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Page 1
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.
Keskus AG, 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, Bi C, Walter A, Gibson M, 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 AG, et al. Among authors: kolmogorov m. Nat Biotechnol. 2025 Apr 4. doi: 10.1038/s41587-025-02618-8. Online ahead of print. Nat Biotechnol. 2025. PMID: 40185952
Unraveling the hidden complexity of cancer through long-read sequencing.
Li Q, Keskus AG, Wagner J, Izydorczyk MB, Timp W, Sedlazeck FJ, Klein AP, Zook JM, Kolmogorov M, Schatz MC. Li Q, et al. Among authors: kolmogorov m. Genome Res. 2025 Apr 14;35(4):599-620. doi: 10.1101/gr.280041.124. Genome Res. 2025. PMID: 40113261 Free PMC article. Review.
Genetic regulation of TERT splicing affects cancer risk by altering cellular longevity and replicative potential.
Florez-Vargas O, Ho M, Hogshead MH, Papenberg BW, Lee CH, Forsythe K, Jones K, Luo W, Teshome K, Blauwendraat C, Billingsley KJ, Kolmogorov M, Meredith M, Paten B, Chari R, Zhang C, Schneekloth JS, Machiela MJ, Chanock SJ, Gadalla SM, Savage SA, Mbulaiteye SM, Prokunina-Olsson L. Florez-Vargas O, et al. Among authors: kolmogorov m. Nat Commun. 2025 Feb 16;16(1):1676. doi: 10.1038/s41467-025-56947-y. Nat Commun. 2025. PMID: 39956830 Free PMC article.
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection.
Negi S, Stenton SL, Berger SI, Canigiula P, 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: kolmogorov m. Am J Hum Genet. 2025 Feb 6;112(2):428-449. doi: 10.1016/j.ajhg.2025.01.002. Epub 2025 Jan 24. Am J Hum Genet. 2025. PMID: 39862869
Genetic regulation of TERT splicing contributes to reduced or elevated cancer risk by altering cellular longevity and replicative potential.
Florez-Vargas O, Ho M, Hogshead M, Lee CH, Papenberg BW, Forsythe K, Jones K, Luo W, Teshome K, Blauwendraat C, Billingsley KJ, Kolmogorov M, Meredith M, Paten B, Chari R, Zhang C, Schneekloth JS, Machiela MJ, Chanock SJ, Gadalla S, Savage SA, Mbulaiteye SM, Prokunina-Olsson L. Florez-Vargas O, et al. Among authors: kolmogorov m. medRxiv [Preprint]. 2024 Nov 5:2024.11.04.24316722. doi: 10.1101/2024.11.04.24316722. medRxiv. 2024. Update in: Nat Commun. 2025 Feb 16;16(1):1676. doi: 10.1038/s41467-025-56947-y. PMID: 39802763 Free PMC article. Updated. Preprint.
Successful classification of clinical pediatric leukemia genetic subtypes via structural variant detection using HiFi long-read sequencing.
Lansdon LA, Yoo B, Keskus A, Pushel I, Bi C, Ahmad T, Bryant A, Walter A, Gibson M, Rindler M, Li W, Habeebu SM, Cooley LD, Herriges J, Repnikova E, Zhang L, August KJ, Flatt TG, Gamis AS, Guest EM, Hays JA, Hetherington M, Lewing K, Pastinen T, Kolmogorov M, Farooqi MS. Lansdon LA, et al. Among authors: kolmogorov m. medRxiv [Preprint]. 2024 Nov 5:2024.11.05.24316078. doi: 10.1101/2024.11.05.24316078. medRxiv. 2024. PMID: 39802758 Free PMC article. Preprint.
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation.
Billingsley KJ, Meredith M, Daida K, Jerez PA, Negi S, Malik L, Genner RM, Moller A, Zheng X, Gibson SB, Mastoras M, Baker B, Kouam C, Paquette K, Jarreau P, Makarious MB, Moore A, Hong S, Vitale D, Shah S, Monlong J, Pantazis CB, Asri M, Shafin K, Carnevali P, Marenco S, Auluck P, Mandal A, Miga KH, Rhie A, Reed X, Ding J, Cookson MR, Nalls M, Singleton A, Miller DE, Chaisson M, Timp W, Gibbs JR, Phillippy AM, Kolmogorov M, Jain M, Sedlazeck FJ, Paten B, Blauwendraat C. Billingsley KJ, et al. Among authors: kolmogorov m. bioRxiv [Preprint]. 2024 Dec 17:2024.12.16.628723. doi: 10.1101/2024.12.16.628723. bioRxiv. 2024. PMID: 39764002 Free PMC article. Preprint.
The Utility of Long-Read Sequencing in Diagnosing Early Onset Parkinson's Disease.
Daida K, Yoshino H, Malik L, Baker B, Ishiguro M, Genner R, Paquette K, Li Y, Nishioka K, Masuzugawa S, Hirano M, Takahashi K, Kolmogorov M, Billingsley KJ, Funayama M, Blauwendraat C, Hattori N. Daida K, et al. Among authors: kolmogorov m. Ann Neurol. 2025 Apr;97(4):753-765. doi: 10.1002/ana.27155. Epub 2024 Dec 19. Ann Neurol. 2025. PMID: 39699073 Free PMC article.
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.
Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson ZB, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E; 1000 Genomes ONT Sequencing Consortium; University of Washington Center for Rare Disease Research (UW-CRDR); Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium; McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE. Gustafson JA, et al. Among authors: kolmogorov m. Genome Res. 2024 Nov 20;34(11):2061-2073. doi: 10.1101/gr.279273.124. Genome Res. 2024. PMID: 39358015 Free PMC article.
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: kolmogorov m. bioRxiv [Preprint]. 2024 Oct 18:2024.09.18.613544. doi: 10.1101/2024.09.18.613544. bioRxiv. 2024. PMID: 39345378 Free PMC article. Preprint.
40 results