James Galagan, Ph.D.
Associate Professor, Biomedical Engineering and Microbiology
Ph.D., Computational Neuroscience, MIT
B.S., Computer and Electrical Engineering, UC Davis
Systems Biology, Infectious Diseases, Tuberculosis, Computational Biology, Genomics and Microbiology.
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 Recent Publications
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.
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.
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.
Decaprio, D., Vinson, J.P., Pearson, M.D., Montgomery, P., Doherty, M., and Galagan, J.E. (2007). Conrad: Gene prediction using conditional random fields. Genome Res.
Neafsey, D.E. and Galagan, J.E. (2007). Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol. 7: 119.
Neafsey, D.E. and Galagan, J.E. (2007). Dual modes of natural selection on upstream open reading frames. Mol Biol Evol. 24: 1744-1751.
Galagan, J.E., Calvo, S.E., Cuomo, C., Ma, L.J., Wortman, J.R., Batzoglou, S., et al. (2005). Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature. 438: 1105-1115.
Galagan, J.E., Calvo, S.E., Borkovich, K.A., Selker, E.U., et al. (2003). The genome sequence of the filamentous fungus Neurospora crassa. Nature. 422: 859-868.