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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PA, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, Pesout T, Prabakaran J, Carnevali P; North American Brain Expression Consortium (NABEC); Yang J, Rhie A, Scholz SW, Traynor BJ, Miga KH, Jain M, Timp W, Phillippy AM, Chaisson M, Sedlazeck FJ, Blauwendraat C, Paten B. Kolmogorov M, et al. Among authors: phillippy am. bioRxiv [Preprint]. 2023 Apr 5:2023.01.12.523790. doi: 10.1101/2023.01.12.523790. bioRxiv. 2023. PMID: 36711673 Free PMC article. Updated. Preprint.
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.
Sendell-Price AT, Tulenko FJ, Pettersson M, Kang D, Montandon M, Winkler S, Kulb K, Naylor GP, Phillippy A, Fedrigo O, Mountcastle J, Balacco JR, Dutra A, Dale RE, Haase B, Jarvis ED, Myers G, Burgess SM, Currie PD, Andersson L, Schartl M. Sendell-Price AT, et al. Nat Commun. 2023 Oct 19;14(1):6628. doi: 10.1038/s41467-023-42238-x. Nat Commun. 2023. PMID: 37857613 Free PMC article.
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.
Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Balacco JR, Chaisson M, Cheng H, Collins J, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, Formenti G. Larivière D, et al. Among authors: phillippy am. bioRxiv [Preprint]. 2023 Jun 30:2023.06.28.546576. doi: 10.1101/2023.06.28.546576. bioRxiv. 2023. PMID: 37425881 Free PMC article. Updated. Preprint.
A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.
Toh H, Yang C, Formenti G, Raja K, Yan L, Tracey A, Chow W, Howe K, Bergeron LA, Zhang G, Haase B, Mountcastle J, Fedrigo O, Fogg J, Kirilenko B, Munegowda C, Hiller M, Jain A, Kihara D, Rhie A, Phillippy AM, Swanson SA, Jiang P, Clegg DO, Jarvis ED, Thomson JA, Stewart R, Chaisson MJP, Bukhman YV. Toh H, et al. Among authors: phillippy am. BMC Biol. 2022 Nov 8;20(1):245. doi: 10.1186/s12915-022-01427-8. BMC Biol. 2022. PMID: 36344967 Free PMC article.
Population genomics of the critically endangered kākāpō.
Dussex N, van der Valk T, Morales HE, Wheat CW, Díez-Del-Molino D, von Seth J, Foster Y, Kutschera VE, Guschanski K, Rhie A, Phillippy AM, Korlach J, Howe K, Chow W, Pelan S, Mendes Damas JD, Lewin HA, Hastie AR, Formenti G, Fedrigo O, Guhlin J, Harrop TWR, Le Lec MF, Dearden PK, Haggerty L, Martin FJ, Kodali V, Thibaud-Nissen F, Iorns D, Knapp M, Gemmell NJ, Robertson F, Moorhouse R, Digby A, Eason D, Vercoe D, Howard J, Jarvis ED, Robertson BC, Dalén L. Dussex N, et al. Among authors: phillippy am. Cell Genom. 2021 Sep 8;1(1):100002. doi: 10.1016/j.xgen.2021.100002. eCollection 2021 Oct 13. Cell Genom. 2021. PMID: 36777713 Free PMC article.
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, 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. Kolmogorov M, et al. Among authors: phillippy am. Nat Methods. 2023 Oct;20(10):1483-1492. doi: 10.1038/s41592-023-01993-x. Epub 2023 Sep 14. Nat Methods. 2023. PMID: 37710018
Comparative genome assembly.
Pop M, Phillippy A, Delcher AL, Salzberg SL. Pop M, et al. Brief Bioinform. 2004 Sep;5(3):237-48. doi: 10.1093/bib/5.3.237. Brief Bioinform. 2004. PMID: 15383210
Comprehensive DNA signature discovery and validation.
Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL. Phillippy AM, et al. PLoS Comput Biol. 2007 May;3(5):e98. doi: 10.1371/journal.pcbi.0030098. Epub 2007 Apr 20. PLoS Comput Biol. 2007. PMID: 17511514 Free PMC article.
147 results