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Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.
Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ. Meisel JS, et al. Among authors: ghurye j. Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5. Microbiome. 2018. PMID: 30396371 Free PMC article.
A critical assessment of gene catalogs for metagenomic analysis.
Commichaux S, Shah N, Ghurye J, Stoppel A, Goodheart JA, Luque GG, Cummings MP, Pop M. Commichaux S, et al. Among authors: ghurye j. Bioinformatics. 2021 Sep 29;37(18):2848-2857. doi: 10.1093/bioinformatics/btab216. Bioinformatics. 2021. PMID: 33792639 Free PMC article.
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.
Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Myer PR, Ghurye J, Pop M, Weimer PJ, Phillippy AM, Smith TPL. Bickhart DM, et al. Among authors: ghurye j. Genome Biol. 2019 Aug 2;20(1):153. doi: 10.1186/s13059-019-1760-x. Genome Biol. 2019. PMID: 31375138 Free PMC article.
Semi-automated assembly of high-quality diploid human reference genomes.
Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton RS, Fulton LL, Garg S, Gerton JL, Ghurye J, Granat A, Green RE, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger EB, Jain M, Kirsche M, Kolmogorov M, Korbel JO, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell MW, McDaniel J, Nie F, Olsen HE, Olson ND, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg SL, Sanders AD, Schatz MC, Schmitt A, Schneider VA, Selvaraj S, Shafin K, Shumate A, Stitziel NO, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin AV, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook JM, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH; Human Pangenome Reference Consortium. Jarvis ED, et al. Among authors: ghurye j. Nature. 2022 Nov;611(7936):519-531. doi: 10.1038/s41586-022-05325-5. Epub 2022 Oct 19. Nature. 2022. PMID: 36261518 Free PMC article.
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