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  • Choi, H.; Covert, M. W. "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", Accepted in Nucleic Acids Research, 2023.

  • Jeknić, S.; Kudo, T.; Song, J. J.; Covert, M. W. "An Optimized Reporter of the Transcription Factor Hypoxia-Inducible Factor 1α Reveals Complex HIF-1α Activation Dynamics in Single Cells", Journal of Biological Chemistry 2023, 299 (4). doi: 10.1016/j.jbc.2023.104599. [html | pdf]

  • Maritan, M.; Autin, L.; Karr, J.; Covert, M. W.; Olson, A. J.; Goodsell, D. S. "Building Structural Models of a Whole Mycoplasma Cell", Journal of Molecular Biology 2022, 434 (2), 167351. doi: 10.1016/j.jmb.2021.167351. [html | pdf]

  • Kudo, T.; Lane, K.; Covert, M. W. "A Multiplexed Epitope Barcoding Strategy That Enables Dynamic Cellular Phenotypic Screens", Cell Systems 2022, 13 (5), 376-387.e8. doi: 10.1016/j.cels.2022.02.006. [html | pdf]

  • Ahn-Horst, T. A.; Mille, L. S.; Sun, G.; Morrison, J. H.; Covert, M. W. "An Expanded Whole-Cell Model of E. Coli Links Cellular Physiology with Mechanisms of Growth Rate Control", npj Syst Biol Appl 2022, 8 (1), 1–21. doi: 10.1038/s41540-022-00242-9. [html | pdf]

  • Agmon, E.; Spangler, R. K.; Skalnik, C. J.; Poole, W.; Peirce, S. M.; Morrison, J. H.; Covert, M. W. "Vivarium: An Interface and Engine for Integrative Multiscale Modeling in Computational Biology", Bioinformatics 2022, 38 (7), 1972–1979. doi: 10.1093/bioinformatics/btac049. [html | pdf]

  • Sun, G.; Ahn-Horst, T. A.; Covert, M. W. "The E. Coli Whole-Cell Modeling Project", EcoSal plus 2021, 9 (2), eESP-0001. [html | pdf]

  • Covert, M. W.; Gillies, T. E.; Kudo, T.; Agmon, E. "A Forecast for Large-Scale, Predictive Biology: Lessons from Meteorology", Cell Systems 2021, 12 (6), 488–496. doi: 10.1016/j.cels.2021.05.014. [html | pdf]

  • Bodner, K.; Melkonian, A. L.; Covert, M. W. "The Enemy of My Enemy: New Insights Regarding Bacteriophage–Mammalian Cell Interactions", Trends in Microbiology 2021, 29 (6), 528–541. doi: 10.1016/j.tim.2020.10.014. [html | pdf]

  • Macklin DN*, Ahn-Horst TA*, Choi H*, Ruggero NA*, Carrera J*, Mason JC*, Sun G, Agmon E, DeFelice MM, Maayan I, Lane K, Spangler RK, Gillies TE, Paull ML, Akhter S, Bray SR, Weaver DS, Keseler IM, Karp PD, Morrison JH, Covert MW.  "Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation", Science, March 2020. doi: 10.1126/science.aav3751. [html | pdf]

  • Bodner, K.; Melkonian, A. L.; Covert, M. W. "A Protocol to Engineer Bacteriophages for Live-Cell Imaging of Bacterial Prophage Induction Inside Mammalian Cells", STAR Protocols 2020, 1 (2), 100084. doi: 10.1016/j.xpro.2020.100084. [html | pdf]

  • Bodner, K.; Melkonian, A. L.; Barth, A. I. M.; Kudo, T.; Tanouchi, Y.; Covert, M. W. "Engineered Fluorescent E. Coli Lysogens Allow Live-Cell Imaging of Functional Prophage Induction Triggered inside Macrophages", Cell Systems 2020, 10 (3), 254-264.e9. doi: 10.1016/j.cels.2020.02.006. [html | pdf]

