Jonathan M. Monk

8.6k citations

97 papers · 4.3k indexed · 2 hit papers · h-index 31

Impact in

Molecular Biology top 2%
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Enzyme Catalysis and Immobilization
- Metabolomics and Mass Spectrometry Studies
Molecular Medicine top 2%

Papers in

Co-authors: Bernhard Ø. Palsson Zachary A. King Edward J. O’Brien Aarash Bordbar Adam M. Feist Erol Kavvas Yara Seif Ramy K. Aziz
Journals: Proceedings of the National Academy of Sciences (7 papers)PLoS Computational Biology (5 papers)Nature Communications (4 papers)Frontiers in Microbiology (4 papers)Translational Psychiatry (3 papers)
Partner nations: United States Denmark Canada

In The Last Decade

Jonathan M. Monk

91 papers receiving 4.3k citations

Hit Papers

align trajectories log scale

Using Genome-scale Models to Predict Biological Capabilities 2015 · 471 citations

Peers

Countries citing papers authored by Jonathan M. Monk

Since Specialization

Citations

This map shows the geographic impact of Jonathan M. Monk's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Jonathan M. Monk with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Jonathan M. Monk more than expected).

Fields of papers citing papers by Jonathan M. Monk

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Jonathan M. Monk. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Jonathan M. Monk. The network helps show where Jonathan M. Monk may publish in the future.

Co-authorship network

The 25 scholars most cited alongside Jonathan M. Monk, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Jonathan M. Monk Line = papers co-authored together Jonathan M. Monk links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

