Jonathan Monk Ph.D.

San Diego, California 92103 · (971) 645-7785 · jon@pdxmonk.com

Professional Experience

Data Scientist

Systems Biology Research Group
January 2016 - Present

Scientific Consultant

Sinopia Biosciences
January 2017 - Present

Research Scientist

Sinopia Biosceinces
January 2016 - December 2017

Graduate Student Researcher

Systems Biology Research Group, UC San Diego
September 2010 - December 2015

Education

University of California, San Diego

Ph,D., Chemical Engineering
September 2010 - December 2015

University of California, San Diego

M.S., Chemical Engineering
September 2010 - December 2012

Princeton University

B.S.E., Chemical Engineering. Minors: Computer Science and Engineering Biology
September 2004 - June 2008

Publications

All publications

‡corresponding author, * equal contribution For a current list, click here.

2022

  1. Hyun, J. C., Monk, J. M. & Palsson, B. O. Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity. BMC Genomics 23, 7 (2022).
  2. Monk, J. M. Genome-scale metabolic network reconstructions of diverse Escherichia strains reveal strain-specific adaptations. Philos. Trans. R. Soc. Lond. B Biol. Sci. 377, 20210236 (2022).
  3. Mohite, O. S., Lloyd, C., Monk, J., Weber, T. & Palsson, B. Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets. Synthetic and Systems Biology 7, 3. (2022).
  4. Holm, M. K. A., Jørgensen, K. M., Bagge, K., Worning, P., Pedersen, M., Westh, H., Monk, J. M. & Bartels, M. D. Estimated Roles of the Carrier and the Bacterial Strain When Methicillin-Resistant Staphylococcus aureus Decolonization Fails: a Case-Control Study. Microbiol Spectr e0129622 (2022). doi:10.1128/spectrum.01296-22
  5. Li, K., Schön, M., Naviaux, J. C., Monk, J. M., Alchus-Laiferová, N., Wang, L., Straka, I., Matejička, P., Valkovič, P., Ukropec, J., Tarnopolsky, M. A., Naviaux, R. K. & Ukropcová, B. Cerebrospinal fluid and plasma metabolomics of acute endurance exercise. FASEB J. 36, e22408 (2022).
  6. Rodionova, I. A., Gao, Y., Monk, J., Hefner, Y., Wong, N., Szubin, R., Lim, H. G., Rodionov, D. A., Zhang, Z., Saier, M. H., Jr & Palsson, B. O. A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. Sci. Rep. 12, 7274 (2022).
  7. Norsigian, C. J., Danhof, H. A., Brand, C. K., Midani, F. S., Broddrick, J. T., Savidge, T. C., Britton, R. A., Palsson, B. O., Spinler, J. K. & Monk, J. M. Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power. Proc. Natl. Acad. Sci. U. S. A. 119, e2119396119 (2022).
  8. Hawkey, J., Vezina, B., Monk, J. M., Judd, L. M., Harshegyi, T., López-Fernández, S., Rodrigues, C., Brisse, S., Holt, K. E. & Wyres, K. L. A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality. Genome Res. 32, 1004–1014 (2022).
  9. Xavier, J. B., Monk, J. M., Poudel, S., Norsigian, C. J., Sastry, A. V., Liao, C., Bento, J., Suchard, M. A., Arrieta-Ortiz, M. L., Peterson, E. J. R., Baliga, N. S., Stoeger, T., Ruffin, F., Richardson, R. A. K., Gao, C. A., Horvath, T. D., Haag, A. M., Wu, Q., Savidge, T. & Yeaman, M. R. Mathematical models to study the biology of pathogens and the infectious diseases they cause. iScience 25, 104079 (2022).
  10. Vezina, B., Judd, L. M., McDougall, F. K., Boardman, W. S. J., Power, M. L., Hawkey, J., Brisse, S., Monk, J. M., Holt, K. E. & Wyres, K. L. Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies. Environ. Microbiol. (2022). doi:10.1111/1462-2920.16047

