Molecular Evolution, Horizontal Transfer, Molecular Parasites

At present the research in the Gogarten lab is exclusively in computational biology; however, we collaborate with other labs that do research at the bench in molecular biology, virology, and biochemistry.

Research opportunities exist for postdocs, graduate students and undergraduate students majoring in MCB, EEB, biology, computer science or mathematics. We research horizontal transfer of genetic information (which may be genes, genomic islands, selfish genetic elements or molecular parasites).
A current focus is on inteins and group I introns that integrate into a recipient genome using homing endonucleases.

Some basic information on tools and techniques are better communicated in a class room than one on one during research in the laboratory. Before embarking on a research project, it is a good idea to get at least a little familiar with databank searches, sequence alignment, and phylogenetic reconstruction.
Courses in molecular evolution and/or bioinformatics would be an excellent starting point; e.g.,

  • MCB 1201. Virus Hunting: Applied Bioinformatics 4cr
  • MCB/CSE/BME 1401. Honors Core: Computational Molecular Biology 3cr
  • MCB 3421 Introduction to Molecular Evolution and Bioinformatics 3cr
  • MCB 3637. Practical Methods in Microbial Genomics 3cr
  • MCB 5672 Applied Bioinformatics 3cr
  • EEB 4100. Big Data Science for Biologists 4cr
  • EEB 5349 - Phylogenetics 3cr
  • Pavel Pevzner's Bioinformatics courses (UCSD) on Coursera e.g. Bioinformatics for Beginners
  • R-courses from John Hopkins on Coursera, e.g., data-visualization
    You can sign up to audit the course, or take them for free (but you'll not get a certificate).

If you are interested in joining the lab, please send an email to describing your interests, previous training, and ideas for a research project. Also, you are encouraged to check out prior to sending your email and/or to talk to researchers in the lab (Sophia, Danielle, Tian, Danielle, Marlene).

Currently ongoing projects include:

  • Recombination and gene flow in bacteriophages
  • Genomic islands in bacteria and haloarchaea
  • Tracing horizontal transfer in phages, chloroplasts, bacteria and archaea using selfish genetic elements
  • Inteins in actinophages
  • Split inteins in cyanobacteria
  • Population genomics of inteins

Suggested readings from the Gogarten Lab:

On Inteins:

On Horizontal (Gene) Transfer