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A complete pedigree-based graph workflow for rare candidate variant analysis.
Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B. Markello C, et al. Among authors: eizenga j. Genome Res. 2022 May;32(5):893-903. doi: 10.1101/gr.276387.121. Epub 2022 Apr 28. Genome Res. 2022. PMID: 35483961 Free PMC article.
Genome graphs and the evolution of genome inference.
Paten B, Novak AM, Eizenga JM, Garrison E. Paten B, et al. Genome Res. 2017 May;27(5):665-676. doi: 10.1101/gr.214155.116. Epub 2017 Mar 30. Genome Res. 2017. PMID: 28360232 Free PMC article. Review.
Superbubbles, Ultrabubbles, and Cacti.
Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E, Hickey G. Paten B, et al. J Comput Biol. 2018 Jul;25(7):649-663. doi: 10.1089/cmb.2017.0251. Epub 2018 Feb 20. J Comput Biol. 2018. PMID: 29461862 Free PMC article.
A Flow Procedure for Linearization of Genome Sequence Graphs.
Haussler D, Smuga-Otto M, Eizenga JM, Paten B, Novak AM, Nikitin S, Zueva M, Miagkov D. Haussler D, et al. J Comput Biol. 2018 Jul;25(7):664-676. doi: 10.1089/cmb.2017.0248. Epub 2018 May 24. J Comput Biol. 2018. PMID: 29792514 Free PMC article.
Genotyping structural variants in pangenome graphs using the vg toolkit.
Hickey G, Heller D, Monlong J, Sibbesen JA, Sirén J, Eizenga J, Dawson ET, Garrison E, Novak AM, Paten B. Hickey G, et al. Among authors: eizenga j. Genome Biol. 2020 Feb 12;21(1):35. doi: 10.1186/s13059-020-1941-7. Genome Biol. 2020. PMID: 32051000 Free PMC article.
Pangenome Graphs.
Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Sirén J, Garrison E. Eizenga JM, et al. Annu Rev Genomics Hum Genet. 2020 Aug 31;21:139-162. doi: 10.1146/annurev-genom-120219-080406. Epub 2020 May 26. Annu Rev Genomics Hum Genet. 2020. PMID: 32453966 Free PMC article. Review.
31 results