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Page 1
Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads.
Keskus A, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M. Keskus A, et al. Among authors: miga kh. medRxiv [Preprint]. 2024 Mar 26:2024.03.22.24304756. doi: 10.1101/2024.03.22.24304756. medRxiv. 2024. PMID: 38585974 Free PMC article. Preprint.
Comparative genomics of macaques and integrated insights into genetic variation and population history.
Zhang S, Xu N, Fu L, Yang X, Li Y, Yang Z, Feng Y, Ma K, Jiang X, Han J, Hu R, Zhang L, de Gennaro L, Ryabov F, Meng D, He Y, Wu D, Yang C, Paparella A, Mao Y, Bian X, Lu Y, Antonacci F, Ventura M, Shepelev VA, Miga KH, Alexandrov IA, Logsdon GA, Phillippy AM, Su B, Zhang G, Eichler EE, Lu Q, Shi Y, Sun Q, Mao Y. Zhang S, et al. Among authors: miga kh. bioRxiv [Preprint]. 2024 Apr 8:2024.04.07.588379. doi: 10.1101/2024.04.07.588379. bioRxiv. 2024. PMID: 38645259 Free PMC article. Preprint.
The complete sequence and comparative analysis of ape sex chromosomes.
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bornberg-Bauer E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Pond SLK, LaPolice TM, Lee C, Lewis AP, Loh YE, Masterson P, McGarvey KM, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O'Neill RJ, Eichler EE, Phillippy AM. Makova KD, et al. Among authors: miga kh. Nature. 2024 May 29. doi: 10.1038/s41586-024-07473-2. Online ahead of print. Nature. 2024. PMID: 38811727
Phased nanopore assembly with Shasta and modular graph phasing with GFAse.
Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen HE, McNulty B, Porubsky D, Montague TG, Lucas JK, Condon C, Eizenga JM, Juul S, McKenzie SK, Simmonds SE, Park J, Asri M, Koren S, Eichler EE, Axel R, Martin B, Carnevali P, Miga KH, Paten B. Lorig-Roach R, et al. Among authors: miga kh. Genome Res. 2024 Apr 25;34(3):454-468. doi: 10.1101/gr.278268.123. Genome Res. 2024. PMID: 38627094
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautiainen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, Ware D, Schatz MC, Garrison E, Huang S, McCombie WR, Miga KH, Wittenberg AHJ, Phillippy AM. Koren S, et al. Among authors: miga kh. bioRxiv [Preprint]. 2024 Mar 19:2024.03.15.585294. doi: 10.1101/2024.03.15.585294. bioRxiv. 2024. PMID: 38529488 Free PMC article. Preprint.
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O'Neill RJ, Eichler E, Phillippy AM. Makova KD, et al. Among authors: miga kh. bioRxiv [Preprint]. 2023 Dec 1:2023.11.30.569198. doi: 10.1101/2023.11.30.569198. bioRxiv. 2023. PMID: 38077089 Free PMC article. Preprint.
The UCSC Genome Browser database: 2024 update.
Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, Diekhans M, Fischer C, Navarro Gonzalez J, Hickey G, Hinrichs AS, Kuhn RM, Lee BT, Lee CM, Le Mercier P, Miga KH, Nassar LR, Nejad P, Paten B, Perez G, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kent WJ, Haeussler M. Raney BJ, et al. Among authors: miga kh. Nucleic Acids Res. 2024 Jan 5;52(D1):D1082-D1088. doi: 10.1093/nar/gkad987. Nucleic Acids Res. 2024. PMID: 37953330 Free PMC article.
67 results