Publications

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Filters: Keyword is Nanopore Sequencing  [Clear All Filters]
2023
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PAlvarez, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P, Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nat Methods. 2023 ;20(10):1483-1492.
2022
Liu Y, Kearney J, Mahmoud M, Kille B, Sedlazeck FJ, Treangen TJ. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data. Nat Commun. 2022 ;13(1):1321.
2021
Baslan T, Kovaka S, Sedlazeck FJ, Zhang Y, Wappel R, Tian S, Lowe SW, Goodwin S, Schatz MC. High resolution copy number inference in cancer using short-molecule nanopore sequencing. Nucleic Acids Res. 2021 ;49(21):e124.
2020
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. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol. 2020 ;38(9):1044-1053.
Lee I, Razaghi R, Gilpatrick T, Molnar M, Gershman A, Sadowski N, Sedlazeck FJ, Hansen KD, Simpson JT, Timp W. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat Methods. 2020 ;17(12):1191-1199.
Gilpatrick T, Lee I, Graham JE, Raimondeau E, Bowen R, Heron A, Downs B, Sukumar S, Sedlazeck FJ, Timp W. Targeted nanopore sequencing with Cas9-guided adapter ligation. Nat Biotechnol. 2020 ;38(4):433-438.