Advancements in high-throughput biotechnologies have drowned us in a sea of biological data. I aim to develop mathematical methods that leverage this data deluge towards a more predictive biology. My research is focused on the data types of genomics, transcriptomics, fluxomics, and genome-scale reconstructions.
Kavvas ES., Seif Y., Yurkovich JT., Norsigian C., Poudel S., Greenwald WW., Ghatak S., Palsson BO., Monk JM.Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC Systems Biology , (2018) 12:25
- Kavvas ES., Catoui E., Mih N., Yurkovich JT., Seif Y., Dillon N., Heckmann D., Anand A., Yang L., Nizet V., Monk JM., Palsson BO. Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance, Nature Communications, (2018) 9:4306
- Yara Seif, E. Kavvas, JC Lachance, JT. Yurkovich, S. Nuccio, X. Fang, E. Catoiu, M. Raffatellu, Bernhard O. Palsson & Jonathan M. Monk Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nature Communications, 2018
- Xin Fang, JM. Monk, N. Mih, B. Du, AV. Sastry, E. Kavvas, Y. Seif, L. Smarr and BO. Palsson Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Systems Biology, 2018 12:66
- Nathan Mih, E. Brunk, K. Chen, E. Catoiu, A. Sastry, E. Kavvas, JM. Monk, Z. Zhang, BO. Palsson ssbio: a Python framework for structural systems biology. Bioinformatics, 2018
- B. Du, DC. Zielinski, ES. Kavvas, A. Dräger, J. Tan, Z. Zhang, KE. Ruggiero, GA. Arzumanyan and BO. Palsson Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Systems Biology, 2016 10:40