2021

  1. Miller, C. R., Monk, J. M., Szubin, R. & Berti, A. D. Rapid resistance development to three antistaphylococcal therapies in antibiotic-tolerant staphylococcus aureus bacteremia. PLoS One 16, e0258592 (2021).
  2. Lachance, J.-C., Matteau, D., Brodeur, J., Lloyd, C. J., Mih, N., King, Z. A., Knight, T. F., Feist, A. M., Monk, J. M., Palsson, B. O., Jacques, P.-É. & Rodrigue, S. Genome-scale metabolic modeling reveals key features of a minimal gene set. Mol. Syst. Biol. 17, e10099 (2021).
  3. Lloyd, C. J., Monk, J., Yang, L., Ebrahim, A. & Palsson, B. O. Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. PLoS Comput. Biol. 17, e1007817 (2021).
  4. Zolkipli-Cunningham, Z., Naviaux, J. C., Nakayama, T., Hirsch, C. M., Monk, J. M., Li, K., Wang, L., Le, T. P., Meinardi, S., Blake, D. R. & Naviaux, R. K. Metabolic and behavioral features of acute hyperpurinergia and the maternal immune activation mouse model of autism spectrum disorder. PLoS One 16, e0248771 (2021).
  5. Wilken, S. E., Monk, J. M., Leggieri, P. A., Lawson, C. E., Lankiewicz, T. S., Seppälä, S., Daum, C. G., Jenkins, J., Lipzen, A. M., Mondo, S. J., Barry, K. W., Grigoriev, I. V., Henske, J. K., Theodorou, M. K., Palsson, B. O., Petzold, L. R. & O’Malley, M. A. Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. mSystems 6, (2021).
  6. T, M. R. J., Naviaux, J. C., Li, K., Wang, L., Monk, J. M., Taylor, B. A., Figueroa, C. A., Schene, A. H., Ruhé, H. G., Johanna, A., Naviaux, R. K., Metabolic features of recurrent major depressive disorder in remission, and the risk of future recurrence. Translational Psychiatry; London 11, s41398–020 (2021).
  7. Rajput, A., Poudel, S., Tsunemoto, H., Meehan, M., Szubin, R., Olson, C. A., Seif, Y., Lamsa, A., Dillon, N., Vrbanac, A., Sugie, J., Dahesh, S., Monk, J. M., Dorrestein, P. C., Knight, R., Pogliano, J., Nizet, V., Feist, A. M. & Palsson, B. O. Identifying the effect of vancomycin on health care–associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience 10, (2021).
  8. T, M. R. J., Naviaux, J. C., Li, K., Wang, L., Monk, J. M., Taylor, B. A., Figueroa, C. A., Schene, A. H., Ruhé, H. G., Johanna, A., Naviaux, R. K., Metabolic features of recurrent major depressive disorder in remission, and the risk of future recurrence. Translational Psychiatry; London 11, s41398–020 (2021).
  9. Rajput, A., Seif, Y., Choudhary, K. S., Dalldorf, C., Poudel, S., Monk, J. M. & Palsson, B. O. Pangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens. mSystems 6, (2021)

