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Jonathan Monk
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2020 – today
- 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)
2010 – 2019
- 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) - 2015
- [b1]Jonathan Monk:
Comparative Systems Biology Analysis of Microbial Pathogens. University of California, San Diego, USA, 2015
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