Predicting Antimicrobial Resistance and Associated Genomic Features from Whole-Genome Sequencing

Por Monk, Jonathan M.
Publicado no J Clin Microbiol (2019)

Using Genome-Scale Models to Predict Biological Capabilities

Por O’Brien, Edward J., Monk, Jonathan M., Palsson, Bernhard O.
Publicado no Cell (2015)

Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice

Por Du, Bin, Zielinski, Daniel C., Monk, Jonathan M., Palsson, Bernhard O.
Publicado no Proc Natl Acad Sci U S A (2018)

Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, E...

Por Attia, Heba, Szubin, Richard, Yassin, Aymen S., Monk, Jonathan M., Aziz, Ramy K.
Publicado no Microbiol Resour Announc (2019)

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE

Por Norsigian, Charles J., Kavvas, Erol, Seif, Yara, Palsson, Bernhard O., Monk, Jonathan M.
Publicado no Front Genet (2018)

Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology

Por Pekar, Jonathan E., Phaneuf, Patrick, Szubin, Richard, Palsson, Bernhard, Feist, Adam, Monk, Jonathan M.
Publicado no Microbiol Resour Announc (2018)

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

Por Bosi, Emanuele, Monk, Jonathan M., Aziz, Ramy K., Fondi, Marco, Nizet, Victor, Palsson, Bernhard Ø.
Publicado no Proc Natl Acad Sci U S A (2016)

Machine learning in computational biology to accelerate high-throughput protein expression

Por Sastry, Anand, Monk, Jonathan, Tegel, Hanna, Uhlen, Mathias, Palsson, Bernhard O, Rockberg, Johan, Brunk, Elizabeth
Publicado no Bioinformatics (2017)

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

Por Choudhary, Kumari S., Mih, Nathan, Monk, Jonathan, Kavvas, Erol, Yurkovich, James T., Sakoulas, George, Palsson, Bernhard O.
Publicado no Front Microbiol (2018)

Model-driven discovery of underground metabolic functions in Escherichia coli

Por Guzmán, Gabriela I., Utrilla, José, Nurk, Sergey, Brunk, Elizabeth, Monk, Jonathan M., Ebrahim, Ali, Palsson, Bernhard O., Feist, Adam M.
Publicado no Proc Natl Acad Sci U S A (2015)

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

Por Seif, Yara, Monk, Jonathan M., Mih, Nathan, Tsunemoto, Hannah, Poudel, Saugat, Zuniga, Cristal, Broddrick, Jared, Zengler, Karsten, Palsson, Bernhard O.
Publicado no PLoS Comput Biol (2019)

Multi-omics quantification of species variation of Escherichia coli links molecular features with strain phenotypes

Por Monk, Jonathan M., Koza, Anna, Campodonico, Miguel, Machado, Daniel, Seoane, Jose Miguel, Palsson, Bernhard O., Herrgård, Markus J., Feist, Adam M.
Publicado no Cell Syst (2016)

Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions

Por Kavvas, Erol S., Seif, Yara, Yurkovich, James T., Norsigian, Charles, Poudel, Saugat, Greenwald, William W., Ghatak, Sankha, Palsson, Bernhard O., Monk, Jonathan M.
Publicado no BMC Syst Biol (2018)

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Por Fang, Xin, Monk, Jonathan M., Mih, Nathan, Du, Bin, Sastry, Anand V., Kavvas, Erol, Seif, Yara, Smarr, Larry, Palsson, Bernhard O.
Publicado no BMC Syst Biol (2018)

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

Por Monk, Jonathan M., Charusanti, Pep, Aziz, Ramy K., Lerman, Joshua A., Premyodhin, Ned, Orth, Jeffrey D., Feist, Adam M., Palsson, Bernhard Ø.
Publicado em 2013

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Por 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.
Publicado no Nat Commun (2018)

Systems biology of the structural proteome

Por Brunk, Elizabeth, Mih, Nathan, Monk, Jonathan, Zhang, Zhen, O’Brien, Edward J., Bliven, Spencer E., Chen, Ke, Chang, Roger L., Bourne, Philip E., Palsson, Bernhard O.
Publicado no BMC Syst Biol (2016)

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

Por 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.
Publicado no Nat Commun (2018)

BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Por 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
Publicado no PLoS Comput Biol (2019)

Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network

Por Ang, Yen-Sin, Tsai, Su-Yi, Lee, Dung-Fang, Monk, Jonathan, Su, Jie, Ratnakumar, Kajan, Ding, Junjun, Ge, Yongchao, Darr, Henia, Chang, Betty, Wang, Jianlong, Rendl, Michael, Bernstein, Emily, Schaniel, Christoph, Lemischka, Ihor R.
Publicado em 2011