2020

  1. Sales, M. J., Sakoulas, G., Szubin, R., Palsson, B., Arias, C., Singh, K. V., Murray, B. E. & Monk, J. M. Genome Sequence Comparison of Staphylococcus aureus TX0117 and a Beta-Lactamase-Cured Derivative Shows Increased Cationic Peptide Resistance Accompanying Mutations in relA and mnaA. Microbiology Resource Announcements 9, (2020).
  2. Miller, C. R., Dey, S., Smolenski, P. D., Kulkarni, P. S., Monk, J. M., Szubin, R., Sakoulas, G. & Berti, A. D. Distinct Subpopulations of Intravalvular Methicillin-Resistant Staphylococcus aureus with Variable Susceptibility to Daptomycin in Tricuspid Valve Endocarditis. Antimicrob. Agents Chemother. 64, (2020).
  3. Botero, D., Monk, J.M, Rodríguez Cubillos, M. J., Rodríguez Cubillos, A., Restrepo, M., Bernal-Galeano, V., Reyes, A., González Barrios, A., Palsson, B. Ø., Restrepo, S. & Bernal, A. Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level. Front. Genet. 11, 837 (2020).
  4. Norsigian, C. J., Danhof, H. A., Brand, C. K., Oezguen, N., Midani, F. S., Palsson, B. O., Savidge, T. C., Britton, R. A., Spinler, J. K. & Monk, J. M‡. Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. npj Systems Biology and Applications 6, 31 (2020).
  5. Broddrick, J. T., Szubin, R., Norsigian, C. J., Monk, J. M., Palsson, B. O. & Parenteau, M. N. High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. Front. Microbiol. 11, 596626 (2020).
  6. Mih, N., Monk, J. M., Fang, X., Catoiu, E., Heckmann, D., Yang, L. & Palsson, B. O. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinformatics 21, 162 (2020).
  7. Hawkey, J., Monk, J. M., Billman-Jacobe, H., Palsson, B. & Holt, K. E. Impact of insertion sequences on convergent evolution of Shigella species. PLoS Genetics 680777 (2020). doi:10.1101/680777
  8. Mohite, O. S., Lloyd, C., Monk, J.M., Weber, T. & Palsson, B. Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets. bioRxiv 781328 (2020). doi:10.1101/781328
  9. Sales, M. J., Sakoulas, G., Szubin, R., Palsson, B., Arias, C., Singh, K. V., Murray, B. E. & Monk, J. M. Genome Sequence Comparison of Staphylococcus aureus TX0117 and a Beta-Lactamase-Cured Derivative Shows Increased Cationic Peptide Resistance Accompanying Mutations in relA and mnaA. Microbiology Resource Announcements 9, (2020).
  10. Miller, C. R., Dey, S., Smolenski, P. D., Kulkarni, P. S., Monk, J. M., Szubin, R., Sakoulas, G. & Berti, A. D. Distinct Subpopulations of Intravalvular Methicillin-Resistant Staphylococcus aureus with Variable Susceptibility to Daptomycin in Tricuspid Valve Endocarditis. Antimicrob. Agents Chemother. 64, (2020).
  11. Li, K., Naviaux, J. C., Monk, J. M., Wang, L. & Naviaux, R. K. Improved Dried Blood Spot-Based Metabolomics: A Targeted, Broad-Spectrum, Single-Injection Method. Metabolites 10, (2020).
  12. Jensen, C. S., Norsigian, C. J., Fang, X., Nielsen, X. C., Christensen, J. J., Palsson, B. O. & Monk, J. M. Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen. (2020). doi:10.3389/fgene.2020.00116
  13. Kavvas, E. S., Yang, L., Monk, J. M., Heckmann, D. & Palsson, B. O. A biochemically-interpretable machine learning classifier for microbial GWAS. Nat. Commun. 11, 2580 (2020).
  14. Botero, D., Monk, J., Rodríguez Cubillos, M. J., Rodríguez Cubillos, A., Restrepo, M., Bernal-Galeano, V., Reyes, A., González Barrios, A., Palsson, B. Ø., Restrepo, S. & Bernal, A. Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level. Front. Genet. 11, 837 (2020).
  15. Zolkipli-Cunningham, Z., Naviaux, J. C., Nakayama, T., Hirsch, C. M., Monk, J. M., Li, K., Wang, L., Le, T. P., Meinardi, S., Blake, D. & Naviaux, R. K. Metabolic and behavioral features of acute hyperpurinergia and the connection to autism spectrum disorder. Research Square (2020). doi:10.21203/rs.3.rs-63567/v1
  16. Norsigian, C. J., Danhof, H. A., Brand, C. K., Oezguen, N., Midani, F. S., Palsson, B. O., Savidge, T. C., Britton, R. A., Spinler, J. K. & Monk, J. M. Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. npj Systems Biology and Applications 6, 31 (2020).
  17. Broddrick, J. T., Szubin, R., Norsigian, C. J., Monk, J. M., Palsson, B. O. & Parenteau, M. N. High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. Front. Microbiol. 11, 596626 (2020).
  18. Mih, N., Monk, J. M., Fang, X., Catoiu, E., Heckmann, D., Yang, L. & Palsson, B. O. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinformatics 21, 162 (2020).
  19. Li, K., Naviaux, J. C., Monk, J. M., Wang, L. & Naviaux, R. K. Improved Dried Blood Spot-Based Metabolomics: A Targeted, Broad-Spectrum, Single-Injection Method. Metabolites 10, (2020).
  20. Kavvas, E. S., Yang, L., Monk, J. M., Heckmann, D. & Palsson, B. O. A biochemically-interpretable machine learning classifier for microbial GWAS. Nature Communications. 11, 2580 (2020).
  21. Jensen, C. S., Norsigian, C. J., Fang, X., Nielsen, X. C., Christensen, J. J., Palsson, B. O. & Monk, J. M. ‡ Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen. Front. Genet. (2020). doi:10.3389/fgene.2020.00116
  22. Hyun, J. C., Kavvas, E. S., Monk, J. M. ‡ & Palsson, B. O. Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS Comput. Biol. 16, e1007608 (2020).
  23. Lieven, C., Beber, M.E., Olivier, B.G., Bergmann, F.T., Babaei, P., Bartell, J.A., Blank, L.M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B.E., Edirisinghe, J.N., Fleming, R.M.T., Garcia-Jimenez, B., van Helvoirt, W., Henry, C., Hermjakob, H., Herrgard, M.J., Kim, H.U., King, Z., Koehorst, J.J., Klamt, S., Klipp, E., Lakshmanan, M., Le Novere, N., Lee, D.Y., Lee, S.Y., Lee, S., Lewis, N.E., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G.L., Monk, J.M, Nielsen, J., Nielsen, L.K., Nogales, J., Nookaew, I., Resendis, O., Palsson, B.O., Papin, J.A., Patil, K.R., Price, N.D., Richelle, A., Rocha, I., Schaap, P., Sheriff, R.S.M., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaca, P., Vik, J.O., Wodke, J.A., Xavier, J.C., Yuan, Q., Zakhartsev, M., Zhang, C. MEMOTE for standardized genome-scale metabolic model testing. Nat. Biotechnol. 1–5 (2020). doi:10.1038/s41587-020-0446-y
  24. Norsigian, C. J., Fang, X., Seif, Y., Monk, J. M. & Palsson, B. O. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nature Protocols. 15, 1–14 (2020).

