Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 20 of 90

1.

Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex.

Nowakowski TJ, Bhaduri A, Pollen AA, Alvarado B, Mostajo-Radji MA, Di Lullo E, Haeussler M, Sandoval-Espinosa C, Liu SJ, Velmeshev D, Ounadjela JR, Shuga J, Wang X, Lim DA, West JA, Leyrat AA, Kent WJ, Kriegstein AR.

Science. 2017 Dec 8;358(6368):1318-1323. doi: 10.1126/science.aap8809.

2.

The UCSC Genome Browser database: 2018 update.

Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2018 Jan 4;46(D1):D762-D769. doi: 10.1093/nar/gkx1020.

3.

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.

Nat Biotechnol. 2017 Apr 11;35(4):314-316. doi: 10.1038/nbt.3772. No abstract available.

4.

The UCSC Genome Browser database: 2017 update.

Tyner C, Barber GP, Casper J, Clawson H, Diekhans M, Eisenhart C, Fischer CM, Gibson D, Gonzalez JN, Guruvadoo L, Haeussler M, Heitner S, Hinrichs AS, Karolchik D, Lee BT, Lee CM, Nejad P, Raney BJ, Rosenbloom KR, Speir ML, Villarreal C, Vivian J, Zweig AS, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2017 Jan 4;45(D1):D626-D634. doi: 10.1093/nar/gkw1134. Epub 2016 Nov 29.

5.

UCSC Data Integrator and Variant Annotation Integrator.

Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ.

Bioinformatics. 2016 May 1;32(9):1430-2. doi: 10.1093/bioinformatics/btv766. Epub 2016 Jan 6.

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. Epub 2015 Nov 20.

7.

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.

8.

Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments.

Miga KH, Eisenhart C, Kent WJ.

Nucleic Acids Res. 2015 Nov 16;43(20):e133. doi: 10.1093/nar/gkv671. Epub 2015 Jul 10.

9.

Ontology application and use at the ENCODE DCC.

Malladi VS, Erickson DT, Podduturi NR, Rowe LD, Chan ET, Davidson JM, Hitz BC, Ho M, Lee BT, Miyasato S, Roe GR, Simison M, Sloan CA, Strattan JS, Tanaka F, Kent WJ, Cherry JM, Hong EL.

Database (Oxford). 2015 Mar 16;2015. pii: bav010. doi: 10.1093/database/bav010. Print 2015. Review.

10.

The UCSC Ebola Genome Portal.

Haeussler M, Karolchik D, Clawson H, Raney BJ, Rosenbloom KR, Fujita PA, Hinrichs AS, Speir ML, Eisenhart C, Zweig AS, Haussler D, Kent WJ.

PLoS Curr. 2014 Nov 7;6. pii: ecurrents.outbreaks.386ab0964ab4d6c8cb550bfb6071d822. doi: 10.1371/currents.outbreaks.386ab0964ab4d6c8cb550bfb6071d822.

11.

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.

12.

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.

13.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

14.

Navigating protected genomics data with UCSC Genome Browser in a Box.

Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ.

Bioinformatics. 2015 Mar 1;31(5):764-6. doi: 10.1093/bioinformatics/btu712. Epub 2014 Oct 27.

15.

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.

16.

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.

17.

Centromere reference models for human chromosomes X and Y satellite arrays.

Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ.

Genome Res. 2014 Apr;24(4):697-707. doi: 10.1101/gr.159624.113. Epub 2014 Feb 5.

18.

The UCSC Genome Browser database: 2014 update.

Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res. 2014 Jan;42(Database issue):D764-70. doi: 10.1093/nar/gkt1168. Epub 2013 Nov 21.

19.

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.

20.

The UCSC Genome Browser.

Karolchik D, Hinrichs AS, Kent WJ.

Curr Protoc Bioinformatics. 2012 Dec;Chapter 1:Unit1.4. doi: 10.1002/0471250953.bi0104s40.

PMID:
23255150

Supplemental Content

Loading ...
Support Center