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Page 1
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.
Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, Schroth GP, Abaan OD, Talsania K, Lack J, Shen TW, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, Nguyen C, Petitjean V, Sultan M, Cam M, Mehta M, Hung T, Peters E, Kalamegham R, Sahraeian SME, Mohiyuddin M, Guo Y, Yao L, Song L, Lam HYK, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Jensen RV, Pirooznia M, Li Z, Xiao C, Sherry ST, Kusko R, Moos M, Donaldson E, Tezak Z, Ning B, Tong W, Li J, Duerken-Hughes P, Catalanotti C, Maheshwari S, Shuga J, Liang WS, Keats J, Adkins J, Tassone E, Zismann V, McDaniel T, Trent J, Foox J, Butler D, Mason CE, Hong H, Shi L, Wang C, Xiao W; Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium. Fang LT, et al. Among authors: donaldson e. Nat Biotechnol. 2021 Sep;39(9):1151-1160. doi: 10.1038/s41587-021-00993-6. Epub 2021 Sep 9. Nat Biotechnol. 2021. PMID: 34504347 Free PMC article.
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.
Xiao W, Ren L, Chen Z, Fang LT, Zhao Y, Lack J, Guan M, Zhu B, Jaeger E, Kerrigan L, Blomquist TM, Hung T, Sultan M, Idler K, Lu C, Scherer A, Kusko R, Moos M, Xiao C, Sherry ST, Abaan OD, Chen W, Chen X, Nordlund J, Liljedahl U, Maestro R, Polano M, Drabek J, Vojta P, Kõks S, Reimann E, Madala BS, Mercer T, Miller C, Jacob H, Truong T, Moshrefi A, Natarajan A, Granat A, Schroth GP, Kalamegham R, Peters E, Petitjean V, Walton A, Shen TW, Talsania K, Vera CJ, Langenbach K, de Mars M, Hipp JA, Willey JC, Wang J, Shetty J, Kriga Y, Raziuddin A, Tran B, Zheng Y, Yu Y, Cam M, Jailwala P, Nguyen C, Meerzaman D, Chen Q, Yan C, Ernest B, Mehra U, Jensen RV, Jones W, Li JL, Papas BN, Pirooznia M, Chen YC, Seifuddin F, Li Z, Liu X, Resch W, Wang J, Wu L, Yavas G, Miles C, Ning B, Tong W, Mason CE, Donaldson E, Lababidi S, Staudt LM, Tezak Z, Hong H, Wang C, Shi L. Xiao W, et al. Among authors: donaldson e. Nat Biotechnol. 2021 Sep;39(9):1141-1150. doi: 10.1038/s41587-021-00994-5. Epub 2021 Sep 9. Nat Biotechnol. 2021. PMID: 34504346 Free PMC article.
Assessing reproducibility of inherited variants detected with short-read whole genome sequencing.
Pan B, Ren L, Onuchic V, Guan M, Kusko R, Bruinsma S, Trigg L, Scherer A, Ning B, Zhang C, Glidewell-Kenney C, Xiao C, Donaldson E, Sedlazeck FJ, Schroth G, Yavas G, Grunenwald H, Chen H, Meinholz H, Meehan J, Wang J, Yang J, Foox J, Shang J, Miclaus K, Dong L, Shi L, Mohiyuddin M, Pirooznia M, Gong P, Golshani R, Wolfinger R, Lababidi S, Sahraeian SME, Sherry S, Han T, Chen T, Shi T, Hou W, Ge W, Zou W, Guo W, Bao W, Xiao W, Fan X, Gondo Y, Yu Y, Zhao Y, Su Z, Liu Z, Tong W, Xiao W, Zook JM, Zheng Y, Hong H. Pan B, et al. Among authors: donaldson e. Genome Biol. 2022 Jan 3;23(1):2. doi: 10.1186/s13059-021-02569-8. Genome Biol. 2022. PMID: 34980216 Free PMC article.
Standards for sequencing viral genomes in the era of high-throughput sequencing.
Ladner JT, Beitzel B, Chain PS, Davenport MG, Donaldson EF, Frieman M, Kugelman JR, Kuhn JH, O'Rear J, Sabeti PC, Wentworth DE, Wiley MR, Yu GY; Threat Characterization Consortium; Sozhamannan S, Bradburne C, Palacios G. Ladner JT, et al. Among authors: donaldson ef. mBio. 2014 Jun 17;5(3):e01360-14. doi: 10.1128/mBio.01360-14. mBio. 2014. PMID: 24939889 Free PMC article.
Enabling precision medicine via standard communication of HTS provenance, analysis, and results.
Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, Tsang H, Vora JK, Goecks J, Yao J, Almeida JS, Keeney J, Addepalli K, Krampis K, Smith KM, Guo L, Walderhaug M, Schito M, Ezewudo M, Guimera N, Walsh P, Kahsay R, Gottipati S, Rodwell TC, Bloom T, Lai Y, Simonyan V, Mazumder R. Alterovitz G, et al. Among authors: donaldson e. PLoS Biol. 2018 Dec 31;16(12):e3000099. doi: 10.1371/journal.pbio.3000099. eCollection 2018 Dec. PLoS Biol. 2018. PMID: 30596645 Free PMC article.
2018 Ebola virus disease outbreak in Équateur Province, Democratic Republic of the Congo: a retrospective genomic characterisation.
Mbala-Kingebeni P, Pratt CB, Wiley MR, Diagne MM, Makiala-Mandanda S, Aziza A, Di Paola N, Chitty JA, Diop M, Ayouba A, Vidal N, Faye O, Faye O, Karhemere S, Aruna A, Nsio J, Mulangu F, Mukadi D, Mukadi P, Kombe J, Mulumba A, Duraffour S, Likofata J, Pukuta E, Caviness K, Bartlett ML, Gonzalez J, Minogue T, Sozhamannan S, Gross SM, Schroth GP, Kuhn JH, Donaldson EF, Delaporte E, Sanchez-Lockhart M, Peeters M, Muyembe-Tamfum JJ, Alpha Sall A, Palacios G, Ahuka-Mundeke S. Mbala-Kingebeni P, et al. Among authors: donaldson ef. Lancet Infect Dis. 2019 Jun;19(6):641-647. doi: 10.1016/S1473-3099(19)30124-0. Epub 2019 Apr 15. Lancet Infect Dis. 2019. PMID: 31000465
402 results