Genome Designs helps life scientists generate value from their sequencing projects by gaining a much deeper insight into the metabolic machinery of the living cell and its regulation. We also help companies design and improve bioproduction strains (even the super-producing ones), and compute potential biomarkers and drug targets.

Services We Offer:

  1. Radical improvement of gene function recognition via manual re-annotation of genomes. This service dramatically decreases the amount of automatically assigned empty names like "Putative uncharacterized protein" (PUP) or vague unspecific names based on their belonging to a class of proteins that have a common sequence motif. As an example, see comparative statistics of our recent reconstructions of archaeal genomes.
  2. Standardization of protein function names and assignment of EC numbers. Finding gene functions and EC numbers that are missing due to the multifunctional nature of the enzymes and their wide substrate specificity.
  3. Metabolic reconstruction based on the re-annotated genomes, with the help of our proprietary MPW pathway database and its original pathway nomenclature. The reconstructions are organism- and tissue-specific.
  4. Mathematical simulation of the kinetics and dynamics of reconstructed biochemical networks, using a set of original methods requiring minimal experimentally measured kinetic parameters and essential variables. The vast majority of kinetic parameters are computed theoretically, thus making expensive and time-consuming experiments avoidable.
  5. Using results of the re-annotation, functional reconstruction, mathematical simulation, and numerical optimization to assist in metabolic engineering of more efficient biotechnology processes.

Functional reconstructions

  • Recommendations for laboratory and industrial cultivation, including predictions of the required components of the growth media
  • Recommendations for knock-out of pathogens by computing of metabolic bottlenecks
  • Prediction of a large number of regulatory mechanisms
  • Prediction of new kinetic and dynamic features of the reconstructed networks that could be helpful for a deeper understanding of their regulatory strategies.

Metabolic Engineering

Our original mathematical simulation platform gives a much deeper insight into the dynamics of cellular life than oversimplified steady-state flux balance analysis. Yet it does not require an unrealistic amount of experimental data for building a genome-scale dynamic e-cell. The wide use of mathematical asymptotic methods allows us to dramatically simplify the mathematical descriptions and improve the efficiency of metabolic engineering. This shortens the time necessary for improving the existing industrial super-producing strains, and for engineering the novel ones.

In addition to contractual metabolic engineering services, Genome Designs licenses its patented metabolic designs to pharmaceutical, food and bioproduction companies, and partners with academic institutions for government-funded metabolic engineering projects.

Please Contact us for more information.