  • DeFelice MM*, Clark HR*, Hughey JJ*, Maayan I, Kudo T, Gutschow MV, Covert MW, Regot S, “NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop”, Science Signaling. 30 Apr 2019: Vol. 12, Issue 579, eaau3568. doi: 10.1126/scisignal.aau3568. [html | pdf]

  • Jeknić S, Kudo T, Covert MW "Techniques for Studying Decoding of Single Cell Dynamics", Frontiers in Immunology, 11 Apr 2019: Vo. 10 | Article 755: doi: 10.3389/fimmu.2019.00755 [html | pdf]


  • Lane K, Andres-Terre M, Kudo T, Monack DM, Covert MW, “Escalating threat levels of bacterial infection can be discriminated by distinct MAPK and NF-kB signaling dynamics in single host cells", Cell Systems. 27 March 2019, Volume 8, Issue 3, Pages 183-196.e4. [html | pdf]

  • Gutschow MV, Mason JC, Lane K, Maayan I, Hughey JJ, Bajar BT, Amatya DN, Valle SD, Covert MW, “Combinatorial processing of bacterial and host-1 derived innate immune stimuli at the single-cell level”, Molecular Biology of the Cell. 2019 Jan 15;30(2):282-292. doi: 10.1091/mbc.E18-07-0423. [html | pdf]

  • Mason JC, Covert MW, “An energetic reformulation of kinetic rate laws enables scalable parameter estimation for biochemical networks”, Journal of Theoretical Biiology. 2019 Jan 14; Volume 461, Pages 145-156. [html pdf]

  • Mason JC, Covert MW, “Generalizable and scalable techniques for estimating the parameter values of a whole-cell-like system”, Journal of Theoretical Biology. 2018 Oct 24;461:145-156. doi: 10.1016/j.jtbi.2018.10.041. [html | pdf]

  • Kudo T, Jeknić S, Macklin DN, Akhter S, Hughey JJ, Regot S, Covert MW, "Live-cell measurements of kinase activity in single cells using translocation reporters"  Nature Protocols. 2017 Dec 21, 2018 Jan;13(1):155-169. doi: 10.1038/nprot.2017.128. [html | pdf]

  • Tanouchi Y, Covert MW,  "Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology" mBio. 2017 Sep-Oct, 8(5): e01038-17, doi: 10.1128/mBio.01038-17 [html | pdf]

  • Lane K*, Van Valen D*, DeFelice MM, Macklin DN, Kudo T, Jaimovich A, Carr A, Meyer T, Pe'er D, Boutet SC, Covert MW,  "Measuring signaling and RNA-Seq in the same cell links gene expression to dynamic patterns of NF-kappa B activation" Cell Systems. April 26, 2017.  doi: 10.1016/j.cels.2017.03.010 [html | pdf]


  • Koechlein CS*, Harris JR*, Lee TK, Weeks J, Fox RG, Zimdahl B, Ito T, Blevins A, Jung SH, Chute JP, Chourasia A, Covert MW,Reya T High-resolution imaging and computational analysis of haematopoietic cell dynamics in vivo. Nature Communications. July 18, 2016.. doi: 10.1038/ncomms12169 [html | pdf]


  • Karr JR,Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, Kreutz C, DREAM8 Parameter Estimation Challenge Consortium, Wilkinson S, Allgood BA, Bot BM, Hoff BR, Kellen MR, Covert MW, Stolovitzky GA, Meyer P, "Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models" PLoS Comput Biol.2015 May 28 11(5):e1004096. doi: 10.1371/journal.pcbi.1004096. eCollection 2015 May. PMID:26020786 [html | pdf]

  • Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW, "NetworkPainter: dynamic intracellular pathway animation in Cytobank" BMC Bioinformatics. 2015. doi:10.1186/s12859-015-0602-4 [html | pdf]


  • Karr JR, Phillips NC, Covert MW, "WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions" Oxford Journals. 2014. doi: 10.1093/database/bau095 [html | pdf]

  • Bird SW, Maynard NMCovert MW, Kirkegaard K. "Nonlytic viral spread enhanced by autophagy components" PNAS. 2014. 10.1073.1401437111 [html | pdf]

