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Analysis and benchmarking of small and large genomic variants across tandem repeats.
English AC, Dolzhenko E, Ziaei Jam H, McKenzie SK, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. English AC, et al. Among authors: de coster w. Nat Biotechnol. 2024 Apr 26. doi: 10.1038/s41587-024-02225-z. Online ahead of print. Nat Biotechnol. 2024. PMID: 38671154
Towards population-scale long-read sequencing.
De Coster W, Weissensteiner MH, Sedlazeck FJ. De Coster W, et al. Nat Rev Genet. 2021 Sep;22(9):572-587. doi: 10.1038/s41576-021-00367-3. Epub 2021 May 28. Nat Rev Genet. 2021. PMID: 34050336 Free PMC article. Review.
Benchmarking of small and large variants across tandem repeats.
English A, Dolzhenko E, Jam HZ, Mckenzie S, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. English A, et al. Among authors: de coster w. bioRxiv [Preprint]. 2023 Nov 1:2023.10.29.564632. doi: 10.1101/2023.10.29.564632. bioRxiv. 2023. PMID: 37961319 Free PMC article. Updated. Preprint.
Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation.
Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SH, 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: de coster w. medRxiv [Preprint]. 2024 Mar 7:2024.03.05.24303792. doi: 10.1101/2024.03.05.24303792. medRxiv. 2024. PMID: 38496498 Free PMC article. Preprint.
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.
Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AA, Mahmoud M, Paulin LF, Raza MS, Pfeifer SP, Agustinho DP, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LC, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DM, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRR, Kubica J, Lakra P, Lattimer D, Liew CS, Lo BW, Lo C, Lötter A, Majidian S, Mendem SK, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon CL, Prabhakaran R, Saitou M, Sammi A, Sanio P, Sapoval N, Syed N, Treangen T, Wang G, Xu T, Yang J, Zhang S, Zhou W, Sedlazeck FJ, Busby B. Walker K, et al. Among authors: de coster w. F1000Res. 2022 May 16;11:530. doi: 10.12688/f1000research.110194.1. eCollection 2022. F1000Res. 2022. PMID: 36262335 Free PMC article.
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates.
Mc Cartney AM, Mahmoud M, Jochum M, Agustinho DP, Zorman B, Al Khleifat A, Dabbaghie F, K Kesharwani R, Smolka M, Dawood M, Albin D, Aliyev E, Almabrazi H, Arslan A, Balaji A, Behera S, Billingsley K, L Cameron D, Daw J, T Dawson E, De Coster W, Du H, Dunn C, Esteban R, Jolly A, Kalra D, Liao C, Liu Y, Lu TY, M Havrilla J, M Khayat M, Marin M, Monlong J, Price S, Rafael Gener A, Ren J, Sagayaradj S, Sapoval N, Sinner C, C Soto D, Soylev A, Subramaniyan A, Syed N, Tadimeti N, Tater P, Vats P, Vaughn J, Walker K, Wang G, Zeng Q, Zhang S, Zhao T, Kille B, Biederstedt E, Chaisson M, English A, Kronenberg Z, J Treangen T, Hefferon T, Chin CS, Busby B, J Sedlazeck F. Mc Cartney AM, et al. Among authors: de coster w. F1000Res. 2021 Mar 26;10:246. doi: 10.12688/f1000research.51477.2. eCollection 2021. F1000Res. 2021. PMID: 34621504 Free PMC article.
Newest Methods for Detecting Structural Variations.
De Coster W, Van Broeckhoven C. De Coster W, et al. Trends Biotechnol. 2019 Sep;37(9):973-982. doi: 10.1016/j.tibtech.2019.02.003. Epub 2019 Mar 19. Trends Biotechnol. 2019. PMID: 30902345 Free article. Review.
Critical length in long-read resequencing.
De Coster W, Strazisar M, De Rijk P. De Coster W, et al. Among authors: de rijk p. NAR Genom Bioinform. 2020 Jan 13;2(1):lqz027. doi: 10.1093/nargab/lqz027. eCollection 2020 Mar. NAR Genom Bioinform. 2020. PMID: 33575574 Free PMC article.
NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.
De Roeck A, De Coster W, Bossaerts L, Cacace R, De Pooter T, Van Dongen J, D'Hert S, De Rijk P, Strazisar M, Van Broeckhoven C, Sleegers K. De Roeck A, et al. Among authors: de coster w, de pooter t, de rijk p. Genome Biol. 2019 Nov 14;20(1):239. doi: 10.1186/s13059-019-1856-3. Genome Biol. 2019. PMID: 31727106 Free PMC article.
77 results