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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton … See abstract for full author list ➔ Zhou N, et al. Among authors: lee aj. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.
Ten simple rules for large-scale data processing.
Fungtammasan A, Lee A, Taroni J, Wheeler K, Chin CS, Davis S, Greene C. Fungtammasan A, et al. PLoS Comput Biol. 2022 Feb 10;18(2):e1009757. doi: 10.1371/journal.pcbi.1009757. eCollection 2022 Feb. PLoS Comput Biol. 2022. PMID: 35143491 Free PMC article. No abstract available.
Using genome-wide expression compendia to study microorganisms.
Lee AJ, Reiter T, Doing G, Oh J, Hogan DA, Greene CS. Lee AJ, et al. Comput Struct Biotechnol J. 2022 Aug 10;20:4315-4324. doi: 10.1016/j.csbj.2022.08.012. eCollection 2022. Comput Struct Biotechnol J. 2022. PMID: 36016717 Free PMC article. Review.
The Coming of Age of Nucleic Acid Vaccines during COVID-19.
Rando HM, Lordan R, Kolla L, Sell E, Lee AJ, Wellhausen N, Naik A, Kamil JP; COVID-19 Review Consortium; Gitter A, Greene CS. Rando HM, et al. Among authors: lee aj. mSystems. 2023 Apr 27;8(2):e0092822. doi: 10.1128/msystems.00928-22. Epub 2023 Mar 2. mSystems. 2023. PMID: 36861992 Free PMC article. Review.
1,183 results