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Page 1
Efficient dynamic variation graphs.
Eizenga JM, Novak AM, Kobayashi E, Villani F, Cisar C, Heumos S, Hickey G, Colonna V, Paten B, Garrison E. Eizenga JM, et al. Among authors: garrison e. Bioinformatics. 2021 Jan 29;36(21):5139-5144. doi: 10.1093/bioinformatics/btaa640. Bioinformatics. 2021. PMID: 33040146 Free PMC article.
Haplotype-aware graph indexes.
Sirén J, Garrison E, Novak AM, Paten B, Durbin R. Sirén J, et al. Among authors: garrison e. Bioinformatics. 2020 Jan 15;36(2):400-407. doi: 10.1093/bioinformatics/btz575. Bioinformatics. 2020. PMID: 31406990 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: garrison e. 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. Among authors: garrison e. 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.
ODGI: understanding pangenome graphs.
Guarracino A, Heumos S, Nahnsen S, Prins P, Garrison E. Guarracino A, et al. Among authors: garrison e. Bioinformatics. 2022 Jun 27;38(13):3319-3326. doi: 10.1093/bioinformatics/btac308. Bioinformatics. 2022. PMID: 35552372 Free PMC article.
Genome graphs and the evolution of genome inference.
Paten B, Novak AM, Eizenga JM, Garrison E. Paten B, et al. Among authors: garrison e. 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.
A graph-based approach to diploid genome assembly.
Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T. Garg S, et al. Among authors: garrison e. Bioinformatics. 2018 Jul 1;34(13):i105-i114. doi: 10.1093/bioinformatics/bty279. Bioinformatics. 2018. PMID: 29949989 Free PMC article.
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.
Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM, Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, Gupta N, Gabriel S, Blackwell TW, Ratan A, Taylor KD, Rich SS, Rotter JI, Haussler D, Garrison E, Paten B. Sirén J, et al. Among authors: garrison e. Science. 2021 Dec 17;374(6574):abg8871. doi: 10.1126/science.abg8871. Epub 2021 Dec 17. Science. 2021. PMID: 34914532 Free PMC article.
Superbubbles, Ultrabubbles, and Cacti.
Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E, Hickey G. Paten B, et al. Among authors: garrison e. 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.
205 results