I have several rotations available for students who are interested in problems in computational biology. These fall into a variety of areas, described briefly below:
1. Algorithm development. Members of my lab work on developing new methods for hard problems in computational biology. These include, but are not restricted to: protein structure prediction, multiple sequence alignment, enzyme active site prediction, prediction of protein-protein interaction, biological network inference, phylogenetic tree construction for protein superfamilies and phylogenomic inference of gene function. Students interested in this area need strong programming skills; some training in machine learning and/or statistical modeling is very helpful.
2. Comparative genomics of human pathogens and parasites. This project involves a collaboration with scientists in Brazil, Canada and elsewhere working on various human pathogens. We are focusing on the phylogenomic analysis of pathogens and parasites that represent significant health problems in developing countries, such as Plasmodium falciparum (the malaria parasite). This project is part of our participation in the Center for Emerging and Neglected Diseases (CEND, http://globalhealth.berkeley.edu/cend/). This project includes reconstruction of the species phylogenies using phylogenomic approaches, and comparative genomics analyses to detect the genes responsible for pathogenicity and other important traits. Students interested in this area need good programming skills and some experience in genomics/bioinformatics.
3. Metagenomics: inferring the function and taxonomic origin of environmental sequences (e.g., from the human gut, ocean waters and soil). There are many technical challenges in this area, due to the fragmentary and noisy nature of environmental sequences. Students interested in this area need good programming skills and some background in genomics/bioinformatics.