Jonathan Monk

Computational & Data Science Researcher

I am Researcher in the Systems Biology Research Group. My research interests are in constructing and applying metabolic network reconstructions with a focus on infectious disease applications. I compare metabolic network reconstructions of related microbes to interpret and classify their evolutionary differences. Furthermore, I am particularly interested in applying high-throughput techniques to build and improve metabolic network reconstructions.

Google scholar


  1. Monk, J. M.; Charusanti, P.; Aziz, R. K.; Lerman, J. A.; Premyodhin, N.; Orth, J. D.; Feist, A. M.; Palsson, B. O., Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A 2013, 110 (50), 20338-43.
  2. Bordbar, A.; Monk, J. M.; King, Z. A.; Palsson, B. O., Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet 2014, 15 (2), 107-20.
  3. Monk, J.; Nogales, J.; Palsson, B. O., Optimizing genome-scale network reconstructions. Nat Biotechnol 2014, 32 (5), 447-52.
  4. Monk, J.; Palsson, B. O., Genetics. Predicting microbial growth. Science 2014, 344 (6191), 1448-9.
  5. Aziz, R. K.; Khaw, V. L.; Monk, J. M.; Brunk, E.; Lewis, R.; Loh, S. I.; Mishra, A.; Nagle, A. A.; Satyanarayana, C.; Dhakshinamoorthy, S.; Luche, M.; Kitchen, D. B.; Andrews, K. A.; Palsson, B. O.; Charusanti, P., Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC. Front Microbiol 2015, 6, 958.
  6. Guzman, G. I.; Utrilla, J.; Nurk, S.; Brunk, E.; Monk, J. M.; Ebrahim, A.; Palsson, B. O.; Feist, A. M., Model-driven discovery of underground metabolic functions in Escherichia coli. Proc Natl Acad Sci U S A 2015, 112 (3), 929-34.
  7. O'Brien, E. J.; Monk, J. M.; Palsson, B. O., Using Genome-scale Models to Predict Biological Capabilities. Cell 2015, 161 (5), 971-87.
  8. Yang, L.; Tan, J.; O'Brien, E. J.; Monk, J. M.; Kim, D.; Li, H. J.; Charusanti, P.; Ebrahim, A.; Lloyd, C. J.; Yurkovich, J. T.; Du, B.; Drager, A.; Thomas, A.; Sun, Y.; Saunders, M. A.; Palsson, B. O., Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proc Natl Acad Sci U S A 2015, 112 (34), 10810-5.
  9. Aziz, R. K.; Monk, J. M.; Lewis, R. M.; In Loh, S.; Mishra, A.; Abhay Nagle, A.; Satyanarayana, C.; Dhakshinamoorthy, S.; Luche, M.; Kitchen, D. B.; Andrews, K. A.; Fong, N. L.; Li, H. J.; Palsson, B. O.; Charusanti, P., Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. Sci Rep 2015, 5, 16025.
  10. Fouts, D. E.; Matthias, M. A.; Adhikarla, H.; Adler, B.; Amorim-Santos, L.; Berg, D. E.; Bulach, D.; Buschiazzo, A.; Chang, Y. F.; Galloway, R. L.; Haake, D. A.; Haft, D. H.; Hartskeerl, R.; Ko, A. I.; Levett, P. N.; Matsunaga, J.; Mechaly, A. E.; Monk, J. M.; Nascimento, A. L.; Nelson, K. E.; Palsson, B.; Peacock, S. J.; Picardeau, M.; Ricaldi, J. N.; Thaipandungpanit, J.; Wunder, E. A., Jr.; Yang, X. F.; Zhang, J. J.; Vinetz, J. M., What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PLoS Negl Trop Dis 2016, 10 (2), e0004403.
  11. Brunk, E.; Mih, N.; Monk, J.; Zhang, Z.; O'Brien, E. J.; Bliven, S. E.; Chen, K.; Chang, R. L.; Bourne, P. E.; Palsson, B. O., Systems biology of the structural proteome. BMC Syst Biol 2016, 10 (1), 26.
  12. Brunk, E.; George, K. W.; Alonso-Gutierrez, J.; Thompson, M.; Baidoo, E.; Wang, G.; Petzold, C. J.; McCloskey, D.; Monk, J.; Yang, L.; O'Brien, E. J.; Batth, T. S.; Martin, H. G.; Feist, A.; Adams, P. D.; Keasling, J. D.; Palsson, B. O.; Lee, T. S., Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Syst 2016, 2 (5), 335-46.
  13. Bosi, E.; Monk, J. M.; Aziz, R. K.; Fondi, M.; Nizet, V.; Palsson, B. O., Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. Proc Natl Acad Sci U S A 2016, 113 (26), E3801-9.
  14. Monk, J. M.; Koza, A.; Campodonico, M. A.; Machado, D.; Seoane, J. M.; Palsson, B. O.; Herrgard, M. J.; Feist, A. M., Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst 2016, 3 (3), 238-251 e12.
  15. Monk, J. M.; Lloyd, C. J.; Brunk, E.; Mih, N.; Sastry, A.; King, Z.; Takeuchi, R.; Nomura, W.; Zhang, Z.; Mori, H.; Feist, A. M.; Palsson, B. O., iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol 2017, 35 (10), 904-908.


B.S.E Chemical Engineering, Princeton University, 2008 Ph.D. Chemical Engineering, UC San Diego, 2015

Contact Information

Email Address: jmonk at ucsd dot edu
Phone: (858) 822 1144
Mailing Address: 9500 Gilman Drive, Mail Code 0412 , La Jolla, CA 92093-0412