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Items: 1 to 20 of 138

1.

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.

Karnovsky A, Weymouth T, Hull T, Tarcea VG, Scardoni G, Laudanna C, Sartor MA, Stringer KA, Jagadish HV, Burant C, Athey B, Omenn GS.

Bioinformatics. 2012 Feb 1;28(3):373-80. doi: 10.1093/bioinformatics/btr661. Epub 2011 Nov 30.

2.

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks.

Gao J, Tarcea VG, Karnovsky A, Mirel BR, Weymouth TE, Beecher CW, Cavalcoli JD, Athey BD, Omenn GS, Burant CF, Jagadish HV.

Bioinformatics. 2010 Apr 1;26(7):971-3. doi: 10.1093/bioinformatics/btq048. Epub 2010 Feb 7.

3.

MetDisease--connecting metabolites to diseases via literature.

Duren W, Weymouth T, Hull T, Omenn GS, Athey B, Burant C, Karnovsky A.

Bioinformatics. 2014 Aug 1;30(15):2239-41. doi: 10.1093/bioinformatics/btu179. Epub 2014 Apr 8.

4.

Sparse network modeling and Metscape-based visualization methods for the analysis of large-scale metabolomics data.

Basu S, Duren W, Evans CR, Burant CF, Michailidis G, Karnovsky A.

Bioinformatics. 2017 Jan 30. pii: btx012. doi: 10.1093/bioinformatics/btx012. [Epub ahead of print]

PMID:
28137712
5.
6.

LeishCyc: a biochemical pathways database for Leishmania major.

Doyle MA, MacRae JI, De Souza DP, Saunders EC, McConville MJ, Likić VA.

BMC Syst Biol. 2009 Jun 5;3:57. doi: 10.1186/1752-0509-3-57.

7.

Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data.

García-Alcalde F, García-López F, Dopazo J, Conesa A.

Bioinformatics. 2011 Jan 1;27(1):137-9. doi: 10.1093/bioinformatics/btq594. Epub 2010 Nov 23.

8.

MGV: a generic graph viewer for comparative omics data.

Symons S, Nieselt K.

Bioinformatics. 2011 Aug 15;27(16):2248-55. doi: 10.1093/bioinformatics/btr351. Epub 2011 Jun 11.

PMID:
21666268
9.

ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts.

Cavalcante RG, Patil S, Weymouth TE, Bendinskas KG, Karnovsky A, Sartor MA.

Bioinformatics. 2016 May 15;32(10):1536-43. doi: 10.1093/bioinformatics/btw016. Epub 2016 Jan 21.

PMID:
26794319
10.

1D-¹H-nuclear magnetic resonance metabolomics reveals age-related changes in metabolites associated with experimental venous thrombosis.

Obi AT, Stringer KA, Diaz JA, Finkel MA, Farris DM, Yeomans L, Wakefield T, Myers DD Jr.

J Vasc Surg Venous Lymphat Disord. 2016 Apr;4(2):221-30. doi: 10.1016/j.jvsv.2015.09.010. Epub 2015 Nov 24.

PMID:
26993871
11.

Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA.

Kamburov A, Cavill R, Ebbels TM, Herwig R, Keun HC.

Bioinformatics. 2011 Oct 15;27(20):2917-8. doi: 10.1093/bioinformatics/btr499. Epub 2011 Sep 4.

PMID:
21893519
12.

Kiwi: a tool for integration and visualization of network topology and gene-set analysis.

Väremo L, Gatto F, Nielsen J.

BMC Bioinformatics. 2014 Dec 11;15:408. doi: 10.1186/s12859-014-0408-9.

13.

INVEX--a web-based tool for integrative visualization of expression data.

Xia J, Lyle NH, Mayer ML, Pena OM, Hancock RE.

Bioinformatics. 2013 Dec 15;29(24):3232-4. doi: 10.1093/bioinformatics/btt562. Epub 2013 Sep 26.

14.

Integration of metabolic networks and gene expression in virtual reality.

Yang Y, Engin L, Wurtele ES, Cruz-Neira C, Dickerson JA.

Bioinformatics. 2005 Sep 15;21(18):3645-50. Epub 2005 Jul 14.

PMID:
16020466
15.

integrOmics: an R package to unravel relationships between two omics datasets.

Lê Cao KA, González I, Déjean S.

Bioinformatics. 2009 Nov 1;25(21):2855-6. doi: 10.1093/bioinformatics/btp515. Epub 2009 Aug 25.

16.

The ConsensusPathDB interaction database: 2013 update.

Kamburov A, Stelzl U, Lehrach H, Herwig R.

Nucleic Acids Res. 2013 Jan;41(Database issue):D793-800. doi: 10.1093/nar/gks1055. Epub 2012 Nov 11.

17.

Integrating and annotating the interactome using the MiMI plugin for cytoscape.

Gao J, Ade AS, Tarcea VG, Weymouth TE, Mirel BR, Jagadish HV, States DJ.

Bioinformatics. 2009 Jan 1;25(1):137-8. doi: 10.1093/bioinformatics/btn501. Epub 2008 Sep 23.

18.

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W132-7. doi: 10.1093/nar/gkq312. Epub 2010 May 5.

19.

MetPA: a web-based metabolomics tool for pathway analysis and visualization.

Xia J, Wishart DS.

Bioinformatics. 2010 Sep 15;26(18):2342-4. doi: 10.1093/bioinformatics/btq418. Epub 2010 Jul 13.

PMID:
20628077
20.

Systems biology approaches and pathway tools for investigating cardiovascular disease.

Wheelock CE, Wheelock AM, Kawashima S, Diez D, Kanehisa M, van Erk M, Kleemann R, Haeggström JZ, Goto S.

Mol Biosyst. 2009 Jun;5(6):588-602. doi: 10.1039/b902356a. Epub 2009 Apr 27. Review.

PMID:
19462016

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