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Page 1
A draft human pangenome reference.
Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichl… See abstract for full author list ➔ Liao WW, et al. Among authors: novak am. Nature. 2023 May;617(7960):312-324. doi: 10.1038/s41586-023-05896-x. Epub 2023 May 10. Nature. 2023. PMID: 37165242 Free PMC article.
The NIH BD2K center for big data in translational genomics.
Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van't Veer L, Wold B, Haussler D. Paten B, et al. Among authors: novak am. J Am Med Inform Assoc. 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047. Epub 2015 Jul 13. J Am Med Inform Assoc. 2015. PMID: 26174866 Free PMC article.
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.
44 results