Publications by authors named "Markus Covert"

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The EcoCyc database (2025).
Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Markus W Covert

EcoSal Plus· December 2025

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Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy.
John W Hickey, Eran Agmon, Nina Horowitz, Tze-Kai Tan, Matthew Lamore, Markus W Covert

Cell Syst· April 2024

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Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons.
Gwanggyu Sun, Mialy M DeFelice, Taryn E Gillies, Travis A Ahn-Horst, Cecelia J Andrews, Markus W Covert

Cell Syst· March 2024

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Cell biology is….
Julie A Theriot, Anne Simonsen, Iva Tolić, Manuel D Leonetti, Satyajit Mayor, Markus W Covert

Cell· January 2024

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The EcoCyc Database (2023).
Peter D Karp, Suzanne Paley, Ron Caspi, Anamika Kothari, Markus Krummenacker, Markus W Covert

EcoSal Plus· December 2023

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Context-dependent regulation of lipid accumulation in adipocytes by a HIF1α-PPARγ feedback network.
Takamasa Kudo, Michael L Zhao, Stevan Jeknić, Kyle M Kovary, Edward L LaGory, Markus W Covert

Cell Syst· December 2023

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T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
John W Hickey, Maximillian Haist, Nina Horowitz, Chiara Caraccio, Yuqi Tan, Markus Covert

Cell Rep· December 2023

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Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical Component of Therapeutic T Cell Efficacy.
John W Hickey, Eran Agmon, Nina Horowitz, Matthew Lamore, John Sunwoo, Markus Covert

bioRxiv· December 2023

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Whole-cell modeling of E. coli confirms that in vitro tRNA aminoacylation measurements are insufficient to support cell growth and predicts a positive feedback mechanism regulating arginine biosynthesis.
Heejo Choi, Markus W Covert

Nucleic Acids Res· July 2023

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Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses.
Christopher J Skalnik, Sean Y Cheah, Mica Y Yang, Mattheus B Wolff, Ryan K Spangler, Markus W Covert

PLoS Comput Biol· June 2023

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An optimized reporter of the transcription factor hypoxia-inducible factor 1α reveals complex HIF-1α activation dynamics in single cells.
Stevan Jeknić, Takamasa Kudo, Joanna J Song, Markus W Covert

J Biol Chem· April 2023

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An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control.
Travis A Ahn-Horst, Luis Santiago Mille, Gwanggyu Sun, Jerry H Morrison, Markus W Covert

NPJ Syst Biol Appl· August 2022

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A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens.
Takamasa Kudo, Keara Lane, Markus W Covert

Cell Syst· May 2022

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Microbial metabolites in the marine carbon cycle.
Mary Ann Moran, Elizabeth B Kujawinski, William F Schroer, Shady A Amin, Nicholas R Bates, Markus W Covert

Nat Microbiol· April 2022

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Vivarium: an interface and engine for integrative multiscale modeling in computational biology.
Eran Agmon, Ryan K Spangler, Christopher J Skalnik, William Poole, Shayn M Peirce, Markus W Covert

Bioinformatics· March 2022

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Building Structural Models of a Whole Mycoplasma Cell.
Martina Maritan, Ludovic Autin, Jonathan Karr, Markus W Covert, Arthur J Olson

J Mol Biol· January 2022

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The E. coli Whole-Cell Modeling Project.
Gwanggyu Sun, Travis A Ahn-Horst, Markus W Covert

EcoSal Plus· December 2021

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The Enemy of My Enemy: New Insights Regarding Bacteriophage-Mammalian Cell Interactions.
Katie Bodner, Arin L Melkonian, Markus W Covert

Trends Microbiol· June 2021

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A forecast for large-scale, predictive biology: Lessons from meteorology.
Markus W Covert, Taryn E Gillies, Takamasa Kudo, Eran Agmon

Cell Syst· June 2021

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A Protocol to Engineer Bacteriophages for Live-Cell Imaging of Bacterial Prophage Induction Inside Mammalian Cells.
Katie Bodner, Arin L Melkonian, Markus W Covert

STAR Protoc· September 2020

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Simultaneous cross-evaluation of heterogeneous datasets via mechanistic simulation.
Derek N Macklin, Travis A Ahn-Horst, Heejo Choi, Nicholas A Ruggero, Javier Carrera, Markus W Covert

Science· July 2020

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Stress-mediated exit to quiescence restricted by increasing persistence in CDK4/6 activation.
Hee Won Yang, Steven D Cappell, Ariel Jaimovich, Chad Liu, Mingyu Chung, Markus Covert

Elife· April 2020

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Engineered Fluorescent E. coli Lysogens Allow Live-Cell Imaging of Functional Prophage Induction Triggered inside Macrophages.
Katie Bodner, Arin L Melkonian, Angela I M Barth, Takamasa Kudo, Yu Tanouchi, Markus W Covert

Cell Syst· March 2020

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Deep learning for cellular image analysis.
Erick Moen, Dylan Bannon, Takamasa Kudo, William Graf, Markus Covert

Nat Methods· December 2019

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NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop.
Mialy M DeFelice, Helen R Clark, Jacob J Hughey, Inbal Maayan, Takamasa Kudo, Markus W Covert

Sci Signal· April 2019

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