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Books and Theses
- 2015
[b1]Jonathan Monk:
Comparative Systems Biology Analysis of Microbial Pathogens. University of California, San Diego, USA, 2015
Journal Articles
- 2022
- [j12]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): 566 (2022) - 2021
- [j11]Colton J. Lloyd, Jonathan Monk, Laurence Yang, Ali Ebrahim, Bernhard O. Palsson:
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. PLoS Comput. Biol. 17(6) (2021) - 2020
- [j10]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): 162 (2020) - [j9]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) - 2019
- [j8]Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, 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) - [j7]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) - [j6]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) - 2018
- [j5]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): 2155-2157 (2018) - [j4]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): 25:1-25:15 (2018) - [j3]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): 66:1-66:10 (2018) - 2017
- [j2]Anand Sastry, Jonathan Monk, Hanna Tegel, Mathias Uhlen, Bernhard O. Palsson, Johan Rockberg, Elizabeth Brunk:
Machine learning in computational biology to accelerate high-throughput protein expression. Bioinform. 33(16): 2487-2495 (2017) - 2016
- [j1]Elizabeth Brunk, Nathan Mih, Jonathan Monk, Zhen Zhang, Edward J. O'Brien, Spencer E. Bliven, Ke Chen, Roger L. Chang, Philip E. Bourne, Bernhard O. Palsson:
Systems biology of the structural proteome. BMC Syst. Biol. 10: 26 (2016)
Coauthor Index
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