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Results: 1 to 20 of 28

1.

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.

PMID:
25689317
2.

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. Epub 2015 Feb 16.

PMID:
25686389
3.

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. Epub 2015 Jan 7.

PMID:
25565268
4.

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. Epub 2014 Dec 11.

PMID:
25504731
5.

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. Epub 2014 Nov 26.

6.

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. Epub 2014 Sep 28.

PMID:
25274305
7.

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. Epub 2014 Oct 1.

8.

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. Epub 2014 Aug 18.

PMID:
25138168
9.

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.

10.

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.

11.

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. Epub 2013 Nov 13.

12.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

13.

HAL: a hierarchical format for storing and analyzing multiple genome alignments.

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

Bioinformatics. 2013 May 15;29(10):1341-2. doi: 10.1093/bioinformatics/btt128. Epub 2013 Mar 16.

14.

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics.

Westesson O, Lunter G, Paten B, Holmes I.

PLoS One. 2012;7(4):e34572. doi: 10.1371/journal.pone.0034572. Epub 2012 Apr 20.

15.

Integrating genomes.

Zerbino DR, Paten B, Haussler D.

Science. 2012 Apr 13;336(6078):179-82. doi: 10.1126/science.1216830. Review.

PMID:
22499938
16.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

17.

Cactus: Algorithms for genome multiple sequence alignment.

Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D.

Genome Res. 2011 Sep;21(9):1512-28. doi: 10.1101/gr.123356.111. Epub 2011 Jun 10.

18.

Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelization.

Roskin KM, Paten B, Haussler D.

BMC Bioinformatics. 2011 May 10;12:144. doi: 10.1186/1471-2105-12-144.

19.

Cactus graphs for genome comparisons.

Paten B, Diekhans M, Earl D, John JS, Ma J, Suh B, Haussler D.

J Comput Biol. 2011 Mar;18(3):469-81. doi: 10.1089/cmb.2010.0252.

PMID:
21385048
20.

Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation.

Haudry Y, Ramialison M, Paten B, Wittbrodt J, Ettwiller L.

Nat Protoc. 2010 Feb;5(2):323-34. doi: 10.1038/nprot.2009.158. Epub 2010 Feb 4.

PMID:
20134431
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