James Galagan, PhD

Associate Director, Information Technology/Systems Biology Core

Associate Professor, Biomedical Engineering and Microbiology
Associate Director, Microbial Genome Analysis, Broad Institute

Education/Training

BS, Computer and Electrical Engineering, UC Davis Ph.D.
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

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.