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Items: 10

1.

A graph-based approach to diploid genome assembly.

Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T.

Bioinformatics. 2018 Jul 1;34(13):i105-i114. doi: 10.1093/bioinformatics/bty279.

2.

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.

Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A, Bishara A, Rosenkrantz JL, Lorig-Roach R, Field AR, Haeussler M, Russo L, Bhaduri A, Nowakowski TJ, Pollen AA, Dougherty ML, Nuttle X, Addor MC, Zwolinski S, Katzman S, Kriegstein A, Eichler EE, Salama SR, Jacobs FMJ, Haussler D.

Cell. 2018 May 31;173(6):1356-1369.e22. doi: 10.1016/j.cell.2018.03.051. Epub 2018 May 31.

PMID:
29856954
3.

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.

J Comput Biol. 2018 Jul;25(7):664-676. doi: 10.1089/cmb.2017.0248. Epub 2018 May 24.

PMID:
29792514
4.

Superbubbles, Ultrabubbles, and Cacti.

Paten B, Eizenga JM, Rosen YM, Novak AM, Garrison E, Hickey G.

J Comput Biol. 2018 Jul;25(7):649-663. doi: 10.1089/cmb.2017.0251. Epub 2018 Feb 20.

PMID:
29461862
5.

TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.

Newton Y, Novak AM, Swatloski T, McColl DC, Chopra S, Graim K, Weinstein AS, Baertsch R, Salama SR, Ellrott K, Chopra M, Goldstein TC, Haussler D, Morozova O, Stuart JM.

Cancer Res. 2017 Nov 1;77(21):e111-e114. doi: 10.1158/0008-5472.CAN-17-0580.

6.

A graph extension of the positional Burrows-Wheeler transform and its applications.

Novak AM, Garrison E, Paten B.

Algorithms Mol Biol. 2017 Jul 11;12:18. doi: 10.1186/s13015-017-0109-9. eCollection 2017.

7.

Genome graphs and the evolution of genome inference.

Paten B, Novak AM, Eizenga JM, Garrison E.

Genome Res. 2017 May;27(5):665-676. doi: 10.1101/gr.214155.116. Epub 2017 Mar 30. Review.

8.

Canonical, stable, general mapping using context schemes.

Novak AM, Rosen Y, Haussler D, Paten B.

Bioinformatics. 2015 Nov 15;31(22):3569-76. doi: 10.1093/bioinformatics/btv435. Epub 2015 Jul 27.

9.

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.

J Am Med Inform Assoc. 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047. Epub 2015 Jul 13.

10.

Modeling the role of negative cooperativity in metabolic regulation and homeostasis.

Bush EC, Clark AE, DeBoever CM, Haynes LE, Hussain S, Ma S, McDermott MB, Novak AM, Wentworth JS.

PLoS One. 2012;7(11):e48920. doi: 10.1371/journal.pone.0048920. Epub 2012 Nov 9. Erratum in: PLoS One. 2013;8(9). doi: 10.1371/annotation/0e4bae85-55dd-4235-a39b-38d02cfd481e. McDermott, Matthew M [corrected to McDermott, Matthew B A].

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