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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 JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I. Zhou N, et al. Among authors: o donovan c, lichtarge o. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.
Mutational Landscape of the BAP1 Locus Reveals an Intrinsic Control to Regulate the miRNA Network and the Binding of Protein Complexes in Uveal Melanoma.
Sharma A, Biswas A, Liu H, Sen S, Paruchuri A, Katsonis P, Lichtarge O, Chand Dakal T, Maulik U, Gromiha MM, Bandyopadhyay S, Ludwig M, Holz FG, Loeffler KU, Herwig-Carl MC. Sharma A, et al. Among authors: lichtarge o. Cancers (Basel). 2019 Oct 19;11(10):1600. doi: 10.3390/cancers11101600. Cancers (Basel). 2019. PMID: 31635116 Free PMC article.
Evolutionary action score identifies a subset of TP53 mutated myelodysplastic syndrome with favorable prognosis.
Kanagal-Shamanna R, Montalban-Bravo G, Katsonis P, Sasaki K, Class CA, Jabbour E, Sallman D, Hunter AM, Benton C, Chien KS, Luthra R, Bueso-Ramos CE, Kadia T, Andreeff M, Komrokji RS, Al Ali NH, Short N, Daver N, Routbort MJ, Khoury JD, Patel K, Ganan-Gomez I, Wei Y, Borthakur G, Ravandi F, Do KA, Soltysiak KA, Lichtarge O, Medeiros LJ, Kantarjian H, Garcia-Manero G. Kanagal-Shamanna R, et al. Among authors: lichtarge o. Blood Cancer J. 2021 Mar 6;11(3):52. doi: 10.1038/s41408-021-00446-y. Blood Cancer J. 2021. PMID: 33677472 Free PMC article. No abstract available.
Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain.
Marbach F, Stoyanov G, Erger F, Stratakis CA, Settas N, London E, Rosenfeld JA, Torti E, Haldeman-Englert C, Sklirou E, Kessler E, Ceulemans S, Nelson SF, Martinez-Agosto JA, Palmer CGS, Signer RH; Undiagnosed Diseases Network, Andrews MV, Grange DK, Willaert R, Person R, Telegrafi A, Sievers A, Laugsch M, Theiß S, Cheng Y, Lichtarge O, Katsonis P, Stocco A, Schaaf CP. Marbach F, et al. Among authors: lichtarge o. Genet Med. 2021 Aug;23(8):1465-1473. doi: 10.1038/s41436-021-01152-7. Epub 2021 Apr 8. Genet Med. 2021. PMID: 33833410 Free PMC article.
Structure and evolutionary trace-assisted screening of a residue swapping the substrate ambiguity and chiral specificity in an esterase.
Cea-Rama I, Coscolín C, Katsonis P, Bargiela R, Golyshin PN, Lichtarge O, Ferrer M, Sanz-Aparicio J. Cea-Rama I, et al. Among authors: lichtarge o. Comput Struct Biotechnol J. 2021 Apr 18;19:2307-2317. doi: 10.1016/j.csbj.2021.04.041. eCollection 2021. Comput Struct Biotechnol J. 2021. PMID: 33995922 Free PMC article.
176 results