Met­Ex­plore

Find­ing your path through net­work complexity

Cit­ing MetExplore

[Met­Ex­plore V1] Ludovic Cot­tret, David Wildridge, Flo­rence Vin­son, Michael P. Bar­rett, Huber Charles, Marie-​France Sagot and Fabien Jour­dan. Met­Ex­plore: a web server to link metabolomic exper­i­ments and genome-​scale meta­bolic net­works. (2010) Nucleic Acids Research. 1;38 Suppl:W132-7. PMID:20444866. [Paper]

[Arti­cles, in PubMed, cit­ing MetExplore]

Met­Ex­plore applications

[Endosym­bionts in the white­fly Bemisia tabaci] Q. Rao, P.-A. Rollat-​Farnier, D.-T. Zhu, D. Santos-​Garcia, F. J. Silva, A. Moya, A. Latorre, C. C. Klein, F. Vavre, M.-F. Sagot, S.-S. Liu, L. Mou­ton, and X.-W. Wang, “Genome reduc­tion and poten­tial meta­bolic com­ple­men­ta­tion of the dual endosym­bionts in the white­fly Bemisia tabaci,” BMC Genomics, vol. 16, no. 1, p. 226, Mar. 2015.

[Try­panosoma bru­cei] Shameer S, Logan-​Klumpler FJ, Vin­son F, Cot­tret L, Mer­let B, Achcar F, BoshartM, Ber­ri­man M, Bre­itling R, Bringaud F, Bütikofer P, Cat­tanach AM , Bannerman-​Chukualim B, Creek D, Crouch K, de Kon­ing HP, Denise H, Ebikeme C, Fair­lamb AH, Fer­gu­son MAJ, Gin­ger ML, Hertz-​Fowler C, Kerk­hoven EJ, Mäser P, Michels PAM, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-​Franco F, Smith TK, Tay­lor MC, Tie­lens AGM, Urba­niak MD, van Helle­mond JJ, Vin­cent IM, Wilkin­son SR, Wyl­lie S, Opper­does FR, Bar­rett MP, Jour­dan F. Try­panoCyc: A community-​led bio­chem­i­cal path­ways data­base for Try­panosoma bru­cei. (2014) Nucleic Acids Research, pub­lished online. [paper]

Algo­rithms imple­mented in MetExplore

[Gap filler] Fabien Jour­dan, Ludovic Cot­tret, David Wildridge, Richard Schel­tema, Anne Hil­len­weck, Michael P. Bar­rett, Daniel Zalko, David G. Wat­son and Lau­rent Debrauwer. Use of recon­sti­tuted meta­bolic net­works to assist in metabolomic data visu­al­iza­tion and min­ing. (2010) Metabolomics, 6(2):312321. [Paper]
[Scope]
Han­dorf, T. Eben­höh, O. & Hein­rich. Expand­ing meta­bolic net­works: scopes of com­pounds, robust­ness, and evo­lu­tion. (2005) R.J Mol Evol 61(4), 498512. [Paper]
[Choke Points] Yeh, I. Hanekamp, T. Tsoka, S. Karp, P. D. & Alt­man, R. B. Com­pu­ta­tional analy­sis of Plas­mod­ium fal­ci­parum metab­o­lism: orga­niz­ing genomic infor­ma­tion to facil­i­tate drug dis­cov­ery. (2004) Genome Res 14(5), 917924. [Paper]