Jonathan M. Monk

Publication Activity (10 Years)

Years Active: 2018-2022
Publications (10 Years): 9

Top Topics

Random Subspaces

Nearest Neighbor Classifiers

Metabolic Pathways

Systems Biology

Top Venues

PLoS Comput. Biol.

BMC Syst. Biol.

Publications

Max van 't Hof, Omkar S. Mohite, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson, Morten O. A. Sommer
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. BMC Bioinform. 23 (1) (2022)
Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang, Bernhard O. Palsson
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. BMC Bioinform. 21 (1) (2020)
Jason C. Hyun, Erol S. Kavvas, Jonathan M. Monk, Bernhard O. Palsson
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. PLoS Comput. Biol. 16 (3) (2020)
Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuniga, Jared Broddrick, Karsten Zengler, Bernhard O. Palsson
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput. Biol. 15 (1) (2019)
Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M. Monk, Rayees Rahman, Mini Kamboj, Bernhard O. Palsson, Weigang Qiu, João B. Xavier
Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PLoS Comput. Biol. 15 (12) (2019)
Jean-Christophe Lachance, Colton J. Lloyd, Jonathan M. Monk, Laurence Yang, Anand Sastry, Yara Seif, Bernhard O. Palsson, Sébastien Rodrigue, Adam M. Feist, Zachary A. King, Pierre-Étienne Jacques
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. PLoS Comput. Biol. 15 (4) (2019)
Erol S. Kavvas, Yara Seif, James T. Yurkovich, Charles J. Norsigian, Saugat Poudel, William W. Greenwald, Sankha Ghatak, Bernhard O. Palsson, Jonathan M. Monk
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions. BMC Syst. Biol. 12 (1) (2018)
Nathan Mih, Elizabeth Brunk, Ke Chen, Edward Catoiu, Anand Sastry, Erol S. Kavvas, Jonathan M. Monk, Zhen Zhang, Bernhard O. Palsson
ssbio: a Python framework for structural systems biology. Bioinform. 34 (12) (2018)
Xin Fang, Jonathan M. Monk, Nathan Mih, Bin Du, Anand Sastry, Erol S. Kavvas, Yara Seif, Larry Smarr, Bernhard O. Palsson
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. BMC Syst. Biol. 12 (1) (2018)