Network Biology Approaches to Identify Molecular and Systems-Level Differences Between Salmonella Pathovars

Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level

“…Through the development of a more compatible structure between SalmoNet2 and other accessible large-scale evolutionary genomics tools such as OMA, there is enhanced potential to produce interaction networks for specific Salmonella strains on demand, or build analogous data resources for other nonmodel organisms ( 58 ). With the implementation of SalmoNet2 with OMA to determine orthologous SalmoNet2 interactions, there are more opportunities to study the evolutionary history of proteins and interactions.…”

“…To address this, we created a tutorial and GitHub repository showing the necessary initial steps to generate custom SalmoNet2 networks for interested researchers, and provided helper scripts to handle the outputs of OMA standalone. For more in-depth steps, interested researchers can consult our previous publication on constructing interaction networks for nonmodel organisms that focused specifically on Salmonella ( 58 ).…”

Multi-layered networks of SalmoNet2 enable strain comparisons of the Salmonella genus on a molecular level

“…By increasing the number of strains to 20 from the previous 11, SalmoNet now extends out of subspecies I., adding information on members of other subspecies (subspecies arizonae ), or an entirely different species ( Salmonella bongori ). Developing a more compatible structure between SalmoNet, and other available large-scale evolutionary genomics tools such as OMA, there is increased potential to generate interaction networks for specific Salmonella strains on request, or build similar data resources for other non-model organisms 44 . With the change to OMA as the backbone of SalmoNet interactions, there is a great potential to study the evolutionary history of proteins, and interactions.…”