2019

  1. Dey, S., Gudipati, S., Giuliano, C., Zervos, M. J., Monk, J. M., Szubin, R., Jorgensen, S. C. J., Sakoulas, G. & Berti, A. D. Reduced Production of Bacterial Membrane Vesicles Predicts Mortality in ST45/USA600 Methicillin-Resistant Staphylococcus aureus Bacteremia. Antibiotics (Basel) 9, (2019).
  2. Dey, S., Gudipati, S., Giuliano, C., Zervos, M. J., Monk, J. M., Szubin, R., Jorgensen, S. C. J., Sakoulas, G. & Berti, A. D. Reduced Production of Bacterial Membrane Vesicles Predicts Mortality in ST45/USA600 Methicillin-Resistant Staphylococcus aureus Bacteremia. Antibiotics (Basel) 9, (2019).
  3. Yan, J., Estanbouli, H., Liao, C., Kim, W., Monk, J. M., Rahman, R., Kamboj, M., Palsson, B. O., Qiu, W. & Xavier, J. B. Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PLoS Comput. Biol. 15, e1007562 (2019).
  4. Rajput, A., Poudel, S., Tsunemoto, H., Meehan, M., Szubin, R., Olson, C. A., Lamsa, A., Seif, Y., Dillon, N., Vrbanac, A., Sugie, J., Dahesh, S., Monk, J. M., Dorrestein, P. C., Knight, R., Nizet, V., Palsson, B. O., Feist, A. M. & Pogliano, J. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Sci Data 6, 322 (2019).
  5. Naviaux, R. K., Naviaux, J. C., Li, K., Wang, L., Monk, J. M., Bright, A. T., Koslik, H. J., Ritchie, J. B. & Golomb, B. A. Metabolic features of Gulf War illness.PLoS One 14, e0219531 (2019).
  6. Yang, L., Mih, N., Anand, A., Park, J. H., Tan, J., Yurkovich, J. T., Monk, J. M., Lloyd, C. J., Sandberg, T. E., Seo, S. W., Kim, D., Sastry, A. V., Phaneuf, P., Gao, Y., Broddrick, J. T., Chen, K., Heckmann, D., Szubin, R., Hefner, Y., Feist, A. M. & Palsson, B. O. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. PNAS. 116, 14368–14373 (2019).
  7. Seif, Y., Monk, J. M., Machado, H., Kavvas, E. & Palsson, B. O. Systems Biology and Pangenome of Salmonella O-Antigens. MBio 10, (2019).
  8. Machado, H., Weng, L. L., Dillon, N., Seif, Y., Holland, M., Pekar, J. E., Monk, J. M., Nizet, V., Palsson, B. O. & Feist, A. M. A defined minimal medium for systems analyses of Staphylococcus aureus reveals strain-specific metabolic requirements. Appl. Environ. Microbiol. AEM–01773 (2019).
  9. Miller, C. R., Dey, S., Smolenski, P., Kulkarni, P. S., Sakoulas, G., Monk, J. M., Szubin, R. & Berti, A. D. Distinct, Segregated Daptomycin-Susceptible and Daptomycin-Nonsusceptible Staphylococcus aureus Populations Associated with Tricuspid-Valve Infective Endocarditis. Open Forum Infectious Diseases 6, (2019).
  10. Nogales, J., Mueller, J., Gudmundsson, S., Canalejo, F. J., Duque, E., Monk, J.M., Feist, A. M., Ramos, J. L., Niu, W. & Palsson, B. O. High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities. Environ. Microbiol. (2019). doi:10.1111/1462-2920.14843
  11. Machado, H., Weng, L. L., Dillon, N., Seif, Y., Holland, M., Pekar, J. E., Monk, J. M., Nizet, V., Palsson, B. O. & Feist, A. M. Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus. Appl. Environ. Microbiol. 85, (2019).
  12. Poudel, S., Tsunemoto, H., Meehan, M., Szubin, R., Olson, C. A., Lamsa, A., Seif, Y., Dillon, N., Vrbanac, A., Sugie, J., Dahesh, S., Monk, J. M., Dorrestein, P. C., Pogliano, J., Knight, R., Nizet, V., Palsson, B. O. & Feist, A. M. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Scientific Data 6, 43 (2019).
