Constraint-based models predict metabolic and associated cellular functions
Bordbar, Aarash, Monk, Jonathan M, King, Zachary A, Palsson, Bernhard O
Published in Nature reviews. Genetics (01.02.2014)
Published in Nature reviews. Genetics (01.02.2014)
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A biochemically-interpretable machine learning classifier for microbial GWAS
Kavvas, Erol S, Yang, Laurence, Monk, Jonathan M, Heckmann, David, Palsson, Bernhard O
Published in Nature communications (22.05.2020)
Published in Nature communications (22.05.2020)
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Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
Kavvas, Erol S, Catoiu, Edward, Mih, Nathan, Yurkovich, James T, Seif, Yara, Dillon, Nicholas, Heckmann, David, Anand, Amitesh, Yang, Laurence, Nizet, Victor, Monk, Jonathan M, Palsson, Bernhard O
Published in Nature communications (17.10.2018)
Published in Nature communications (17.10.2018)
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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
Seif, Yara, Kavvas, Erol, Lachance, Jean-Christophe, Yurkovich, James T, Nuccio, Sean-Paul, Fang, Xin, Catoiu, Edward, Raffatellu, Manuela, Palsson, Bernhard O, Monk, Jonathan M
Published in Nature communications (14.09.2018)
Published in Nature communications (14.09.2018)
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Impact of insertion sequences on convergent evolution of Shigella species
Hawkey, Jane, Monk, Jonathan M, Billman-Jacobe, Helen, Palsson, Bernhard, Holt, Kathryn E
Published in PLoS genetics (09.07.2020)
Published in PLoS genetics (09.07.2020)
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Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
Monk, Jonathan M., Charusanti, Pep, Aziz, Ramy, Lerman, Joshua A., Premyodhin, Ned, Orth, Jeffrey D., Feist, Adam M., Palsson, Bernhard Ø.
Published in Proceedings of the National Academy of Sciences - PNAS (10.12.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (10.12.2013)
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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
Lachance, Jean-Christophe, Lloyd, Colton J, Monk, Jonathan M, Yang, Laurence, Sastry, Anand V, Seif, Yara, Palsson, Bernhard O, Rodrigue, Sébastien, Feist, Adam M, King, Zachary A, Jacques, Pierre-Étienne
Published in PLoS computational biology (01.04.2019)
Published in PLoS computational biology (01.04.2019)
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Model-driven discovery of underground metabolic functions in Escherichia coli
Guzmán, Gabriela I, Utrilla, José, Nurk, Sergey, Brunk, Elizabeth, Monk, Jonathan M, Ebrahim, Ali, Palsson, Bernhard O, Feist, Adam M
Published in Proceedings of the National Academy of Sciences - PNAS (20.01.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (20.01.2015)
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A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types
Seif, Yara, Monk, Jonathan M, Mih, Nathan, Tsunemoto, Hannah, Poudel, Saugat, Zuniga, Cristal, Broddrick, Jared, Zengler, Karsten, Palsson, Bernhard O
Published in PLoS computational biology (01.01.2019)
Published in PLoS computational biology (01.01.2019)
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Metabolic and behavioral features of acute hyperpurinergia and the maternal immune activation mouse model of autism spectrum disorder
Zolkipli-Cunningham, Zarazuela, Naviaux, Jane C, Nakayama, Tomohiro, Hirsch, Charlotte M, Monk, Jonathan M, Li, Kefeng, Wang, Lin, Le, Thuy P, Meinardi, Simone, Blake, Donald R, Naviaux, Robert K
Published in PloS one (18.03.2021)
Published in PloS one (18.03.2021)
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Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
Mih, Nathan, Monk, Jonathan M, Fang, Xin, Catoiu, Edward, Heckmann, David, Yang, Laurence, Palsson, Bernhard O
Published in BMC bioinformatics (29.04.2020)
Published in BMC bioinformatics (29.04.2020)
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Metabolic features of Gulf War illness
Naviaux, Robert K, Naviaux, Jane C, Li, Kefeng, Wang, Lin, Monk, Jonathan M, Bright, A Taylor, Koslik, Hayley J, Ritchie, Janis B, Golomb, Beatrice A
Published in PloS one (26.07.2019)
Published in PloS one (26.07.2019)
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Improved Dried Blood Spot-Based Metabolomics: A Targeted, Broad-Spectrum, Single-Injection Method
Li, Kefeng, Naviaux, Jane C, Monk, Jonathan M, Wang, Lin, Naviaux, Robert K
Published in Metabolites (27.02.2020)
Published in Metabolites (27.02.2020)
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Genome‐scale metabolic modeling reveals key features of a minimal gene set
Lachance, Jean‐Christophe, Matteau, Dominick, Brodeur, Joëlle, Lloyd, Colton J, Mih, Nathan, King, Zachary A, Knight, Thomas F, Feist, Adam M, Monk, Jonathan M, Palsson, Bernhard O, Jacques, Pierre‐Étienne, Rodrigue, Sébastien
Published in Molecular systems biology (01.07.2021)
Published in Molecular systems biology (01.07.2021)
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