#	Work
1	Colistin exerts potent activity against mcr+ Enterobacteriaceae via synergistic interactions with the host defense Journal of Clinical Investigation ·Monika Kumaraswamy, Angelica M. Riestra, Andrzej Ciebiera, Samira Dahesh, Fatemeh Askarian, Satoshi Uchiyama, Jonathan M. Monk, Sang‐Hun Jung, Е. В. Шелег, 陳德遠, N Marse Evalina, Jürgen B. Bulitta, Yinzhi Lang, Armin Kousha, Elisabet Bjånes, М. В. Шавнина, T.E. Clark, Hideya Seo, George Sakoulas, Victor Nizet	2025	2
2	Sequencing and genome-scale virulome reconstruction of Enterococcus faecalis clinical isolates delineate genes involved in gelatinase activity and biofilm formation Microbial Pathogenesis ·George Lewis Amos, G. Umarova, Richard Szubin, Jonathan M. Monk, Mona T. Kashef, Ramy K. Aziz	2025	1
3	The thermal dependent biology of cultured lumpfish (Cyclopterus lumpus Linnaeus 1758): Differences due to temperatures during early life and how tolerance is measured Aquaculture ·R. M. Eisenberg, Rebeccah M. Sandrelli, Dennis S. Tucker, Jonathan M. Monk, Daniel G. Boyce, Ruchi Singhal, 智明高柳, A. Kurt Gamperl	2024	0
4	A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex Microbial Genomics ·JD Choi, Ben Vezina, Jane Hawkey, Virginie Passet, Helena Mölter, Jonathan M. Monk, Sylvain Brisse, Kathryn E. Holt, Kelly L. Wyres	2024	1
5	CyuR is a dual regulator for L-cysteine dependent antimicrobial resistance in Escherichia coli Communications Biology ·Irina A. Rodionova, Hyun Gyu Lim, Ye Gao, Dmitry A. Rodionov, Y. Auger, Richard Szubin, Maria Marília Mesquita Patela Bação, Jonathan M. Monk, Bernhard Ø. Palsson	2024	1
6	Decomposition of the pangenome matrix reveals a structure in gene distribution in the Escherichia coli species mSphere ·Siddharth Chauhan, P. A. HARDING, Jason C. Hyun, Jonathan M. Monk, Patrick V. Phaneuf, Bernhard Ø. Palsson	2024	2
7	Rev1 deficiency induces a metabolic shift in MEFs that can be manipulated by the NAD+ precursor nicotinamide riboside Heliyon ·健佐々木, Zhiquan Li, Yuan Li, Fay B. West, Yili Di, Lin Wang, Jonathan M. Monk, Niels de Wind, Vilhelm A. Bohr, Claus Desler, Robert K. Naviaux, Lene Juel Rasmussen	2023	1
8	A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli Scientific Reports ·Irina A. Rodionova, Ye Gao, Jonathan M. Monk, Ying Hefner, Shubham Dabas, Richard Szubin, Hyun Gyu Lim, Dmitry A. Rodionov, Zhongge Zhang, Milton H. Saier, Bernhard Ø. Palsson	2022	14
9	Mathematical models to study the biology of pathogens and the infectious diseases they cause iScience ·João B. Xavier, Jonathan M. Monk, Saugat Poudel, Charles J. Norsigian, Anand V. Sastry, Chen Liao, José Maurício S. Bento, Marc A. Suchard, Mario L. Arrieta‐Ortiz, Eliza J. R. Peterson, Nitin S. Baliga, Thomas Stoeger, Felicia Ruffin, S. Czuzi, Catherine A. Gao, Thomas D. Horvath, Anthony M. Haag, Qinglong Wu, Tor Savidge, Michael R. Yeaman	2022	11
10	A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality Genome Research ·Jane Hawkey, Ben Vezina, Jonathan M. Monk, Louise M. Judd, С.Н. Лысенков, Helena Mölter, Carla Rodrigues, Sylvain Brisse, Kathryn E. Holt, Kelly L. Wyres	2022	8
11	Historical biomonitoring of pollution trends in the North Pacific using archived samples from the Continuous Plankton Recorder Survey The Science of The Total Environment ·Kefeng Li, Jane C. Naviaux, Timothy Pinion, Lin Wang, Jonathan M. Monk, P Micera, Clare Ostle, Sonia Batten, Robert K. Naviaux	2022	1
12	Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus mSystems ·St. Elmo Wilken, Jonathan M. Monk, S.Sn. Prijono Susilo Ahmad, Christopher E. Lawson, Thomas S. Lankiewicz, Susanna Seppälä, Chris Daum, Jerry Jenkins, Anna Lipzen, Stephen J. Mondo, Kerrie Barry, Igor V. Grigoriev, John K. Henske, Michael K. Theodorou, Bernhard Ø. Palsson, Linda Petzold, Michelle O’Malley	2021	45
13	A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types PLoS Computational Biology ·Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zúñiga, Jared T. Broddrick, Karsten Zengler, Bernhard Ø. Palsson	2019	35
14	BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data PLoS Computational Biology ·Jean‐Christophe Lachance, Colton J. Lloyd, Jonathan M. Monk, Laurence Yang, Anand V. Sastry, Yara Seif, Bernhard Ø. Palsson, Sébastien Rodrigue, Adam M. Feist, Zachary A. King, Pierre‐Étienne Jacques	2019	72
15	ssbio: a Python framework for structural systems biology Bioinformatics ·Nathan Mih, Elizabeth Brunk, Ke Chen, Edward Catoiu, Anand V. Sastry, Erol Kavvas, Jonathan M. Monk, Zhen Zhang, Bernhard Ø. Palsson	2018	26
16	Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits Nature Communications ·Yara Seif, Erol Kavvas, Jean‐Christophe Lachance, James T. Yurkovich, Sean‐Paul Nuccio, Xin Fang, Edward Catoiu, Manuela Raffatellu, Bernhard Ø. Palsson, Jonathan M. Monk	2018	95
17	Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa BMC Systems Biology ·Xin Fang, Jonathan M. Monk, Nathan Mih, Bin Du, Anand V. Sastry, Erol Kavvas, Yara Seif, Larry Smarr, Bernhard Ø. Palsson	2018	35
18	Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance Nature Communications ·Erol Kavvas, Edward Catoiu, Nathan Mih, James T. Yurkovich, Yara Seif, Nicholas Dillon, David Heckmann, Amitesh Anand, Laurence Yang, Victor Nizet, Jonathan M. Monk, Bernhard Ø. Palsson	2018	129
19	Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions BMC Systems Biology ·Erol Kavvas, Yara Seif, James T. Yurkovich, Charles J. Norsigian, Saugat Poudel, William W. Greenwald, Yize Wang R, Bernhard Ø. Palsson, Jonathan M. Monk	2018	45
20	Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences Methods in molecular biology ·Jonathan M. Monk, Emanuele Bosi	2017	3

About Jonathan M. Monk

Jonathan M. Monk is a scholar working on Molecular Medicine, Biological Psychiatry, Microbiology, Clinical Biochemistry and Molecular Biology, having authored 97 papers that have together received 4.3k indexed citations. Recurring topics across this work include Microbial Metabolic Engineering and Bioproduction (41 papers), Bacterial Genetics and Biotechnology (19 papers), Genomics and Phylogenetic Studies (15 papers), Biofuel production and bioconversion (15 papers), Antimicrobial Resistance in Staphylococcus (11 papers), RNA and protein synthesis mechanisms (10 papers), Gene Regulatory Network Analysis (10 papers) and Bioinformatics and Genomic Networks (10 papers). The work is most often cited by research in Molecular Biology (3.6k citations), Molecular Medicine (198 citations), Endocrinology (172 citations), Biomedical Engineering (1.0k citations) and Clinical Biochemistry (133 citations). Jonathan M. Monk has collaborated with scholars based in United States, Denmark and Canada. Frequent co-authors include Bernhard Ø. Palsson, Zachary A. King, Edward J. O’Brien, Aarash Bordbar, Adam M. Feist, Erol Kavvas, Yara Seif, Ramy K. Aziz, Juan Nogales and Nathan Mih. Their work appears in journals such as Proceedings of the National Academy of Sciences, PLoS Computational Biology, Nature Communications, Frontiers in Microbiology and Translational Psychiatry.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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