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- person_outline Alfonso Jaramillo
Publication for Desharky
A review of computational tools for design and reconstruction of metabolic pathways
[…] st at each edge, RouteSearch defined an additional criterion at each edge for non-static atom lost and applied branch-and-bound search to find the best paths to minimize the loss . On the other hand, DESHARKY applied Monte Carlo method to search for reaction combinations. To find the shortest path by S matrix representation, stoichiometry-based pathway design algorithms that use MILP is the commo […]
A review of parameters and heuristics for guiding metabolic pathfinding
[…] ny others require the user to select which organism or group of organisms to look at [, ]. Other methods do not require user input. In Cho et al. , enzymes are ranked based on organism specificity. DESHARKY  limits the number of compounds that are not organism-specific to only one non-specific reactant and one non-specific product. In GEM-Path , there is an association between reactions and […]
Development of bio based fine chemical production through synthetic bioengineering
[…] are identified, one can move to pathway design and optimization for microbial production of the target compound. Several computational tools are available, such as BNICE , FMM , RetroPath , and DESHARKY  and M-path  for designing de novo metabolic pathways. These resources provide different views of metabolic pathways for microbial production that are generated using the enormous amount […]
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