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Page 1
Efficient indexing and querying of annotations in a pangenome graph.
Novak AM, Chung D, Hickey G, Djebali S, Yokoyama TT, Garrison E, Narzisi G, Paten B, Monlong J. Novak AM, et al. Among authors: paten b. bioRxiv [Preprint]. 2024 Oct 15:2024.10.12.618009. doi: 10.1101/2024.10.12.618009. bioRxiv. 2024. PMID: 39464141 Free PMC article. Preprint.
Complex genetic variation in nearly complete human genomes.
Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, Paisie CA, Harvey WT, Zhao X, Martino GV, Henglin M, Munson KM, Rabbani K, Chin CS, Gu B, Ashraf H, Austine-Orimoloye O, Balachandran P, Bonder MJ, Cheng H, Chong Z, Crabtree J, Gerstein M, Guethlein LA, Hasenfeld P, Hickey G, Hoekzema K, Hunt SE, Jensen M, Jiang Y, Koren S, Kwon Y, Li C, Li H, Li J, Norman PJ, Oshima KK, Paten B, Phillippy AM, Pollock NR, Rausch T, Rautiainen M, Scholz S, Song Y, Söylev A, Sulovari A, Surapaneni L, Tsapalou V, Zhou W, Zhou Y, Zhu Q, Zody MC, Mills RE, Devine SE, Shi X, Talkowski ME, Chaisson MJP, Dilthey AT, Konkel MK, Korbel JO, Lee C, Beck CR, Eichler EE, Marschall T. Logsdon GA, et al. Among authors: paten b. bioRxiv [Preprint]. 2024 Sep 25:2024.09.24.614721. doi: 10.1101/2024.09.24.614721. bioRxiv. 2024. PMID: 39372794 Free PMC article. Preprint.
Highly accurate assembly polishing with DeepPolisher.
Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K. Mastoras M, et al. Among authors: paten b. bioRxiv [Preprint]. 2024 Sep 19:2024.09.17.613505. doi: 10.1101/2024.09.17.613505. bioRxiv. 2024. PMID: 39345401 Free PMC article. Preprint.
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.
McDaniel JH, Patel V, Olson ND, He HJ, He Z, Cole KD, Schmitt A, Sikkink K, Sedlazeck FJ, Doddapaneni H, Jhangiani SN, Muzny DM, Gingras MC, Mehta H, Paulin LF, Hastie AR, Yu HC, Weigman V, Rojas A, Kennedy K, Remington J, Gonzalez I, Sudkamp M, Wiseman K, Lajoie BR, Levy S, Jain M, Akeson S, Narzisi G, Steinsnyder Z, Reeves C, Shelton J, Kingan SB, Lambert C, Bayabyan P, Wenger AM, McLaughlin IJ, Adamson A, Kingsley C, Wescott M, Kim Y, Paten B, Park J, Violich I, Miga KH, Gardner J, McNulty B, Rosen G, McCoy R, Brundu F, Sayyari E, Scheffler K, Truong S, Catreux S, Hannah LC, Lipson D, Benjamin H, Iremadze N, Soifer I, Eacker S, Wood M, Cross E, Husar G, Gross S, Vernich M, Kolmogorov M, Ahmad T, Keskus A, Bryant A, Thibaud-Nissen F, Trow J, Proszynski J, Hirschberg JW, Ryon K, Mason CE, Wagner J, Xiao C, Liss AS, Zook JM. McDaniel JH, et al. Among authors: paten b. bioRxiv [Preprint]. 2024 Oct 18:2024.09.18.613544. doi: 10.1101/2024.09.18.613544. bioRxiv. 2024. PMID: 39345378 Free PMC article. Preprint.
A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability.
Jadhav B, Garg P, van Vugt JJFA, Ibanez K, Gagliardi D, Lee W, Shadrina M, Mokveld T, Dolzhenko E, Martin-Trujillo A, Gies SJ, Altman G, Rocca C, Barbosa M, Jain M, Lahiri N, Lachlan K, Houlden H, Paten B; Genomics England Research Consortium; Project MinE ALS Sequencing Consortium; Veldink J, Tucci A, Sharp AJ. Jadhav B, et al. Among authors: paten b. Nat Genet. 2024 Nov;56(11):2322-2332. doi: 10.1038/s41588-024-01917-1. Epub 2024 Sep 23. Nat Genet. 2024. PMID: 39313615
Personalized pangenome references.
Sirén J, Eskandar P, Ungaro MT, Hickey G, Eizenga JM, Novak AM, Chang X, Chang PC, Kolmogorov M, Carroll A, Monlong J, Paten B. Sirén J, et al. Among authors: paten b. Nat Methods. 2024 Nov;21(11):2017-2023. doi: 10.1038/s41592-024-02407-2. Epub 2024 Sep 11. Nat Methods. 2024. PMID: 39261641
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.
Park J, Cook DE, Chang PC, Kolesnikov A, Brambrink L, Mier JC, Gardner J, McNulty B, Sacco S, Keskus A, Bryant A, Ahmad T, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Yoo B, Pushel I, Lansdon LA, Bi C, Walter A, Gibson M, Pastinen T, Farooqi MS, Robine N, Miga KH, Carroll A, Kolmogorov M, Paten B, Shafin K. Park J, et al. Among authors: paten b. bioRxiv [Preprint]. 2024 Aug 19:2024.08.16.608331. doi: 10.1101/2024.08.16.608331. bioRxiv. 2024. PMID: 39229187 Free PMC article. Preprint.
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection.
Negi S, Stenton SL, Berger SI, McNulty B, Violich I, Gardner J, Hillaker T, O'Rourke SM, O'Leary MC, Carbonell E, Austin-Tse C, Lemire G, Serrano J, Mangilog B, VanNoy G, Kolmogorov M, Vilain E, O'Donnell-Luria A, Délot E, Miga KH, Monlong J, Paten B. Negi S, et al. Among authors: paten b. medRxiv [Preprint]. 2024 Aug 22:2024.08.22.24312327. doi: 10.1101/2024.08.22.24312327. medRxiv. 2024. PMID: 39228712 Free PMC article. Preprint.
Complete sequencing of ape genomes.
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Roha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT… See abstract for full author list ➔ Yoo D, et al. Among authors: paten b. bioRxiv [Preprint]. 2024 Oct 5:2024.07.31.605654. doi: 10.1101/2024.07.31.605654. bioRxiv. 2024. PMID: 39131277 Free PMC article. Preprint.
Local read haplotagging enables accurate long-read small variant calling.
Kolesnikov A, Cook D, Nattestad M, Brambrink L, McNulty B, Gorzynski J, Goenka S, Ashley EA, Jain M, Miga KH, Paten B, Chang PC, Carroll A, Shafin K. Kolesnikov A, et al. Among authors: paten b. Nat Commun. 2024 Jul 13;15(1):5907. doi: 10.1038/s41467-024-50079-5. Nat Commun. 2024. PMID: 39003259 Free PMC article.
191 results