Covert, Markus W.

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B., Assad-Garcia, N., Glass, J. I., & Covert, M. W. (2012) · Cell

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 1,300

Deep learning for cellular image analysis

Moen, E., Bannon, D., Kudo, T., Graf, W., Covert, M., & Van Valen, D. (2019) · Nature Methods

Cell Image Analysis TechniquesAdvanced Neural Network Applications

Cited by 1,225

Integrating high-throughput and computational data elucidates bacterial networks

Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., & Palsson, B. O. (2004) · Nature

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 792

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

Van Valen, D. A., Kudo, T., Lane, K. M., Macklin, D. N., Quach, N. T., DeFelice, M. M., Maayan, I., Tanouchi, Y., Ashley, E. A., & Covert, M. W. (2016) · PLoS Computational Biology

Cell Image Analysis TechniquesAdvanced Neural Network Applications

Cited by 557

Metabolic modelling of microbes: the flux‐balance approach

Edwards, J. S., Covert, M., & Palsson, B. (2002) · Environmental Microbiology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 365

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation

Macklin, D. N., Ahn-Horst, T. A., Choi, H., Ruggero, N. A., Carrera, J., Mason, J. C., Sun, G., Agmon, E., DeFelice, M. M., Maayan, I., et al. (2020) · Science

Gene Regulatory Network AnalysisMicrobial Metabolic Engineering and Bioproduction

Cited by 151

Building structural models of a whole mycoplasma cell

Maritan, M., Autin, L., Karr, J., Covert, M. W., Olson, A. J., & Goodsell, D. S. (2022) · Journal of Molecular Biology

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 75

An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control

Ahn-Horst, T. A., Mille, L. S., Sun, G., Morrison, J. H., & Covert, M. W. (2022) · npj Systems Biology and Applications

Gene Regulatory Network AnalysisBacterial Genetics and Biotechnology

Cited by 53

Cross-evaluation of E. coli’s operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons

Sun, G., DeFelice, M. M., Gillies, T. E., Ahn-Horst, T. A., Andrews, C. J., Krummenacker, M., Karp, P. D., Morrison, J. H., & Covert, M. W. (2024) · Cell Systems

Gene Regulatory Network AnalysisBacterial Genetics and Biotechnology

Cited by 9