Welcome to the Systems Biology Research Group at the University of California, San Diego. We study the complexity of cellular life using experimental and computational methods that span the genome to the phenotype. Developing, integrating, and applying new methods allow us to gain a systems view of life - from bacterial to human.
Open Positions and Projects
- I am trying to understand the logic behind seemingly redundant prokaryotic energy generation pathways by leveraging adaptive laboratory evolution. I am also interested in bestowing context to ‘pseudo’genes. Amitesh Anand, Post Doctoral Researcher.
- My research interests center on executing comparative genome analytics on microbial pathogens. In particular using metabolic network reconstructions in conjunction with other systems biology techniques, I investigate the pan-genomes of these species for evolutionary drivers of pathogenesis. Charles Norsigian, 5th Year PhD Student
- I combine calculated and experimental features of genome sequences with machine learning at scale to make predictions of phenotype just from sequence. I focus on bacterial genomes with the goal of expediting rational engineering of these genomes. Cameron Lamoureux, 3rd Year PhD Student.
- My research is centered around the use of machine learning to understand the regulation of gene expression in bacteria. I find and characterize independent modules in bacterial transcriptomes. This has led to a comprehensive understanding of the soil and gut bacterium Bacillus subtilis, and the same methods are now being applied to adaptive laboratory evolution experiments and other datasets with genetic alterations. Ultimately, this "genome analysis" will hopefully inform "genome design" by providing data-driven, modular building blocks for the functions of life. Kevin Rychel, 3rd Year PhD Student.