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PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.
Olson ND, Wagner J, McDaniel J, Stephens SH, Westreich ST, Prasanna AG, Johanson E, Boja E, Maier EJ, Serang O, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Kyriakidis K, Malousi A, Shafin K, Pesout T, Jain M, Paten B, Chang PC, Kolesnikov A, Nattestad M, Baid G, Goel S, Yang H, Carroll A, Eveleigh R, Bourgey M, Bourque G, Li G, Ma C, Tang L, Du Y, Zhang S, Morata J, Tonda R, Parra G, Trotta JR, Brueffer C, Demirkaya-Budak S, Kabakci-Zorlu D, Turgut D, Kalay Ö, Budak G, Narcı K, Arslan E, Brown R, Johnson IJ, Dolgoborodov A, Semenyuk V, Jain A, Tetikol HS, Jain V, Ruehle M, Lajoie B, Roddey C, Catreux S, Mehio R, Ahsan MU, Liu Q, Wang K, Sahraeian SME, Fang LT, Mohiyuddin M, Hung C, Jain C, Feng H, Li Z, Chen L, Sedlazeck FJ, Zook JM. Olson ND, et al. Among authors: paten b. Cell Genom. 2022 May 11;2(5):100129. doi: 10.1016/j.xgen.2022.100129. Epub 2022 Apr 27. Cell Genom. 2022. PMID: 35720974 Free PMC article.
Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research.
Ahalt S, Avillach P, Boyles R, Bradford K, Cox S, Davis-Dusenbery B, Grossman RL, Krishnamurthy A, Manning A, Paten B, Philippakis A, Borecki I, Chen SH, Kaltman J, Ladwa S, Schwartz C, Thomson A, Davis S, Leaf A, Lyons J, Sheets E, Bis JC, Conomos M, Culotti A, Desain T, Digiovanna J, Domazet M, Gogarten S, Gutierrez-Sacristan A, Harris T, Heavner B, Jain D, O'Connor B, Osborn K, Pillion D, Pleiness J, Rice K, Rupp G, Serret-Larmande A, Smith A, Stedman JP, Stilp A, Barsanti T, Cheadle J, Erdmann C, Farlow B, Gartland-Gray A, Hayes J, Hiles H, Kerr P, Lenhardt C, Madden T, Mieczkowska JO, Miller A, Patton P, Rathbun M, Suber S, Asare J. Ahalt S, et al. Among authors: paten b. J Am Med Inform Assoc. 2023 Jun 20;30(7):1293-1300. doi: 10.1093/jamia/ocad048. J Am Med Inform Assoc. 2023. PMID: 37192819 Free PMC article.
Improved data analysis for the MinION nanopore sequencer.
Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Jain M, et al. Among authors: paten b. Nat Methods. 2015 Apr;12(4):351-6. doi: 10.1038/nmeth.3290. Epub 2015 Feb 16. Nat Methods. 2015. PMID: 25686389 Free PMC article.
Mapping DNA methylation with high-throughput nanopore sequencing.
Rand AC, Jain M, Eizenga JM, Musselman-Brown A, Olsen HE, Akeson M, Paten B. Rand AC, et al. Among authors: paten b. Nat Methods. 2017 Apr;14(4):411-413. doi: 10.1038/nmeth.4189. Epub 2017 Feb 20. Nat Methods. 2017. PMID: 28218897 Free PMC article.
Haplotype-aware diplotyping from noisy long reads.
Ebler J, Haukness M, Pesout T, Marschall T, Paten B. Ebler J, et al. Among authors: paten b. Genome Biol. 2019 Jun 3;20(1):116. doi: 10.1186/s13059-019-1709-0. Genome Biol. 2019. PMID: 31159868 Free PMC article.
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B. Shafin K, et al. Among authors: paten b. Nat Biotechnol. 2020 Sep;38(9):1044-1053. doi: 10.1038/s41587-020-0503-6. Epub 2020 May 4. Nat Biotechnol. 2020. PMID: 32686750 Free PMC article.
A strategy for building and using a human reference pangenome.
Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Marschall T, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Rautiainen M, Regier A, Sedlazeck FJ, Siren J, Souilmi Y, Wagner J, Wrightsman T, Yokoyama TT, Zeng Q, Zook JM, Paten B, Busby B. Llamas B, et al. Among authors: paten b. F1000Res. 2019 Oct 14;8:1751. doi: 10.12688/f1000research.19630.2. eCollection 2019. F1000Res. 2019. PMID: 34386196 Free PMC article.
179 results