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Items: 1 to 20 of 113

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.

'Multi-omic' data analysis using O-miner.

Sangaralingam A, Dayem Ullah AZ, Marzec J, Gadaleta E, Nagano A, Ross-Adams H, Wang J, Lemoine NR, Chelala C.

Brief Bioinform. 2017 Aug 4. doi: 10.1093/bib/bbx080. [Epub ahead of print]

PMID:
28981577
3.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

Velmeshev D, Lally P, Magistri M, Faghihi MA.

BMC Genomics. 2016 Jan 13;17:49. doi: 10.1186/s12864-015-2346-y.

4.

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.

5.

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.

6.

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
7.

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files.

Hart SN, Duffy P, Quest DJ, Hossain A, Meiners MA, Kocher JP.

Brief Bioinform. 2016 Mar;17(2):346-51. doi: 10.1093/bib/bbv051. Epub 2015 Jul 25.

8.

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.

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.

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.

11.

canEvolve: a web portal for integrative oncogenomics.

Samur MK, Yan Z, Wang X, Cao Q, Munshi NC, Li C, Shah PK.

PLoS One. 2013;8(2):e56228. doi: 10.1371/journal.pone.0056228. Epub 2013 Feb 13.

12.

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.

13.

CS-MINER: A Tool for Association Mining in Binding-Database.

Mani-Varnosfaderani A, Valadkhani A, Jalali-Heravi M.

Mol Inform. 2015 Apr;34(4):185-96. doi: 10.1002/minf.201400142. Epub 2015 Mar 10.

PMID:
27490165
14.

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.

15.

web cellHTS2: a web-application for the analysis of high-throughput screening data.

Pelz O, Gilsdorf M, Boutros M.

BMC Bioinformatics. 2010 Apr 12;11:185. doi: 10.1186/1471-2105-11-185.

16.

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.

17.

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.

Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, Väremo L, Nookaew I, Nielsen J.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W175-81. doi: 10.1093/nar/gku371. Epub 2014 May 3.

18.

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.

19.

Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.

Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X; MSeqDR Consortium Participants; MSeqDR Consortium participants: Sherri Bale, Jirair Bedoyan, Doron Behar, Penelope Bonnen, Lisa Brooks, Claudia Calabrese, Sarah Calvo, Patrick Chinnery, John Christodoulou, Deanna Church,; Rosanna Clima, Bruce H. Cohen, Richard G. Cotton, IFM de Coo, Olga Derbenevoa, Johan T. den Dunnen, David Dimmock, Gregory Enns, Giuseppe Gasparre,; Amy Goldstein, Iris Gonzalez, Katrina Gwinn, Sihoun Hahn, Richard H. Haas, Hakon Hakonarson, Michio Hirano, Douglas Kerr, Dong Li, Maria Lvova, Finley Macrae, Donna Maglott, Elizabeth McCormick, Grant Mitchell, Vamsi K. Mootha, Yasushi Okazaki,; Aurora Pujol, Melissa Parisi, Juan Carlos Perin, Eric A. Pierce, Vincent Procaccio, Shamima Rahman, Honey Reddi, Heidi Rehm, Erin Riggs, Richard Rodenburg, Yaffa Rubinstein, Russell Saneto, Mariangela Santorsola, Curt Scharfe,; Claire Sheldon, Eric A. Shoubridge, Domenico Simone, Bert Smeets, Jan A. Smeitink, Christine Stanley, Anu Suomalainen, Mark Tarnopolsky, Isabelle Thiffault, David R. Thorburn, Johan Van Hove, Lynne Wolfe, and Lee-Jun Wong.

Mol Genet Metab. 2015 Mar;114(3):388-96. doi: 10.1016/j.ymgme.2014.11.016. Epub 2014 Dec 4. Review.

20.

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.

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