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Canonical, stable, general mapping using context schemes.
Novak AM, Rosen Y, Haussler D, Paten B. Novak AM, et al. Bioinformatics. 2015 Nov 15;31(22):3569-76. doi: 10.1093/bioinformatics/btv435. Epub 2015 Jul 27. Bioinformatics. 2015. PMID: 26220960 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: novak am. 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.
Toil enables reproducible, open source, big biomedical data analyses.
Vivian J, Rao AA, Nothaft FA, Ketchum C, Armstrong J, Novak A, Pfeil J, Narkizian J, Deran AD, Musselman-Brown A, Schmidt H, Amstutz P, Craft B, Goldman M, Rosenbloom K, Cline M, O'Connor B, Hanna M, Birger C, Kent WJ, Patterson DA, Joseph AD, Zhu J, Zaranek S, Getz G, Haussler D, Paten B. Vivian J, et al. Nat Biotechnol. 2017 Apr 11;35(4):314-316. doi: 10.1038/nbt.3772. Nat Biotechnol. 2017. PMID: 28398314 Free PMC article. No abstract available.
Superbubbles, Ultrabubbles, and Cacti.
Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E, Hickey G. Paten B, et al. Among authors: novak am. 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. Among authors: novak am. 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.
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: novak am. Bioinformatics. 2018 Jul 1;34(13):i105-i114. doi: 10.1093/bioinformatics/bty279. Bioinformatics. 2018. PMID: 29949989 Free PMC article.
Sequence tube maps: making graph genomes intuitive to commuters.
Beyer W, Novak AM, Hickey G, Chan J, Tan V, Paten B, Zerbino DR. Beyer W, et al. Among authors: novak am. Bioinformatics. 2019 Dec 15;35(24):5318-5320. doi: 10.1093/bioinformatics/btz597. Bioinformatics. 2019. PMID: 31368484 Free PMC article.
Haplotype-aware graph indexes.
Sirén J, Garrison E, Novak AM, Paten B, Durbin R. Sirén J, et al. Among authors: novak am. Bioinformatics. 2020 Jan 15;36(2):400-407. doi: 10.1093/bioinformatics/btz575. Bioinformatics. 2020. PMID: 31406990 Free PMC article.
54 results