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2023 2
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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, 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. Nat Methods. 2023 Oct;20(10):1483-1492. doi: 10.1038/s41592-023-01993-x. Epub 2023 Sep 14. Nat Methods. 2023. PMID: 37710018 Free PMC article.
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. Nat Commun. 2025 Feb 16;16(1):1676. doi: 10.1038/s41467-025-56947-y. Nat Commun. 2025. PMID: 39956830 Free PMC article.
Assessing methylation detection for primary human tissue using Nanopore sequencing.
Genner R, Akeson S, Meredith M, Jerez PA, Malik L, Baker B, Miano-Burkhardt A; CARD-long-read Team; Paten B, Billingsley KJ, Blauwendraat C, Jain M. Genner R, et al. bioRxiv [Preprint]. 2024 Mar 1:2024.02.29.581569. doi: 10.1101/2024.02.29.581569. bioRxiv. 2024. Update in: Genome Res. 2025 Apr 14;35(4):632-643. doi: 10.1101/gr.279159.124. PMID: 38464144 Free PMC article. Updated. Preprint.
African ancestry neurodegeneration risk variant disrupts an intronic branchpoint in GBA1.
Álvarez Jerez P, Wild Crea P, Ramos DM, Gustavsson EK, Radefeldt M, Damianov A, Makarious MB, Ojo OO, Billingsley KJ, Malik L, Daida K, Bromberek S, Hu F, Schneider Z, Surapaneni AL, Stadler J, Rizig M, Morris HR, Pantazis CB, Leonard HL, Screven L, Qi YA, Nalls MA, Bandres-Ciga S, Hardy J, Houlden H, Eng C, Burchard EG, Kachuri L, Lin CH, Black DL; Global Parkinson’s Genetics Program (GP2); Singleton AB, Fischer S, Bauer P, Reed X, Ryten M, Beetz C, Ward M, Okubadejo NU, Blauwendraat C. Álvarez Jerez P, et al. Nat Struct Mol Biol. 2024 Dec;31(12):1955-1963. doi: 10.1038/s41594-024-01423-2. Epub 2024 Dec 12. Nat Struct Mol Biol. 2024. PMID: 39668204 Free PMC article.
The ZFHX3 GGC Repeat Expansion Underlying Spinocerebellar Ataxia Type 4 has a Common Ancestral Founder.
Chen Z, Alvarez Jerez P, Anderson C, Paucar M, Lee J, Nilsson D, Macpherson H, Scardamaglia A, Montgomery K, Hardy J, Singleton AB, Tucci A, Mathews KD, Fu YH, Engvall M, Laffita-Mesa J, Nennesmo I, Wedell A, Ptáček LJ, Blauwendraat C, Gustavsson EK, Svenningsson P, Ryten M, Houlden H. Chen Z, et al. Mov Disord. 2025 Feb;40(2):363-369. doi: 10.1002/mds.30077. Epub 2024 Dec 5. Mov Disord. 2025. PMID: 39635987 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, 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. bioRxiv [Preprint]. 2023 Apr 5:2023.01.12.523790. doi: 10.1101/2023.01.12.523790. bioRxiv. 2023. Update in: Nat Methods. 2023 Oct;20(10):1483-1492. doi: 10.1038/s41592-023-01993-x. PMID: 36711673 Free PMC article. Updated. 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. 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. 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.
13 results