Publications

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Filters: Author is Farek, Jesse  [Clear All Filters]
2023
Behera S, LeFaive J, Orchard P, Mahmoud M, Paulin LF, Farek J, Soto DC, Parker SCJ, Smith AV, Dennis MY, Zook JM, Sedlazeck FJ. FixItFelix: improving genomic analysis by fixing reference errors. Genome Biol. 2023 ;24(1):31.
2022
Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, Schatz MC, Narzisi G, Byrska-Bishop M, Clarke W, Evani US, Markello C, Shafin K, Zhou X, Sidow A, Bansal V, Ebert P, Marschall T, Lansdorp P, Hanlon V, Mattsson C-A, Barrio AMartinez, Fiddes IT, Xiao C, Fungtammasan A, Chin C-S, Wenger AM, Rowell WJ, Sedlazeck FJ, Carroll A, Salit M, Zook JM. Benchmarking challenging small variants with linked and long reads. Cell Genom. 2022 ;2(5).
Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, Fungtammasan A, Hwang Y-C, Gupta R, Wenger AM, Rowell WJ, Khan ZM, Farek J, Zhu Y, Pisupati A, Mahmoud M, Xiao C, Yoo B, Sahraeian SMohammad E, Miller DE, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Narzisi G, Evani UShanker, Clarke WE, Lee J, Mason CE, Lincoln SE, Miga KH, Ebbert MTW, Shumate A, Li H, Chin C-S, Zook JM, Sedlazeck FJ. Curated variation benchmarks for challenging medically relevant autosomal genes. Nat Biotechnol. 2022 ;40(5):672-680.
Farek J, Hughes D, Salerno W, Zhu Y, Pisupati A, Mansfield A, Krasheninina O, English AC, Metcalf GA, Boerwinkle E, Muzny DM, Gibbs RA, Khan Z, Sedlazeck FJ. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments. Gigascience. 2022 ;12.
2020
Chin C-S, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautiainen M, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, Sedlazeck FJ, Bansal V, Yoo B, Miller N, Zhou X, Carroll A, Barrio AMartinez, Salit M, Marschall T, Dilthey AT, Zook JM. A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nat Commun. 2020 ;11(1):4794.