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Personalized Pangenome References.
Sirén J, Eskandar P, Ungaro MT, Hickey G, Eizenga JM, Novak AM, Chang X, Chang PC, Kolmogorov M, Carroll A, Monlong J, Paten B. Sirén J, et al. Among authors: paten b. bioRxiv [Preprint]. 2023 Dec 15:2023.12.13.571553. doi: 10.1101/2023.12.13.571553. bioRxiv. 2023. PMID: 38168361 Free PMC article. Preprint.
Canonical, stable, general mapping using context schemes.
Novak AM, Rosen Y, Haussler D, Paten B. Novak AM, et al. Among authors: paten b. 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. 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. Among authors: paten b. 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.
Chromosome assembly of large and complex genomes using multiple references.
Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S. Kolmogorov M, et al. Among authors: paten b. Genome Res. 2018 Nov;28(11):1720-1732. doi: 10.1101/gr.236273.118. Epub 2018 Oct 19. Genome Res. 2018. PMID: 30341161 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: paten b. Bioinformatics. 2019 Dec 15;35(24):5318-5320. doi: 10.1093/bioinformatics/btz597. Bioinformatics. 2019. PMID: 31368484 Free PMC article.
179 results