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Assessment of the evidence yield for the calibrated PP3/BP4 computational recommendations.
Stenton SL, Pejaver V, Bergquist T, Biesecker LG, Byrne AB, Nadeau E, Greenblatt MS, Harrison S, Tavtigian S, Radivojac P, Brenner SE, O'Donnell-Luria A. Stenton SL, et al. Among authors: brenner se. medRxiv [Preprint]. 2024 Mar 7:2024.03.05.24303807. doi: 10.1101/2024.03.05.24303807. medRxiv. 2024. PMID: 38496501 Free PMC article. Preprint.
Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria.
Pejaver V, Byrne AB, Feng BJ, Pagel KA, Mooney SD, Karchin R, O'Donnell-Luria A, Harrison SM, Tavtigian SV, Greenblatt MS, Biesecker LG, Radivojac P, Brenner SE; ClinGen Sequence Variant Interpretation Working Group. Pejaver V, et al. Among authors: brenner se. Am J Hum Genet. 2022 Dec 1;109(12):2163-2177. doi: 10.1016/j.ajhg.2022.10.013. Epub 2022 Nov 21. Am J Hum Genet. 2022. PMID: 36413997 Free PMC article.
Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer.
Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, Sun Y, Shen Y, Garg A, Pal D, Yu Y, Huff CD, Tavtigian SV, Young E, Neuhausen SL, Ziv E, Pal LR, Andreoletti G, Brenner SE, Kann MG. Voskanian A, et al. Among authors: brenner se. Hum Mutat. 2019 Sep;40(9):1612-1622. doi: 10.1002/humu.23849. Epub 2019 Aug 17. Hum Mutat. 2019. PMID: 31241222 Free PMC article.
Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016.
Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Mooney SD, Nodzak C, Pal LR, Radivojac P, Savojardo C, Shi X, Zhou Y, Uppal A, Xu Q, Yin Y, Pejaver V, Wang M, Wei L, Moult J, Yu GK, Brenner SE, LeBowitz JH. Clark WT, et al. Among authors: brenner se. Hum Mutat. 2019 Sep;40(9):1519-1529. doi: 10.1002/humu.23875. Hum Mutat. 2019. PMID: 31342580 Free PMC article.
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, Lar… See abstract for full author list ➔ Zhou N, et al. Among authors: brenner se. Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8. Genome Biol. 2019. PMID: 31744546 Free PMC article.
Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat RR, Li X, Pal LR, Kundu K, Yin Y, Moult J, Jiang Y, Pejaver V, Pagel KA, Li B, Mooney SD, Radivojac P, Shah S, Carraro M, Gasparini A, Leonardi E, Giollo M, Ferrari C, Tosatto SCE, Bachar E, Azaria JR, Ofran Y, Unger R, Niroula A, Vihinen M, Chang B, Wang MH, Franke A, Petersen BS, Pirooznia M, Zandi P, McCombie R, Potash JB, Altman RB, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA. Daneshjou R, et al. Among authors: brenner se. Hum Mutat. 2017 Sep;38(9):1182-1192. doi: 10.1002/humu.23280. Epub 2017 Jul 7. Hum Mutat. 2017. PMID: 28634997 Free PMC article.
186 results