A Whole-Cell Computational Model Predicts Phenotype from Genotype
Karr, Jonathan R., Sanghvi, Jayodita C., Macklin, Derek N., Gutschow, Miriam V., Jacobs, Jared M., Bolival, Benjamin, Assad-Garcia, Nacyra, Glass, John I., Covert, Markus W.
Published in Cell (20.07.2012)
Published in Cell (20.07.2012)
Get full text
Journal Article
The principles of whole-cell modeling
Karr, Jonathan R, Takahashi, Koichi, Funahashi, Akira
Published in Current opinion in microbiology (01.10.2015)
Published in Current opinion in microbiology (01.10.2015)
Get full text
Journal Article
Self-guarding of MORC3 enables virulence factor-triggered immunity
Gaidt, Moritz M., Morrow, Alyssa, Fairgrieve, Marian R., Karr, Jonathan P., Yosef, Nir, Vance, Russell E.
Published in Nature (London) (02.12.2021)
Published in Nature (London) (02.12.2021)
Get full text
Journal Article
Increased stray gas abundance in a subset of drinking water wells near Marcellus shale gas extraction
Jackson, Robert B., Vengosh, Avner, Darrah, Thomas H., Warner, Nathaniel R., Down, Adrian, Poreda, Robert J., Osborn, Stephen G., Zhao, Kaiguang, Karr, Jonathan D.
Published in Proceedings of the National Academy of Sciences - PNAS (09.07.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (09.07.2013)
Get full text
Journal Article
Geochemical and isotopic variations in shallow groundwater in areas of the Fayetteville Shale development, north-central Arkansas
Warner, Nathaniel R., Kresse, Timothy M., Hays, Phillip D., Down, Adrian, Karr, Jonathan D., Jackson, Robert B., Vengosh, Avner
Published in Applied geochemistry (01.08.2013)
Published in Applied geochemistry (01.08.2013)
Get full text
Journal Article
Building Structural Models of a Whole Mycoplasma Cell
Maritan, Martina, Autin, Ludovic, Karr, Jonathan, Covert, Markus W., Olson, Arthur J., Goodsell, David S.
Published in Journal of molecular biology (30.01.2022)
Published in Journal of molecular biology (30.01.2022)
Get full text
Journal Article
Datanator: an integrated database of molecular data for quantitatively modeling cellular behavior
Roth, Yosef D, Lian, Zhouyang, Pochiraju, Saahith, Shaikh, Bilal, Karr, Jonathan R
Published in Nucleic acids research (08.01.2021)
Published in Nucleic acids research (08.01.2021)
Get full text
Journal Article
Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm
Tourigny, David S., Goldberg, Arthur P., Karr, Jonathan R.
Published in Biophysical journal (07.12.2021)
Published in Biophysical journal (07.12.2021)
Get full text
Journal Article
Mapping urban pipeline leaks: Methane leaks across Boston
Phillips, Nathan G., Ackley, Robert, Crosson, Eric R., Down, Adrian, Hutyra, Lucy R., Brondfield, Max, Karr, Jonathan D., Zhao, Kaiguang, Jackson, Robert B.
Published in Environmental pollution (1987) (01.02.2013)
Published in Environmental pollution (1987) (01.02.2013)
Get full text
Journal Article
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
Shaikh, Bilal, Marupilla, Gnaneswara, Wilson, Mike, Blinov, Michael L, Moraru, Ion I, Karr, Jonathan R
Published in Nucleic acids research (02.07.2021)
Published in Nucleic acids research (02.07.2021)
Get full text
Journal Article
Emerging whole-cell modeling principles and methods
Goldberg, Arthur P, Szigeti, Balázs, Chew, Yin Hoon, Sekar, John AP, Roth, Yosef D, Karr, Jonathan R
Published in Current opinion in biotechnology (01.06.2018)
Published in Current opinion in biotechnology (01.06.2018)
Get full text
Journal Article
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems
Dräger, Andreas, Helikar, Tomáš, Barberis, Matteo, Birtwistle, Marc, Calzone, Laurence, Chaouiya, Claudine, Hasenauer, Jan, Karr, Jonathan R, Niarakis, Anna, Rodríguez Martínez, María, Saez-Rodriguez, Julio, Thakar, Juilee
Published in Bioinformatics (Oxford, England) (05.11.2021)
Published in Bioinformatics (Oxford, England) (05.11.2021)
Get full text
Journal Article
p300 is an obligate integrator of combinatorial transcription factor inputs
Ferrie, John J., Karr, Jonathan P., Graham, Thomas G.W., Dailey, Gina M., Zhang, Gloria, Tjian, Robert, Darzacq, Xavier
Published in Molecular cell (18.01.2024)
Published in Molecular cell (18.01.2024)
Get full text
Journal Article
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
Covert, Markus W., Xiao, Nan, Chen, Tiffany J., Karr, Jonathan R.
Published in Bioinformatics (15.09.2008)
Published in Bioinformatics (15.09.2008)
Get full text
Journal Article
Organizing genome engineering for the gigabase scale
Bartley, Bryan A., Beal, Jacob, Karr, Jonathan R., Strychalski, Elizabeth A.
Published in Nature communications (04.02.2020)
Published in Nature communications (04.02.2020)
Get full text
Journal Article
Guidelines for Reproducibly Building and Simulating Systems Biology Models
Medley, J. Kyle, Goldberg, Arthur P., Karr, Jonathan R.
Published in IEEE transactions on biomedical engineering (01.10.2016)
Published in IEEE transactions on biomedical engineering (01.10.2016)
Get full text
Journal Article
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks
Lang, Paul F, Chebaro, Yassmine, Zheng, Xiaoyue, P Sekar, John A, Shaikh, Bilal, Natale, Darren A, Karr, Jonathan R
Published in Genome Biology (18.05.2020)
Published in Genome Biology (18.05.2020)
Get full text
Journal Article