Jonathan Monk - Publications

Affiliations: 
2015 University of California, San Diego, La Jolla, CA 

37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Nogales J, Mueller J, Gudmundsson S, Canalejo FJ, Duque E, Monk J, Feist AM, Ramos JL, Niu W, Palsson BO. High-quality genome-scale metabolic modeling of Pseudomonas putida highlights its broad metabolic capabilities. Environmental Microbiology. PMID 31657101 DOI: 10.1111/1462-2920.14843  0.84
2019 Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM. A defined minimal medium for systems analyses of reveals strain-specific metabolic requirements. Applied and Environmental Microbiology. PMID 31471305 DOI: 10.1128/AEM.01773-19  0.84
2019 Seif Y, Monk JM, Machado H, Kavvas E, Palsson BO. Systems Biology and Pangenome of O-Antigens. Mbio. 10. PMID 31455646 DOI: 10.1128/mBio.01247-19  0.84
2019 Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270234 DOI: 10.1073/pnas.1905039116  0.84
2019 Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ, Aziz RK, Monk JM. Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Clinical Isolates. Frontiers in Cellular and Infection Microbiology. 9: 161. PMID 31179245 DOI: 10.3389/fcimb.2019.00161  0.84
2019 Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, et al. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Scientific Data. 6: 43. PMID 31028276 DOI: 10.1038/s41597-019-0051-4  0.84
2019 Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ. BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. Plos Computational Biology. 15: e1006971. PMID 31009451 DOI: 10.1371/journal.pcbi.1006971  0.84
2019 Attia H, Szubin R, Yassin AS, Monk JM, Aziz RK. 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. PMID 30801061 DOI: 10.1128/MRA.01418-18  0.52
2019 Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. Plos Computational Biology. 15: e1006644. PMID 30625152 DOI: 10.1371/journal.pcbi.1006644  0.84
2018 Pekar JE, Phaneuf P, Szubin R, Palsson B, Feist A, Monk JM. Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiology Resource Announcements. 7. PMID 30533692 DOI: 10.1128/MRA.00890-18  0.52
2018 Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, et al. Metagenomics-Based, Strain-Level Analysis of From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Frontiers in Microbiology. 9: 2559. PMID 30425690 DOI: 10.3389/fmicb.2018.02559  0.84
2018 Kavvas ES, Catoiu 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. 9: 4306. PMID 30333483 DOI: 10.1038/s41467-018-06634-y  0.84
2018 Du B, Zielinski DC, Monk JM, Palsson BO. Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. Proceedings of the National Academy of Sciences of the United States of America. PMID 30309961 DOI: 10.1073/pnas.1805367115  0.84
2018 Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM. Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nature Communications. 9: 3771. PMID 30218022 DOI: 10.1038/s41467-018-06112-5  0.84
2018 Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO. 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. PMID 29890970 DOI: 10.1186/s12918-018-0587-5  0.84
2018 Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO. The Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Frontiers in Microbiology. 9: 1082. PMID 29887846 DOI: 10.3389/fmicb.2018.01082  0.84
2018 Norsigian CJ, Kavvas E, Seif Y, Palsson BO, Monk JM. iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of AYE. Frontiers in Genetics. 9: 121. PMID 29692801 DOI: 10.3389/fgene.2018.00121  0.84
2018 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. 12: 25. PMID 29499714 DOI: 10.1186/s12918-018-0557-y  0.84
2018 Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO, Valencia A. ssbio: A Python Framework for Structural Systems Biology. Bioinformatics (Oxford, England). PMID 29444205 DOI: 10.1093/bioinformatics/bty077  0.84
2017 Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. iML1515, a knowledgebase that computes Escherichia coli traits. Nature Biotechnology. 35: 904-908. PMID 29020004 DOI: 10.1038/nbt.3956  0.84
2017 Sastry A, Monk J, Tegel H, Uhlén M, Palsson BO, Rockberg J, Brunk E. Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression. Bioinformatics (Oxford, England). PMID 28398465 DOI: 10.1093/bioinformatics/btx207  0.84
2017 Aziz RK, Monk JM, Andrews KA, Nhan J, Khaw VL, Wong H, Palsson BO, Charusanti P. The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microbiological Research. 194: 47-52. PMID 27938862 DOI: 10.1016/j.micres.2016.10.006  0.84
2016 Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Systems. PMID 27667363 DOI: 10.1016/j.cels.2016.08.013  0.84
2016 Bosi E, Monk JM, Aziz RK, Fondi M, Nizet V, Palsson BØ. Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. Proceedings of the National Academy of Sciences of the United States of America. PMID 27286824 DOI: 10.1073/pnas.1523199113  0.76
2016 Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, et al. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Systems. PMID 27211860 DOI: 10.1016/j.cels.2016.04.004  0.76
2016 Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. Systems biology of the structural proteome. Bmc Systems Biology. 10: 26. PMID 26969117 DOI: 10.1186/s12918-016-0271-6  0.76
2016 Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, ... ... Monk JM, et al. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. Plos Neglected Tropical Diseases. 10: e0004403. PMID 26890609 DOI: 10.1371/journal.pntd.0004403  0.76
2015 Aziz RK, Monk JM, Lewis RM, In Loh S, Mishra A, Abhay Nagle A, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Fong NL, Li HJ, Palsson BO, Charusanti P. Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. Scientific Reports. 5: 16025. PMID 26531810 DOI: 10.1038/srep16025  0.76
2015 Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, 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 in Microbiology. 6: 958. PMID 26441892 DOI: 10.3389/fmicb.2015.00958  0.76
2015 Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, et al. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences of the United States of America. PMID 26261351 DOI: 10.1073/pnas.1501384112  0.76
2015 O'Brien EJ, Monk JM, Palsson BO. Using Genome-scale Models to Predict Biological Capabilities. Cell. 161: 971-987. PMID 26000478 DOI: 10.1016/j.cell.2015.05.019  0.76
2015 Guzmán GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM. Model-driven discovery of underground metabolic functions in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 112: 929-34. PMID 25564669 DOI: 10.1073/pnas.1414218112  0.76
2014 Monk J, Palsson BO. Genetics. Predicting microbial growth. Science (New York, N.Y.). 344: 1448-9. PMID 24970063 DOI: 10.1126/science.1253388  0.76
2014 Monk J, Nogales J, Palsson BO. Optimizing genome-scale network reconstructions. Nature Biotechnology. 32: 447-52. PMID 24811519 DOI: 10.1038/nbt.2870  0.76
2014 Bordbar A, Monk JM, King ZA, Palsson BO. Constraint-based models predict metabolic and associated cellular functions. Nature Reviews. Genetics. 15: 107-20. PMID 24430943 DOI: 10.1038/nrg3643  0.76
2013 Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proceedings of the National Academy of Sciences of the United States of America. 110: 20338-43. PMID 24277855 DOI: 10.1073/pnas.1307797110  0.76
2011 Ang YS, Tsai SY, Lee DF, Monk J, Su J, Ratnakumar K, Ding J, Ge Y, Darr H, Chang B, Wang J, Rendl M, Bernstein E, Schaniel C, Lemischka IR. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell. 145: 183-97. PMID 21477851 DOI: 10.1016/j.cell.2011.03.003  0.76
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