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2019 1
2020 1
2021 2
2022 4
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Page 1
Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting.
Gorzynski JE, Goenka SD, Shafin K, Jensen TD, Fisk DG, Grove ME, Spiteri E, Pesout T, Monlong J, Baid G, Bernstein JA, Ceresnak S, Chang PC, Christle JW, Chubb H, Dalton KP, Dunn K, Garalde DR, Guillory J, Knowles JW, Kolesnikov A, Ma M, Moscarello T, Nattestad M, Perez M, Ruzhnikov MRZ, Samadi M, Setia A, Wright C, Wusthoff CJ, Xiong K, Zhu T, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA. Gorzynski JE, et al. Among authors: pesout t. N Engl J Med. 2022 Feb 17;386(7):700-702. doi: 10.1056/NEJMc2112090. Epub 2022 Jan 12. N Engl J Med. 2022. PMID: 35020984 No abstract available.
Towards complete and error-free genome assemblies of all vertebrate species.
Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW 3rd, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED. Rhie A, et al. Among authors: pesout t. Nature. 2021 Apr;592(7856):737-746. doi: 10.1038/s41586-021-03451-0. Epub 2021 Apr 28. Nature. 2021. PMID: 33911273 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: pesout t. Genome Biol. 2019 Jun 3;20(1):116. doi: 10.1186/s13059-019-1709-0. Genome Biol. 2019. PMID: 31159868 Free PMC article.
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing.
Goenka SD, Gorzynski JE, Shafin K, Fisk DG, Pesout T, Jensen TD, Monlong J, Chang PC, Baid G, Bernstein JA, Christle JW, Dalton KP, Garalde DR, Grove ME, Guillory J, Kolesnikov A, Nattestad M, Ruzhnikov MRZ, Samadi M, Sethia A, Spiteri E, Wright CJ, Xiong K, Zhu T, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA. Goenka SD, et al. Among authors: pesout t. Nat Biotechnol. 2022 Jul;40(7):1035-1041. doi: 10.1038/s41587-022-01221-5. Epub 2022 Mar 28. Nat Biotechnol. 2022. PMID: 35347328 Free PMC article.
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: pesout t. 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.
Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock.
Gorzynski JE, Goenka SD, Shafin K, Jensen TD, Fisk DG, Grove ME, Spiteri E, Pesout T, Monlong J, Bernstein JA, Ceresnak S, Chang PC, Christle JW, Chubb H, Dunn K, Garalde DR, Guillory J, Ruzhnikov MRZ, Wright C, Wusthoff CJ, Xiong K, Hollander SA, Berry GJ, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA. Gorzynski JE, et al. Among authors: pesout t. Circ Genom Precis Med. 2022 Apr;15(2):e003591. doi: 10.1161/CIRCGEN.121.003591. Epub 2022 Feb 8. Circ Genom Precis Med. 2022. PMID: 35133172 No abstract available.
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: pesout t. 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.