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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: bhat p. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A… See abstract for full author list ➔ Jiang Y, et al. Among authors: bhat p. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
A large-scale evaluation of computational protein function prediction.
Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. Radivojac P, et al. Among authors: bhat p. Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27. Nat Methods. 2013. PMID: 23353650 Free PMC article.
Search for exotic decays of the Higgs boson to a pair of pseudoscalars in the μμbb and ττbb final states.
CMS Collaboration; Hayrapetyan A, Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, Damanakis K, Dragicevic M, Del Valle AE, Hussain PS, Jeitler M, Krammer N, Liko D, Mikulec I, Schieck J, Schöfbeck R, Schwarz D, Sonawane M, Templ S, Waltenberger W, Wulz CE, Darwish MR, Janssen T, Van Mechelen P, Bols ES, D'Hondt J, Dansana S, De Moor A, Delcourt M, El Faham H, Lowette S, Makarenko I, Müller D, Sahasransu AR, Tavernier S, Tytgat M, Van Putte S, Vannerom D, Clerbaux B, De Lentdecker G, Favart L, Hohov D, Jaramillo J, Khalilzadeh A, Lee K, Mahdavikhorrami M, Malara A, Paredes S, Pétré L, Postiau N, Thomas L, Bemden MV, Velde CV, Vanlaer P, De Coen M, Dobur D, Hong Y, Knolle J, Lambrecht L, Mestdach G, Rendón C, Samalan A, Skovpen K, Van Den Bossche N, Wezenbeek L, Benecke A, Bruno G, Caputo C, Delaere C, Donertas IS, Giammanco A, Jaffel K, Jain S, Lemaitre V, Lidrych J, Mastrapasqua P, Mondal K, Tran TT, Wertz S, Alves GA, Coelho E, Hensel C, Menezes De Oliveira T, Moraes A, Rebello Teles P, Soeiro M, Aldá Júnior WL, Alves Gallo Pereira M, Barroso Ferreira Filho M, Brandao Malbouisson H, Carvalho W, Chinellato J, Da Costa EM, Da Silveira GG, De Jesus Damiao D, Fonseca De… See abstract for full author list ➔ CMS Collaboration, et al. Among authors: bhat pc. Eur Phys J C Part Fields. 2024;84(5):493. doi: 10.1140/epjc/s10052-024-12727-4. Epub 2024 May 14. Eur Phys J C Part Fields. 2024. PMID: 38757620 Free PMC article.
Genome organization around nuclear speckles drives mRNA splicing efficiency.
Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, Takei Y, Burr A, Goronzy IN, Chen AW, Huang W, Ferrer JLM, Soehalim E, Goh ST, Chari T, Sullivan DK, Blanco MR, Guttman M. Bhat P, et al. Nature. 2024 May;629(8014):1165-1173. doi: 10.1038/s41586-024-07429-6. Epub 2024 May 8. Nature. 2024. PMID: 38720076
1,285 results