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Items: 1 to 20 of 37

1.

DATA SHARING AND REPRODUCIBLE CLINICAL GENETIC TESTING: SUCCESSES AND CHALLENGES.

Yang S, Cline M, Zhang C, Paten B, Lincoln SE.

Pac Symp Biocomput. 2016;22:166-176.

2.

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community.

Jain M, Olsen HE, Paten B, Akeson M.

Genome Biol. 2016 Nov 25;17(1):239.

PMID:
27887629
3.

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.

Zerbino DR, Ballinger T, Paten B, Hickey G, Haussler D.

BMC Bioinformatics. 2016 Sep 29;17(1):400.

4.

Long-read sequence assembly of the gorilla genome.

Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin CS, Eichler EE.

Science. 2016 Apr 1;352(6281):aae0344. doi: 10.1126/science.aae0344.

5.

MinION Analysis and Reference Consortium: Phase 1 data release and analysis.

Ip CL, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE; MinION Analysis and Reference Consortium..

F1000Res. 2015 Oct 15;4:1075. doi: 10.12688/f1000research.7201.1.

6.

The UCSC Genome Browser database: 2016 update.

Speir ML, Zweig AS, Rosenbloom KR, Raney BJ, Paten B, Nejad P, Lee BT, Learned K, Karolchik D, Hinrichs AS, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Fujita PA, Eisenhart C, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D717-25. doi: 10.1093/nar/gkv1275.

7.

The Matchmaker Exchange: a platform for rare disease gene discovery.

Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL.

Hum Mutat. 2015 Oct;36(10):915-21. doi: 10.1002/humu.22858.

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.

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.

10.

The Genome 10K Project: a way forward.

Koepfli KP, Paten B; Genome 10K Community of Scientists., O'Brien SJ.

Annu Rev Anim Biosci. 2015;3:57-111. doi: 10.1146/annurev-animal-090414-014900. Review.

PMID:
25689317
11.

Improved data analysis for the MinION nanopore sequencer.

Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M.

Nat Methods. 2015 Apr;12(4):351-6. doi: 10.1038/nmeth.3290.

12.

Building a pan-genome reference for a population.

Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B.

J Comput Biol. 2015 May;22(5):387-401. doi: 10.1089/cmb.2014.0146.

13.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA.

Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449.

14.

The UCSC Genome Browser database: 2015 update.

Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hickey G, Hinrichs AS, Hubley R, Karolchik D, Learned K, Lee BT, Li CH, Miga KH, Nguyen N, Paten B, Raney BJ, Smit AF, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2015 Jan;43(Database issue):D670-81. doi: 10.1093/nar/gku1177.

15.

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.

Jacobs FM, Greenberg D, Nguyen N, Haeussler M, Ewing AD, Katzman S, Paten B, Salama SR, Haussler D.

Nature. 2014 Dec 11;516(7530):242-5. doi: 10.1038/nature13760.

16.

Alignathon: a competitive assessment of whole-genome alignment methods.

Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B.

Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114.

17.

Comparative assembly hubs: web-accessible browsers for comparative genomics.

Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B.

Bioinformatics. 2014 Dec 1;30(23):3293-301. doi: 10.1093/bioinformatics/btu534.

18.

A unifying model of genome evolution under parsimony.

Paten B, Zerbino DR, Hickey G, Haussler D.

BMC Bioinformatics. 2014 Jun 19;15:206. doi: 10.1186/1471-2105-15-206.

19.

Ragout-a reference-assisted assembly tool for bacterial genomes.

Kolmogorov M, Raney B, Paten B, Pham S.

Bioinformatics. 2014 Jun 15;30(12):i302-9. doi: 10.1093/bioinformatics/btu280.

20.

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ.

Bioinformatics. 2014 Apr 1;30(7):1003-5. doi: 10.1093/bioinformatics/btt637.

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