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Items: 16

1.

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery.

Krishnakumar V, Contrino S, Cheng CY, Belyaeva I, Ferlanti ES, Miller JR, Vaughn MW, Micklem G, Town CD, Chan AP.

Plant Cell Physiol. 2017 Jan 1;58(1):e4. doi: 10.1093/pcp/pcw200.

PMID:
28013278
2.

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.

3.

Araport: the Arabidopsis information portal.

Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, Rosen BD, Cheng CY, Moreira W, Mock SA, Stubbs J, Sullivan JM, Krampis K, Miller JR, Micklem G, Vaughn M, Town CD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1003-9. doi: 10.1093/nar/gku1200. Epub 2014 Nov 20.

4.

InterMine: extensive web services for modern biology.

Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, Hu F, Smith R, Stěpán R, Sullivan J, Micklem G.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W468-72. doi: 10.1093/nar/gku301. Epub 2014 Apr 21.

5.

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE.

Trinh QM, Jen FY, Zhou Z, Chu KM, Perry MD, Kephart ET, Contrino S, Ruzanov P, Stein LD.

BMC Genomics. 2013 Jul 22;14:494. doi: 10.1186/1471-2164-14-494.

6.

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G.

Bioinformatics. 2012 Dec 1;28(23):3163-5. doi: 10.1093/bioinformatics/bts577. Epub 2012 Sep 27.

7.

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.

8.

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.

9.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium., Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

10.

Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.

Mukherjee G, Abeygunawardena N, Parkinson H, Contrino S, Durinck S, Farne A, Holloway E, Lilja P, Moreau Y, Oezcimen A, Rayner T, Sharma A, Brazma A, Sarkans U, Shojatalab M.

Plant Physiol. 2005 Oct;139(2):632-6.

11.

ArrayExpress--a public repository for microarray gene expression data at the EBI.

Parkinson H, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, Coulson R, Farne A, Lara GG, Holloway E, Kapushesky M, Lilja P, Mukherjee G, Oezcimen A, Rayner T, Rocca-Serra P, Sharma A, Sansone S, Brazma A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D553-5.

12.

The ArrayExpress gene expression database: a software engineering and implementation perspective.

Sarkans U, Parkinson H, Lara GG, Oezcimen A, Sharma A, Abeygunawardena N, Contrino S, Holloway E, Rocca-Serra P, Mukherjee G, Shojatalab M, Kapushesky M, Sansone SA, Farne A, Rayner T, Brazma A.

Bioinformatics. 2005 Apr 15;21(8):1495-501. Epub 2004 Nov 25.

PMID:
15564302
13.

COMe: the ontology of bioinorganic proteins.

Degtyarenko K, Contrino S.

BMC Struct Biol. 2004 Feb 27;4:3.

14.

ArrayExpress: a public database of gene expression data at EBI.

Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA.

C R Biol. 2003 Oct-Nov;326(10-11):1075-8.

PMID:
14744115
15.

The role SWISS-PROT and TrEMBL play in the genome research environment.

Junker V, Contrino S, Fleischmann W, Hermjakob H, Lang F, Magrane M, Martin MJ, Mitaritonna N, O'Donovan C, Apweiler R.

J Biotechnol. 2000 Mar 31;78(3):221-34.

PMID:
10751683
16.

Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.

Apweiler R, Gateau A, Contrino S, Martin MJ, Junker V, O'Donovan C, Lang F, Mitaritonna N, Kappus S, Bairoch A.

Proc Int Conf Intell Syst Mol Biol. 1997;5:33-43.

PMID:
9322012

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