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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: violich i. 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 Free PMC article.
Highly accurate assembly polishing with DeepPolisher.
Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K; and the Human Pangenome Reference Consortium. Mastoras M, et al. Genome Res. 2025 Jul 1;35(7):1595-1608. doi: 10.1101/gr.280149.124. Genome Res. 2025. PMID: 40389286
Multi-modality machine learning predicting Parkinson's disease.
Makarious MB, Leonard HL, Vitale D, Iwaki H, Sargent L, Dadu A, Violich I, Hutchins E, Saffo D, Bandres-Ciga S, Kim JJ, Song Y, Maleknia M, Bookman M, Nojopranoto W, Campbell RH, Hashemi SH, Botia JA, Carter JF, Craig DW, Van Keuren-Jensen K, Morris HR, Hardy JA, Blauwendraat C, Singleton AB, Faghri F, Nalls MA. Makarious MB, et al. Among authors: violich i. NPJ Parkinsons Dis. 2022 Apr 1;8(1):35. doi: 10.1038/s41531-022-00288-w. NPJ Parkinsons Dis. 2022. PMID: 35365675 Free PMC article.
Decreased SNCA Expression in Whole-Blood RNA Analysis of Parkinson's Disease Adjusting for Lymphocytes.
Xu K, Violich I, Hutchins E, Alsop E, Nalls MA, Blauwendraat C, Gibbs JR, Cookson MR, Moore A, Van Keuren-Jensen K, Craig DW. Xu K, et al. Among authors: violich i. bioRxiv [Preprint]. 2024 Nov 19:2024.11.18.623684. doi: 10.1101/2024.11.18.623684. bioRxiv. 2024. Update in: NPJ Parkinsons Dis. 2025 Oct 14;11(1):292. doi: 10.1038/s41531-025-01062-4. PMID: 39605721 Free PMC article. Updated. Preprint.
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, Gooden AA, Schmitt A, Sikkink K, Sedlazeck FJ, Doddapaneni H, Jhangiani SN, Muzny DM, Gingras MC, Mehta H, Behera S, Paulin LF, Hastie AR, Yu HC, Weigman V, Rojas A, Kennedy K, Remington J, Salas-González 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, Baybayan 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 GL, McCoy R, Brundu F, Sayyari E, Scheffler K, Truong S, Catreux S, Hannah LC, Lipson D, Benjamin H, Iremadze N, Soifer I, Krieger G, Eacker S, Wood M, Cross E, Husar G, Gross S, Vernich M, Kolmogorov M, Ahmad T, Keskus AG, Bryant A, Thibaud-Nissen F, Trow J, Proszynski J, Hirschberg JW, Ryon K, Mason CE, Bhakta MS, Sanborn JZ, Munding EM, Wagner J, Xiao C, Liss AS, Zook JM. McDaniel JH, et al. Among authors: violich i. Sci Data. 2025 Jul 16;12(1):1195. doi: 10.1038/s41597-025-05438-2. Sci Data. 2025. PMID: 40670386 Free PMC article.
The Foundational Data Initiative for Parkinson Disease: Enabling efficient translation from genetic maps to mechanism.
Bressan E, Reed X, Bansal V, Hutchins E, Cobb MM, Webb MG, Alsop E, Grenn FP, Illarionova A, Savytska N, Violich I, Broeer S, Fernandes N, Sivakumar R, Beilina A, Billingsley KJ, Berghausen J, Pantazis CB, Pitz V, Patel D, Daida K, Meechoovet B, Reiman R, Courtright-Lim A, Logemann A, Antone J, Barch M, Kitchen R, Li Y, Dalgard CL; American Genome Center; Rizzu P, Hernandez DG, Hjelm BE, Nalls M, Gibbs JR, Finkbeiner S, Cookson MR, Van Keuren-Jensen K, Craig DW, Singleton AB, Heutink P, Blauwendraat C. Bressan E, et al. Among authors: violich i. Cell Genom. 2023 Feb 6;3(3):100261. doi: 10.1016/j.xgen.2023.100261. eCollection 2023 Mar 8. Cell Genom. 2023. PMID: 36950378 Free PMC article.
Deep sequencing of sncRNAs reveals hallmarks and regulatory modules of the transcriptome during Parkinson's disease progression.
Kern F, Fehlmann T, Violich I, Alsop E, Hutchins E, Kahraman M, Grammes NL, Guimarães P, Backes C, Poston KL, Casey B, Balling R, Geffers L, Krüger R, Galasko D, Mollenhauer B, Meese E, Wyss-Coray T, Craig DW, Van Keuren-Jensen K, Keller A. Kern F, et al. Among authors: violich i. Nat Aging. 2021 Mar;1(3):309-322. doi: 10.1038/s43587-021-00042-6. Epub 2021 Mar 15. Nat Aging. 2021. PMID: 37118411
RNA sequencing of whole blood reveals early alterations in immune cells and gene expression in Parkinson's disease.
Craig DW, Hutchins E, Violich I, Alsop E, Gibbs JR, Levy S, Robison M, Prasad N, Foroud T, Crawford KL, Toga AW, Whitsett TG, Kim S, Casey B, Reimer A, Hutten SJ, Frasier M, Kern F, Fehlman T, Keller A, Cookson MR, Van Keuren-Jensen K; Parkinson Progression Marker Initiative. Craig DW, et al. Among authors: violich i. Nat Aging. 2021 Aug;1(8):734-747. doi: 10.1038/s43587-021-00088-6. Epub 2021 Aug 5. Nat Aging. 2021. PMID: 37117765
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection.
Negi S, Stenton SL, Berger SI, 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: violich i. medRxiv [Preprint]. 2024 Aug 22:2024.08.22.24312327. doi: 10.1101/2024.08.22.24312327. medRxiv. 2024. Update in: Am J Hum Genet. 2025 Feb 06;112(2):428-449. doi: 10.1016/j.ajhg.2025.01.002. PMID: 39228712 Free PMC article. Updated. Preprint.
13 results