A new tool to analyze bipartite networks in community networks

A new study in which Sergi Valverde, from the Complex Systems Lab  at DCEXS-UPF has collaborated, provides an open source MATLAB package to study the structure of bipartite ecological networks inspired by real problems in microbiology and with broader applications.   Bipartite networks are a special type of ecological network where individuals of a certain species interact with individuals of different species. They are ubiquitous in community ecology, such as the relation between phages (viruses that infect bacteria) and their bacterial hosts. You can read more about this tool, called BiMat, at the group’s blog. Continue reading A new tool to analyze bipartite networks in community networks

How does genotype determine phenotype?

Very interesting talk by Edward Marcotte today at the PRBB! He is an expert in proteomics, but touches all aspects of systems biology, and today he asked the following question: how does genotype determine phenotype? Can we predict the outcome of all the genomic variation we are uncovering with the many genomic projects we are doing nowadays? Well, his lab is certainly trying to do so, and using three different strategies which I will summarise very briefly: 1.  Using functional gene networks, which are based on data such as mRNA expression, protein-protein interactions (PPI), etc. These networks presumably are formed … Continue reading How does genotype determine phenotype?