Hintsanen P, Khan SA, Mpindi JP, Kallioniemi O, Honkela A, Aittokallio T, Wennerberg K; NCI DREAM Community; Collins JJ, Gallahan D, Singer D, Saez-Rodriguez J, Kaski S, Gray JW, Stolovitzky G. Costello JC, et al. Nat Biotechnol. 2014 Dec;32(12):1202-12. doi: 10.1038/nbt.2877. Epub 2014 Jun 1. Nat Biotechnol. 2014. PMID: 24880487 Free PMC article.
Prediction of human population responses to toxic compounds by a collaborative competition.
Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration; Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J. Eduati F, et al. Nat Biotechnol. 2015 Sep;33(9):933-40. doi: 10.1038/nbt.3299. Epub 2015 Aug 10. Nat Biotechnol. 2015. PMID: 26258538 Free PMC article.
Wisdom of crowds for robust gene network inference.
Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR; DREAM5 Consortium; Kellis M, Collins JJ, Stolovitzky G. Marbach D, et al. Nat Methods. 2012 Jul 15;9(8):796-804. doi: 10.1038/nmeth.2016. Nat Methods. 2012. PMID: 22796662 Free PMC article.
93 results