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PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
PLoS Comput Biol. 2021 Aug 9;17(8):e1008844. doi: 10.1371/journal.pcbi.1008844. eCollection 2021 Aug.
PLoS Comput Biol. 2021.
PMID: 34370723
Free PMC article.
Computational discovery of direct associations between GO terms and protein domains.
Alborzi SZ, Ritchie DW, Devignes MD.
Alborzi SZ, et al.
BMC Bioinformatics. 2018 Nov 20;19(Suppl 14):413. doi: 10.1186/s12859-018-2380-2.
BMC Bioinformatics. 2018.
PMID: 30453875
Free PMC article.
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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: alborzi sz.
Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.
Genome Biol. 2019.
PMID: 31744546
Free PMC article.
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ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains.
Alborzi SZ, Devignes MD, Ritchie DW.
Alborzi SZ, et al.
BMC Bioinformatics. 2017 Feb 13;18(1):107. doi: 10.1186/s12859-017-1519-x.
BMC Bioinformatics. 2017.
PMID: 28193156
Free PMC article.
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A structure-based classification and analysis of protein domain family binding sites and their interactions.
Ghoorah AW, Devignes MD, Alborzi SZ, Smaïl-Tabbone M, Ritchie DW.
Ghoorah AW, et al. Among authors: alborzi sz.
Biology (Basel). 2015 Apr 9;4(2):327-43. doi: 10.3390/biology4020327.
Biology (Basel). 2015.
PMID: 25860777
Free PMC article.
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