Desharky statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool Desharky

Tool usage distribution map

This map represents all the scientific publications referring to Desharky per scientific context
info info

Associated diseases


Popular tool citations

chevron_left Metabolic pathway prediction chevron_right
Want to access the full stats & trends on this tool?

Desharky specifications


Unique identifier OMICS_04877
Name Desharky
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Alfonso Jaramillo

Publication for Desharky

Desharky citations


A review of computational tools for design and reconstruction of metabolic pathways

PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] 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

J Cheminform
PMCID: 5602787
PMID: 29086092
DOI: 10.1186/s13321-017-0239-6

[…] 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

Microb Cell Fact
PMCID: 4302092
PMID: 25494636
DOI: 10.1186/s12934-014-0173-5

[…] 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 […]

Want to access the full list of citations?
Desharky institution(s)
Instituto de Biologia Molecular y Celular de Plantas, CSIC, Spain

Desharky reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Desharky