Loyola University Chicago

Department of Biology

Catherine Putonti

Ph.D. 2006, University of Houston
Phone: 773.508.3277
Fax: 773.508.3646


The areas of my current research are computational biology and microbial evolution, blending traditional bench molecular biology techniques and applied computer science. As such, the line between biology and computer science is often blurred. Specifically, I have concentrated my scientific interests on the two areas below.

1. The evolution of virus-host genome compatibility. Previous bioinformatic analyses, including analyses conducted in our lab, have identified correlations between the nucleotide usage of viruses and their hosts. This stands to reason as viruses are largely dependent upon their hosts for biosynthesis. As such, we have focused on the evolution of pathogen-host nucleotide correspondences and their correlation with virulence. Using the model system of bacteriophages and their hosts, we have created engineered strains by altering their nucleotide usage relative to the preferences of their host and evolved these mutants for hundreds of generations. This has afforded us the opportunity to watch evolution in action! This research integrates computational analysis, both in the design of our mutant strains as well as in the examination of the mutations which arise over the course of our selection experiments, with experimental evolution and molecular biology.

2. The role of bacteriophages in regulating bacterial populations. Looking out at our beloved biology building at Lake Michigan spurred us to expand our questions beyond just model systems to that of the complex aquatic environment. So frequently we hear of Lake Michigan beach closings due to elevated E. coli levels, but what role do bacteriophages play in the fluctuations of bacteria within near-shore waters? The increased throughput and decreased cost of next-generation sequencing allowed us to begin asking questions such as this. Our first challenge, however, was not molecular in nature, rather it was computational. Viruses have no universal markers like rRNA and, despite their omnipresence, few bacteriophage species have been fully sequenced and characterized. Thus, we began the development of new computational tools for the analysis of short sequencing reads from environmental viral species. This is in parallel with the molecular investigation of the phage diversity and density in the Chicago area waters.


Watkins SC, Kuehnle N, Ruggeri CA, Malki K, Bruder K, Elayyan J, Damisch K, Vahora N, O’Malley P, Ruggles-Sage B, Romer Z, Putonti C. Assessment of a metaviromic dataset generated from nearshore Lake Michigan. Marine Freshw Res. In Press.

Putonti C, Nowicki B, Shaffer M, Fofanov Y, Nowicki S. Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus. BMC Evol Biol. 2013, 13: 184.

Putonti C, Quach B, Kooistra RL, Kanzok S. The evolution and putative function of phosducin-like proteins in the malaria parasite Plasmodium. Infect Genet Evol. 2013, 13: 49-55.

Cox J, Schubert A, Travisano M, Putonti C. Adaptive evolution and inherent tolerance to extreme thermal environments. BMC Evol Biol. 2010, 10: 75.

Schubert A, Putonti C. Evolution of the sequence composition of Flaviviruses. Infect Genet Evol. 2010, 10: 129-136.

Putonti, C., Luo, Y., Katili, C., Chumakov, S., Fox, G.E., Graur, D., Fofanov, Y. A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Mol Biol Evol. 2006; 23: 1863-1868.

Putonti, C., Chumakov, S., Mitra, R., Fox, G.E., Willson, R.C., Fofanov, Y. Human-blind probes and primers for Dengue virus identification: Exhaustive analysis of subsequences present in the human and 83 Dengue genome sequences. FEBS J. 2006; 273: 398-408.