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Items: 1 to 20 of 124

1.

modMine: flexible access to modENCODE data.

Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, Kephart ET, Lloyd P, Stinson EO, Washington NL, Perry MD, Ruzanov P, Zha Z, Lewis SE, Stein LD, Micklem G.

Nucleic Acids Res. 2012 Jan;40(Database issue):D1082-8. doi: 10.1093/nar/gkr921. Epub 2011 Nov 12.

2.

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.

Washington NL, Stinson EO, Perry MD, Ruzanov P, Contrino S, Smith R, Zha Z, Lyne R, Carr A, Lloyd P, Kephart E, McKay SJ, Micklem G, Stein LD, Lewis SE.

Database (Oxford). 2011 Aug 19;2011:bar023. doi: 10.1093/database/bar023. Print 2011.

3.

Lessons from modENCODE.

Brown JB, Celniker SE.

Annu Rev Genomics Hum Genet. 2015;16:31-53. doi: 10.1146/annurev-genom-090413-025448. Epub 2015 Jun 26. Review.

PMID:
26133010
4.

WormBase 2007.

Rogers A, Antoshechkin I, Bieri T, Blasiar D, Bastiani C, Canaran P, Chan J, Chen WJ, Davis P, Fernandes J, Fiedler TJ, Han M, Harris TW, Kishore R, Lee R, McKay S, Müller HM, Nakamura C, Ozersky P, Petcherski A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW.

Nucleic Acids Res. 2008 Jan;36(Database issue):D612-7. Epub 2007 Nov 8.

5.

FlyBase: anatomical data, images and queries.

Grumbling G, Strelets V.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D484-8.

6.

WormBase: new content and better access.

Bieri T, Blasiar D, Ozersky P, Antoshechkin I, Bastiani C, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Han M, Harris TW, Kishore R, Lee R, McKay S, Müller HM, Nakamura C, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Durbin R, Stein LD, Sternberg PW, Spieth J.

Nucleic Acids Res. 2007 Jan;35(Database issue):D506-10. Epub 2006 Nov 11.

7.

FlyBase 101--the basics of navigating FlyBase.

McQuilton P, St Pierre SE, Thurmond J; FlyBase Consortium..

Nucleic Acids Res. 2012 Jan;40(Database issue):D706-14. doi: 10.1093/nar/gkr1030. Epub 2011 Nov 29.

8.
9.

Navigating and mining modENCODE data.

Boley N, Wan KH, Bickel PJ, Celniker SE.

Methods. 2014 Jun 15;68(1):38-47. doi: 10.1016/j.ymeth.2014.03.007. Epub 2014 Mar 15. Review.

10.

FlyBase: integration and improvements to query tools.

Wilson RJ, Goodman JL, Strelets VB; FlyBase Consortium..

Nucleic Acids Res. 2008 Jan;36(Database issue):D588-93. Epub 2007 Dec 26.

11.

FlyBase : a database for the Drosophila research community.

Drysdale R; FlyBase Consortium..

Methods Mol Biol. 2008;420:45-59. doi: 10.1007/978-1-59745-583-1_3. Review.

PMID:
18641940
12.

WormBase: a multi-species resource for nematode biology and genomics.

Harris TW, Chen N, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Chan J, Chen CK, Chen WJ, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D411-7.

13.

WormBase: better software, richer content.

Schwarz EM, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Harris TW, Kenny EE, Kishore R, Lawson D, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Spooner W, Tuli MA, Van Auken K, Wang D, Durbin R, Spieth J, Stein LD, Sternberg PW.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D475-8.

14.

WormBase: methods for data mining and comparative genomics.

Harris TW, Stein LD.

Methods Mol Biol. 2006;351:31-50. Review.

PMID:
16988424
15.

Cross-organism analysis using InterMine.

Lyne R, Sullivan J, Butano D, Contrino S, Heimbach J, Hu F, Kalderimis A, Lyne M, Smith RN, Štěpán R, Balakrishnan R, Binkley G, Harris T, Karra K, Moxon SA, Motenko H, Neuhauser S, Ruzicka L, Cherry M, Richardson J, Stein L, Westerfield M, Worthey E, Micklem G.

Genesis. 2015 Aug;53(8):547-60. doi: 10.1002/dvg.22869. Epub 2015 Jul 8. Review.

16.

FlyBase: genomes by the dozen.

Crosby MA, Goodman JL, Strelets VB, Zhang P, Gelbart WM; FlyBase Consortium..

Nucleic Acids Res. 2007 Jan;35(Database issue):D486-91. Epub 2006 Nov 11.

17.

Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes.

Maglich JM, Sluder A, Guan X, Shi Y, McKee DD, Carrick K, Kamdar K, Willson TM, Moore JT.

Genome Biol. 2001;2(8):RESEARCH0029. Epub 2001 Jul 24.

18.

WormQTLHD--a web database for linking human disease to natural variation data in C. elegans.

van der Velde KJ, de Haan M, Zych K, Arends D, Snoek LB, Kammenga JE, Jansen RC, Swertz MA, Li Y.

Nucleic Acids Res. 2014 Jan;42(Database issue):D794-801. doi: 10.1093/nar/gkt1044. Epub 2013 Nov 11.

19.

Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis.

Sullivan JC, Reitzel AM, Finnerty JR.

Nucleic Acids Res. 2008 Jan;36(Database issue):D607-11. Epub 2007 Nov 3.

20.

Genetics. Revealing the dark matter of the genome.

Blaxter M.

Science. 2010 Dec 24;330(6012):1758-9. doi: 10.1126/science.1200700. Epub 2010 Dec 22. No abstract available.

PMID:
21177977

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