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Phased nanopore assembly with Shasta and modular graph phasing with GFAse.
Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen H, McNulty B, Porubsky D, Montague T, Lucas J, Condon C, Eizenga J, Juul S, McKenzie S, Simmonds SE, Park J, Asri M, Koren S, Eichler E, Axel R, Martin B, Carnevali P, Miga K, Paten B. Lorig-Roach R, et al. Among authors: mcnulty b. bioRxiv [Preprint]. 2023 Feb 22:2023.02.21.529152. doi: 10.1101/2023.02.21.529152. bioRxiv. 2023. PMID: 36865218 Free PMC article. Updated. Preprint.
Local read haplotagging enables accurate long-read small variant calling.
Kolesnikov A, Cook D, Nattestad M, 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: mcnulty b. bioRxiv [Preprint]. 2023 Sep 12:2023.09.07.556731. doi: 10.1101/2023.09.07.556731. bioRxiv. 2023. PMID: 37745389 Free PMC article. Preprint.
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: mcnulty b. bioRxiv [Preprint]. 2024 Mar 19:2024.03.15.585294. doi: 10.1101/2024.03.15.585294. bioRxiv. 2024. PMID: 38529488 Free PMC article. Preprint.
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: mcnulty b. medRxiv [Preprint]. 2024 Mar 26:2024.03.22.24304756. doi: 10.1101/2024.03.22.24304756. medRxiv. 2024. PMID: 38585974 Free PMC article. Preprint.
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: mcnulty b. Genome Res. 2024 Apr 25;34(3):454-468. doi: 10.1101/gr.278268.123. Genome Res. 2024. PMID: 38627094
Obesity is South Africa's new HIV epidemic.
Chandiwana N, Venter W, Manne-Goehler J, Wade A, Le Roux C, Mbalati N, Grimbeek A, Kruger P, Montsho E, Zimela Z, Yawa A, Tshabalala S, Rambau N, Mpofu N, Stevenson S, McNulty B, Ntusi N, Pillay Y, Dave J, Murphy A, Goldstein S, Hfman K, Mahomedy S, Thomas E, Mrara B, Wing J, Lubbe J, Koto Z, Conradie-Smit M, Wharton S, May W, Marr I, Kaplan H, Forgan M, Alexander G, Turner J, Fourie VR, Hellig J, Banks M, Ragsdale K, Noeth M, Mohamed F, Myer L, Lebina L, Maswime S, Moosa Y, Thomas S, Mbelle M, Sinxadi P, Bekker LG, Bhana S, Fabian J, Decloedt E, Bayat Z, Daya R, Bobat B, Storie F, Goedecke J, Kahn K, Tollman S, Mansfield B, Siedner M, Marconi V, Mody A, Mtshali N, Geng E, Srinivasa S, Ali M, Lalla-Edwards S, Bentley A, Wolvaardt G, Hill A, Nel J. Chandiwana N, et al. Among authors: mcnulty b. S Afr Med J. 2024 Mar 18;114(3):e1927. doi: 10.7196/SAMJ.2024.v114i3.1927. S Afr Med J. 2024. PMID: 38525565 Free article. No abstract available.
Bringing an end to diabetes stigma and discrimination: an international consensus statement on evidence and recommendations.
Speight J, Holmes-Truscott E, Garza M, Scibilia R, Wagner S, Kato A, Pedrero V, Deschênes S, Guzman SJ, Joiner KL, Liu S, Willaing I, Babbott KM, Cleal B, Dickinson JK, Halliday JA, Morrissey EC, Nefs G, O'Donnell S, Serlachius A, Winterdijk P, Alzubaidi H, Arifin B, Cambron-Kopco L, Santa Ana C, Davidsen E, de Groot M, de Wit M, Deroze P, Haack S, Holt RIG, Jensen W, Khunti K, Kragelund Nielsen K, Lathia T, Lee CJ, McNulty B, Naranjo D, Pearl RL, Prinjha S, Puhl RM, Sabidi A, Selvan C, Sethi J, Seyam M, Sturt J, Subramaniam M, Terkildsen Maindal H, Valentine V, Vallis M, Skinner TC. Speight J, et al. Among authors: mcnulty b. Lancet Diabetes Endocrinol. 2024 Jan;12(1):61-82. doi: 10.1016/S2213-8587(23)00347-9. Lancet Diabetes Endocrinol. 2024. PMID: 38128969 Review.
205 results