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 interested in utilizing statistical methods and machine learning techniques on genomic & transcriptomic data to develop useful biological models that can assist in metabolic engineering and strain design. Specifically, my current thesis work revolves around large-scale pangenome analysis of prokaryotic model organisms, namely Escherichia coli and Staphylococcus aureus, and in differentiating wild-type, commensal, and pathogenic strains by their metabolic gene content. Siddharth Chauhan, 4th Year PhD Student.
- My research is based in bridging the gap between constraint-based modeling and kinetic modeling methods to explore large-scale models of metabolism such as the human red blood cell and hepatocyte. My aim is to develop software tools and robust workflows to facilitate the development of comprehensive metabolic models for applications in personalized medicine. Zachary Haiman, 3rd Year PhD Student.
- My research centers around iModulons, which are independently modulated groups of genes that can be computed from transcriptomic data using the machine learning algorithm "independent component analysis." In my first project, I generated iModulons for the soil and gut bacterium Bacillus subtilis and analyzed them to obtain several hypotheses about how Bacillus regulates its genes and quantitatively summarize complex processes like sporulation. In my next project, I show how iModulon analysis can capture changes to the genome in a laboratory evolution study, as well as be useful for predicting phenotypes and modeling a major metabolic tradeoff. Finally, I build online knowledgebases such as imodulondb.org, which provides a searchable and interactive platform for sharing systems biology data and results. Kevin Rychel, 4th Year PhD Student.