PUBLICATIONS AND DATA SETS
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D. Jevremovic, D. Boley, "Parallel Computation of Elementary Flux Modes in Metabolic Networks using Global Arrays", submitted for review, 2012
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D. Jevremovic, D. Boley, "Finding Minimal Generating Set for Metabolic Network with Reversible Pathways", submitted for review, 2012
Accompanying MATLAB script used to compute minimal generating set at MinGen Software
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D. Jevremovic, D. Boley, C.P. Sosa, "Divide-and-conquer approach to
the parallel computation of elementary flux modes in metabolic networks", 10th IEEE workshop on High Performance Computational Biology, 2011 link
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D. Jevremovic, C. Trinh, F. Srienc, D. Boley, "Parallelization of the Nullspace Algorithm for the Computation of Metabolic Pathways", Parallel Computing no. 37, vol. 6-7, (2011) pp. 261-278 link
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D. Jevremovic, C. Trinh, F. Srienc, D. Boley, "A Simple Rank Test to Distinguish Extreme
Pathways from Elementary Modes in Metabolic Networks", technical report 08-029, 2008 link
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D. Jevremovic, C. Trinh, F. Srienc, D. Boley, "On Algebraic Properties of Extreme Pathways in Metabolic Networks", Journal of Computational Biology. February 2010, 17(2): 107-119 link
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Network models used in publications:
- S. cerevisiae central metabolism networks:
# metabolites # reactions (# rev) substrates 62 78 (31) glucose anaerobic tar.gz (5.1 MB) 62 80 (31) glucose aerobic tar.gz () 63 83 (34) glucose, glycerol, acetate allowed uptake of acetate tar.gz -
E. coli central metabolism networks:
# metabolites # reactions (# rev) substrates 47 59 (21) glucose tar.gz 41 61 (19) glucose tar.gz 49 64 (19) xylose, glucose tar.gz 50 66 (19) xylose, glycerol,glucose tar.gz 50 66 (28) xylose, glycerol,glucose succinate,acetate and lactose transport reactions are made reversible
conversion of pyruvate to lactate made reversible;
conversion of CoA to CoASH made reversible;
conversion of ACP to ACE made reversibletar.gz
- S. cerevisiae central metabolism networks:
| Last change: August 2012 |