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Items: 1 to 20 of 129

1.

O-miner: an integrative platform for automated analysis and mining of -omics data.

Cutts RJ, Dayem Ullah AZ, Sangaralingam A, Gadaleta E, Lemoine NR, Chelala C.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W560-8. doi: 10.1093/nar/gks432. Epub 2012 May 17.

2.

Genomics Portals: integrative web-platform for mining genomics data.

Shinde K, Phatak M, Johannes FM, Chen J, Li Q, Vineet JK, Hu Z, Ghosh K, Meller J, Medvedovic M.

BMC Genomics. 2010 Jan 13;11:27. doi: 10.1186/1471-2164-11-27.

3.

Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

Guzzi PH, Cannataro M.

Comput Methods Programs Biomed. 2013 Aug;111(2):402-9. doi: 10.1016/j.cmpb.2013.04.006. Epub 2013 May 31.

PMID:
23731720
4.

mu-CS: an extension of the TM4 platform to manage Affymetrix binary data.

Guzzi PH, Cannataro M.

BMC Bioinformatics. 2010 Jun 10;11:315. doi: 10.1186/1471-2105-11-315.

5.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.

BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.

6.

Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.

Hermida L, Poussin C, Stadler MB, Gubian S, Sewer A, Gaidatzis D, Hotz HR, Martin F, Belcastro V, Cano S, Peitsch MC, Hoeng J.

BMC Genomics. 2013 Jul 29;14:514. doi: 10.1186/1471-2164-14-514.

7.

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.

Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, Soiland-Reyes S, Dunlop I, Nenadic A, Fisher P, Bhagat J, Belhajjame K, Bacall F, Hardisty A, Nieva de la Hidalga A, Balcazar Vargas MP, Sufi S, Goble C.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W557-61. doi: 10.1093/nar/gkt328. Epub 2013 May 2.

8.

Methods for visual mining of genomic and proteomic data atlases.

Boyle J, Kreisberg R, Bressler R, Killcoyne S.

BMC Bioinformatics. 2012 Apr 23;13:58. doi: 10.1186/1471-2105-13-58.

9.

Onto-Tools: new additions and improvements in 2006.

Khatri P, Voichita C, Kattan K, Ansari N, Khatri A, Georgescu C, Tarca AL, Draghici S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W206-11. Epub 2007 Jun 21.

10.

Computational solutions for omics data.

Berger B, Peng J, Singh M.

Nat Rev Genet. 2013 May;14(5):333-46. doi: 10.1038/nrg3433. Review.

11.

eXframe: reusable framework for storage, analysis and visualization of genomics experiments.

Sinha AU, Merrill E, Armstrong SA, Clark TW, Das S.

BMC Bioinformatics. 2011 Nov 21;12:452. doi: 10.1186/1471-2105-12-452.

12.

EDGE(3): a web-based solution for management and analysis of Agilent two color microarray experiments.

Vollrath AL, Smith AA, Craven M, Bradfield CA.

BMC Bioinformatics. 2009 Sep 4;10:280. doi: 10.1186/1471-2105-10-280.

13.

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis.

Merelli I, Viti F, Milanesi L.

BMC Bioinformatics. 2012;13 Suppl 14:S5. doi: 10.1186/1471-2105-13-S14-S5. Epub 2012 Sep 7.

14.

Recent additions and improvements to the Onto-Tools.

Khatri P, Sellamuthu S, Malhotra P, Amin K, Done A, Draghici S.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W762-5.

15.

Online tools for bioinformatics analyses in nutrition sciences.

Malkaram SA, Hassan YI, Zempleni J.

Adv Nutr. 2012 Sep 1;3(5):654-65. doi: 10.3945/an.112.002477. Review.

16.

Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana.

Schuler M, Keller A, Backes C, Philippar K, Lenhof HP, Bauer P.

BMC Plant Biol. 2011 May 18;11:87. doi: 10.1186/1471-2229-11-87.

17.

Functional genomics and proteomics in the clinical neurosciences: data mining and bioinformatics.

Phan JH, Quo CF, Wang MD.

Prog Brain Res. 2006;158:83-108. Review.

PMID:
17027692
18.

SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS.

Merelli I, Calabria A, Cozzi P, Viti F, Mosca E, Milanesi L.

BMC Bioinformatics. 2013;14 Suppl 1:S9. doi: 10.1186/1471-2105-14-S1-S9. Epub 2013 Jan 14.

19.

RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies.

Manduchi E, Grant GR, He H, Liu J, Mailman MD, Pizarro AD, Whetzel PL, Stoeckert CJ Jr.

Bioinformatics. 2004 Mar 1;20(4):452-9. Epub 2004 Jan 22.

20.

Drug discovery applications for KNIME: an open source data mining platform.

Mazanetz MP, Marmon RJ, Reisser CB, Morao I.

Curr Top Med Chem. 2012;12(18):1965-79. Review.

PMID:
23110532
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