  13. Lachance, J.-C., Lloyd, C. J., Monk, J. M., Yang, L., Sastry, A. V., Seif, Y., Palsson, B. O., Rodrigue, S., Feist, A. M., King, Z. A. & Jacques, P.-É. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS Computational Biology. 15, e1006971 (2019).
  14. Attia, H., Szubin, R., Yassin, A. S., Monk, J. M. & Aziz, R. K. Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt. Microbiology Resource Announcements 8, (2019).
  15. Monk, J. M.‡ Predicting Antimicrobial Resistance and Associated Genomic Features from Whole-Genome Sequencing. Journal of Clinical Microbiology. 57, (2019).
  16. Seif, Y., Monk, J. M., Mih, N., Tsunemoto, H., Poudel, S., Zuniga, C., Broddrick, J., Zengler, K. & Palsson, B. O. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Computational Biology. 15, e1006644 (2019).
  17. Norsigian, C., Attia, H., Szubin, R., Yassin, A., Palsson, B., Aziz, R. & Monk, J.M.‡ Comparative Genome-scale Metabolic Modelling of Metallo-beta-Lactamase–producing Multidrug-resistant Klebsiella pneumoniae Clinical Isolates. Frontiers Cellular Infection Microbiology. 9, 161 (2019).

2018

  1. Monk, J. M., Mih, N., Du, B., Sastry, A. V., Kavvas, E., Seif, Y., Smarr, L. & Palsson, B. O. Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Systems Biology. 12, 66 (2018).
  2. Kavvas, E. S., Seif, Y., Yurkovich, J. T., Norsigian, C., Poudel, S., Greenwald, W. W., Ghatak, S., Palsson, B. O. & Monk, J. M‡. Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC Systems Biology. 12, 25 (2018).
  3. Du, B., Zielinski, D. C., Monk, J. M. & Palsson, B. O. Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. PNAS. 115, 11339–11344 (2018).
  4. Kavvas, E. S., Catoiu, E., Mih, N., Yurkovich, J. T., Seif, Y., Dillon, N., Heckmann, D., Anand, A., Yang, L., Nizet, V., Monk, J.M.‡ and Palsson, B.O‡. Others. Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nature Communications. 9, 4306 (2018).
  5. Pekar, J. E., Phaneuf, P., Szubin, R., Palsson, B., Feist, A. & Monk, J. M.‡ Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiology Resource Announcements. 7, (2018).
  6. Seif, Y., Kavvas, E., Lachance, J.-C., Yurkovich, J. T., Nuccio, S.-P., Fang, X., Catoiu, E., Raffatellu, M., Palsson, B. O. & Monk, J. M‡. Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nature Communications. 9, 3771 (2018).
  7. Norsigian, C. J., Kavvas, E., Seif, Y., Palsson, B. O. & Monk, J. M.‡ iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. Frontiers in Genetics. 9, 121 (2018).
  8. Mih, N., Brunk, E., Chen, K., Catoiu, E., Sastry, A., Kavvas, E., Monk, J. M., Zhang, Z. & Palsson, B. O. ssbio: a Python framework for structural systems biology. Bioinformatics. 34, 2155–2157 (2018).
  9. Fang, X., Monk, J. M., Nurk, S., Akseshina, M., Zhu, Q., Gemmell, C., Gianetto-Hill, C., Leung, N., Szubin, R., Sanders, J., Beck, P. L., Li, W., Sandborn, W. J., Gray-Owen, S. D., Knight, R., Allen-Vercoe, E., Palsson, B. O. & Smarr, L. Metagenomics-Based, Strain-Level Analysis of From a Time-Series of Microbiome Samples From a Crohn’s Disease Patient. Frontiers in Microbiology. 9, 2559 (2018).
  10. Choudhary, K. S., Mih, N., Monk, J.M., Kavvas, E., Yurkovich, J. T., Sakoulas, G. & Palsson, B. O. The Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Frontiers in Microbiology. 9, 1082 (2018).

