James Galagan, PhD

Associate Professor, Biomedical Engineering and Microbiology


BS, Computer and Electrical Engineering, UC Davis
PhD, Computational Neuroscience, MIT

Research Interests

Dr. Galagan’s research is focused on Systems Biology of microbial organisms, specficially Mycobacterium tuberculosis – the causative agent of tuberculosis – and the fungus Neurospora crassa.  The Galagan Lab is an interdisciplinary group that combines computational biology, genomics, and experimental lab work.  Specific interests and projects include:

  • Using a genomics, computational modeling, and experimental systems-identification techniques to reconstruct the gene regulatory network of M. tuberculosis.
  • Developing and experimentally validating computational models of microbial metabolism for M. tuberculosis and N. crassa.
  • Using high-throughput sequencing and comparative sequence analysis to study the functional evolution of M. tuberculosis.
  • Developing computational methods for genomic data analysis (including gene prediction, gene expression analysis, and polymorphism discovery)
  • Developing experimental methods for microbial systems identification and analysis, drawing on electrical and mechanical systems identification methods.


Selected  Publications

  1. Colijn, C., Weiner, B., Cheng, T.-Y., Brandes, A., Zucker, J., Lun, D.S., Moody, B., Murray, M., and Galagan, J.E. (In Press). Computational prediction of metabolic flux using expression data: an application to Mycobacterium tuberculosis mycolic acid biosynthesis. PLoS Computational Biology.
  2. Reddy, T.B., Riley, R., Wymore, F., Montgomery, P., et al. (2009). TB database: an integrated platform for tuberculosis research. Nucleic Acids Res. 37: D499-508.
  3. McGuire, A.M., M.D. Pearson, D.E. Neafsey, and J.E. Galagan. (2008). Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biology. 9: R50.