000212953 001__ 212953
000212953 005__ 20190317000312.0
000212953 037__ $$aPOST_TALK
000212953 245__ $$aSystematic Reduction of Genome Scale Metabolic Reconstructions - redGEM
000212953 269__ $$a2015
000212953 260__ $$c2015
000212953 336__ $$aPosters
000212953 520__ $$aGenome-scale metabolic reconstructions (GEMs) are valuable resources for understanding and redesigning cellular networks as they encapsulate all the known biochemistry of the organisms from genes to proteins to their functions. Complexity of these large metabolic networks often hinders their utility in various practical applications. This difficulty calls for models of reduced sizes that are consistent with the genome-scale models. Currently available core models are reduced ad hoc with different aims and criteria, and up to date, there are no systematic reduction methods in the literature. In this work, we have developed redGEM, a systematic model reduction method for constructing core metabolic models from GEMs that is applicable to any genome-scale model. In redGEM, we use as inputs: (i) definition of the metabolic subsystems that are of interest for a physiology under study; (ii) information about the extracellular nutrients; and (iii) any available physiological data. Next, we employ a directed graph search method to find the connections between the selected subsystems, and we then apply a computational method to construct lumped reactions between the biomass building blocks and those subsystems. The result of this procedure is a reduced model that is consistent with the original GEM in terms of flux profiles and essential reactions. We applied the method to generate reduced models for the growth physiology of E. coli and S. cerevisiae under aerobic/anaerobic conditions.
000212953 700__ $$0245962$$g215631$$aAtaman, Meriç
000212953 700__ $$0248468$$g222571$$aHernandez Gardiol, Daniel Federico
000212953 700__ $$0247694$$g241502$$aFengos, Georgios
000212953 700__ $$0243874$$g177860$$aSoh, Keng Cher
000212953 700__ $$0240657$$g174688$$aHatzimanikatis, Vassily
000212953 7112_ $$dSeptember 16-18, 2015$$cCrowne Plaza Heidelberg, Germany$$a4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2015)
000212953 8564_ $$uhttps://infoscience.epfl.ch/record/212953/files/Poster.pdf$$zn/a$$s3131894$$yn/a
000212953 909C0 $$xU11422$$0252131$$pLCSB
000212953 909CO $$ooai:infoscience.tind.io:212953$$qGLOBAL_SET$$pSB$$pposter
000212953 917Z8 $$x215631
000212953 937__ $$aEPFL-POSTER-212953
000212953 973__ $$aOTHER
000212953 980__ $$aPOSTER