For the next couple of months I’ll be working on a project alongside Natalie Gardiner from Life Sciences, with co-conspirators @neilswainston and @porld. Natalie studies diabetic neuropathy: this debilitating nerve damage affects around half of diabetes patients, and can lead to pain or loss of sensation. The causes of the condition are not well-understood, though elevated blood glucose is known to be a key factor.
Natalie’s lab has amassed comprehensive proteomic and metabolomic data sets from nerve cells in diabetic rats. This is a great opportunity for us to put to work some of the tools we’ve developed in the MCISB. ‘Omics measurements can tell us what changes occur in a disease, but not which of these changes are important to its development; for this we require knowledge of the underlying network organisation. We shall apply our Daaaaave algorithm [1, see also “From genes to fluxes”] to rat-nerve specific derivations of Recon 2 [2, “Hambo” see also “Striking a balance with Recon 2.1”], to derive cell–level behaviour from Natalie’s gene-level data.
Watch this space for news on “Super-Daaaaave” and “Rambo”.
References
- Lee D, Smallbone K, Dunn WB, Murabito E, Winder CL, Kell DB, Mendes P, Swainston N (2012) “Improving metabolic flux predictions using absolute gene expression data” BMC Systems Biology 6:73.
doi:10.1186/1752-0509-6-73 - Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Every Man, His Dog, Palsson BØ (2013) “A community-driven global reconstruction of human metabolism” Nature Biotechnology 31:419-425.
doi:10.1038/nbt.2488
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