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StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data.
Holt JM, Harting J, Chen X, Baker D, Saunders CT, Kronenberg Z, Gonzaludo N, Yoo B, Hudjashov G, Jõeloo M, Lawlor JMJ, Lim WK; Estonian Biobank Research Team; Jamuar SS, Cooper GM, Milani L, Pastinen T, Eberle MA. Holt JM, et al. Among authors: pastinen t. bioRxiv [Preprint]. 2024 Dec 11:2024.12.10.627527. doi: 10.1101/2024.12.10.627527. bioRxiv. 2024. PMID: 39713404 Free PMC article. Preprint.
Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort.
Cheung WA, Johnson AF, Rowell WJ, Farrow E, Hall R, Cohen ASA, Means JC, Zion TN, Portik DM, Saunders CT, Koseva B, Bi C, Truong TK, Schwendinger-Schreck C, Yoo B, Johnston JJ, Gibson M, Evrony G, Rizzo WB, Thiffault I, Younger ST, Curran T, Wenger AM, Grundberg E, Pastinen T. Cheung WA, et al. Among authors: pastinen t. Nat Commun. 2023 May 29;14(1):3090. doi: 10.1038/s41467-023-38782-1. Nat Commun. 2023. PMID: 37248219 Free PMC article.
Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans.
Guitart X, Porubsky D, Yoo D, Dougherty ML, Dishuck PC, Munson KM, Lewis AP, Hoekzema K, Knuth J, Chang S, Pastinen T, Eichler EE. Guitart X, et al. Among authors: pastinen t. bioRxiv [Preprint]. 2024 Mar 13:2024.03.12.584650. doi: 10.1101/2024.03.12.584650. bioRxiv. 2024. Update in: Genome Res. 2024 Nov 20;34(11):1798-1810. doi: 10.1101/gr.279299.124 PMID: 38654825 Free PMC article. Updated. Preprint.
A common flanking variant is associated with enhanced stability of the FGF14-SCA27B repeat locus.
Pellerin D, Del Gobbo GF, Couse M, Dolzhenko E, Nageshwaran SK, Cheung WA, Xu IRL, Dicaire MJ, Spurdens G, Matos-Rodrigues G, Stevanovski I, Scriba CK, Rebelo A, Roth V, Wandzel M, Bonnet C, Ashton C, Agarwal A, Peter C, Hasson D, Tsankova NM, Dewar K, Lamont PJ, Laing NG, Renaud M, Houlden H, Synofzik M, Usdin K, Nussenzweig A, Napierala M, Chen Z, Jiang H, Deveson IW, Ravenscroft G, Akbarian S, Eberle MA, Boycott KM, Pastinen T; All of Us Research Program Long Read Working Group; Brais B, Zuchner S, Danzi MC. Pellerin D, et al. Among authors: pastinen t. Nat Genet. 2024 Jul;56(7):1366-1370. doi: 10.1038/s41588-024-01808-5. Epub 2024 Jun 27. Nat Genet. 2024. PMID: 38937606 Free PMC article.
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: pastinen t. medRxiv [Preprint]. 2024 Nov 5:2024.11.05.24316078. doi: 10.1101/2024.11.05.24316078. medRxiv. 2024. PMID: 39802758 Free PMC article. Preprint.
Structural polymorphism and diversity of human segmental duplications.
Jeong H, Dishuck PC, Yoo D, Harvey WT, Munson KM, Lewis AP, Kordosky J, Garcia GH; Human Genome Structural Variation Consortium (HGSVC); Yilmaz F, Hallast P, Lee C, Pastinen T, Eichler EE. Jeong H, et al. Among authors: pastinen t. Nat Genet. 2025 Jan 8. doi: 10.1038/s41588-024-02051-8. Online ahead of print. Nat Genet. 2025. PMID: 39779957
Complex trait associations in rare diseases and impacts on Mendelian variant interpretation.
Smail C, Ge B, Keever-Keigher MR, Schwendinger-Schreck C, Cheung WA, Johnston JJ, Barrett C; Genomic Answers for Kids Consortium; Feldman K, Cohen ASA, Farrow EG, Thiffault I, Grundberg E, Pastinen T. Smail C, et al. Among authors: pastinen t. Nat Commun. 2024 Sep 18;15(1):8196. doi: 10.1038/s41467-024-52407-1. Nat Commun. 2024. PMID: 39294130 Free PMC article.
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.
Park J, Cook DE, Chang PC, Kolesnikov A, Brambrink L, Mier JC, Gardner J, McNulty B, Sacco S, Keskus A, Bryant A, Ahmad T, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Yoo B, Pushel I, Lansdon LA, Bi C, Walter A, Gibson M, Pastinen T, Farooqi MS, Robine N, Miga KH, Carroll A, Kolmogorov M, Paten B, Shafin K. Park J, et al. Among authors: pastinen t. bioRxiv [Preprint]. 2024 Aug 19:2024.08.16.608331. doi: 10.1101/2024.08.16.608331. bioRxiv. 2024. PMID: 39229187 Free PMC article. Preprint.
243 results