2017

  1. 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. Nature Biotechnology. 35, 904–908 (2017).
  2. Sastry, A., Monk, J., Tegel, H., Uhlen, M., Palsson, B. O., Rockberg, J. & Brunk, E. Machine learning in computational biology to accelerate high-throughput protein expression. Bioinformatics 33, 2487–2495 (2017).
  3. Aziz, R. K., Monk, J. M., Andrews, K. A., Nhan, J., Khaw, V. L., Wong, H., Palsson, B. O. & Charusanti, P. The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microbiol. Res. 194, 47–52 (2017).

2016

  1. Brunk, E., Mih, N., Monk, J.M., 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 Systems Biology. 10, 26 (2016).
  2. Monk, J. M., Koza, A., Campodonico, M. A., Machado, D., Seoane, J. M., Palsson, B. O., Herrgård, M. J. & Feist, A. M. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Systems. 3, 238–251.e12 (2016).
  3. Bosi, E., Monk, J. M., Aziz, R. K., Fondi, M., Nizet, V. & Palsson, B. Ø. Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. PNAS. 113, E3801–9 (2016).
  4. Brunk, E., George, K. W., Alonso-Gutierrez, J., Thompson, M., Baidoo, E., Wang, G., Petzold, C. J., McCloskey, D., Monk, J.M., 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 Systems. 2, 335–346 (2016).

2015

  1. 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. T., 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 Neglected Tropical. Diseases. 10, e0004403 (2016).
  2. 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. Scientific Reports. 5, 16025 (2015).
  3. 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. Ø. & 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. Frontiers Microbiology. 6, 958 (2015).
  4. 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., Dräger, 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. PNAS. 112, 10810–10815 (2015).
  5. O’Brien, E. J., Monk, J. M. & Palsson, B. O. Using Genome-scale Models to Predict Biological Capabilities. Cell 161, 971–987 (2015).
  6. Guzmán, 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. PNAS. 112, 929–934 (2015).

2014

  1. Monk, J.M. & Palsson, B. O. Genetics. Predicting microbial growth. Science. 344, 1448–1449 (2014).
  2. Monk, J.M., Nogales, J. & Palsson, B. O. Optimizing genome-scale network reconstructions. Nature Biotechnology. 32, 447–452 (2014).
  3. Bordbar, A., Monk, J. M., King, Z. A. & Palsson, B. O. Constraint-based models predict metabolic and associated cellular functions. Nature Review Genetics. 15, 107–120 (2014).

2013

  1. Monk, J. M., Charusanti, P., Aziz, R. K., Lerman, J. A., Premyodhin, N., Orth, J. D., Feist, A. M. & Palsson, B. Ø. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. PNAS 110, 20338–20343 (2013).

2011

  1. Ang, Y.-S., Tsai, S.-Y., Lee, D.-F., Monk, J.M., Su, J., Ratnakumar, K., Ding, J., Ge, Y., Darr, H., Chang, B., Wang, J., Rendl, M., Bernstein, E., Schaniel, C. & Lemischka, I. R. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145, 183–197 (2011).

Awards & Certifications

  • Outstanding Graduate Student Award - UC San Diego 2015
  • National Science Foundation Fellow - EAPSI 2013