  • Birch EW, Udell M, Covert MW. "Incorporation of flexible objectives and time-linked simulation with flux balance analysis" Journal of Theoretical Biology. 2014. 345: 12-21. [html | pdf]

  • Covert MW. "Simulating a Living Cell" Scientific American.2013.310(1):44-51. [html | pdf]

  • Purcell O., Jain B, Karr JRCovert MW, Lu T. "Towards a whole-cell modeling approach for synthetic biology" Chaos. 2013. 23: 025112. [html | pdf]


  • Freundt EC, Maynard ND, Clancy EK, Roy S, Bousset L, Sourigues Y, Covert MW, Melki R, Kirkegaard K, and Brahic M. "Neuron-to-Neuron Transmission of α-Synuclein Fibrils Through Axonal Transport" Annals of Neurology. 2012. 72(4): 517-24. [html | pdf]

  • Birch EWRuggero NA, Covert MW. "Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation" PLoS Computational Biology. 2012. 8(10): e1002746. [html | pdf]

  • Maynard ND, Macklin DN, Kirkegaard K, Covert MW. "Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting" Molecular Systems Biology. 2012. 8: 567. [html | pdf]

  • Lee TK, Covert MW. "High-throughput, single-cell NF-κB dynamics" Current Opinion in Genetics & Development . 2010. 20(6): 677-83. [html | pdf]

  • Maynard NDBirch EWSanghvi JC, Chen L, Gutschow MV, Covert MW. "A Forward-Genetic Screen and Dynamic Analysis of Lambda Phage Host-Dependencies Reveals an Extensive Interaction Network and a New Anti-Viral Strategy" PLoS Genetics. 2010. 6(7): e1001017. [html | pdf]

  • Tay S*, Hughey JJ*, Lee TK, Lipniacki T, Quake SR, Covert MW. "Single-cell NF-κB dynamics reveal digital activation and analogue information processing" Nature. 2010. 466(7303): 267-271. [html | pdf]

  • Hughey JJLee TK, Covert MW. "Computational modeling of mammalian signaling networks" Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2010. 2(2): 194 - 209. [html | pdf]

  • Terzer M, Maynard ND, Covert MW, Stelling J. "Genome-scale metabolic networks" Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2009. 1(3): 285 - 297. [html | pdf]

  • Seok J, Xiao W, Moldawer LL, Davis RW, Covert MW. "A dynamic network of transcription in LPS-treated human subjects" BMC Syst Biol. 2009. 3: 78. [html | pdf]

  • Covert MW, Xiao N, Chen TJ, and Karr JR. "Integrated Flux Balance Analysis Model of Escherichia coli" Bioinformatics. 2008. 24(18): 2044-2050. [html | pdf]

  • Covert MW*, Leung TH*, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-κB activation" Science. 2005. 309(5742): 1854-7. [html | pdf]

  • Covert MW. "Integrated regulatory and metabolic models" Computational Systems Biology. Academic Press, New York, 2005. [html | pdf]

  • Herrgård MJ, Covert MW, Palsson BØ. "Reconstruction of microbial transcriptional regulatory networks" Curr Opin Biotechnol. 2004. 15(1): 70-7. [html | pdf]

  • Covert MW, Knight EM, Reed JL, Herrgård MJ, Palsson BØ. "Integrating high-throughput and computational data elucidates bacterial networks" Nature. 2004. 429(6987): 92-6. [html | pdf]

  • Covert MW, Palsson BØ. "Constraints-based models: regulation of gene expression reduces the steady-state solution space" J Theor Biol. 2003. 221(3): 309-25. [html | pdf]

  • Herrgård MJ, Covert MW, Palsson BØ. "Reconciling gene expression data with known genome-scale regulatory network structures" Genome Res. 2003. 13(11): 2423-34. [html | pdf]

  • Covert MW, Famili I, Palsson BØ. "Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?" Biotechnol Bioeng. 2003. 84(7): 763-72. [html | pdf]

  • Edwards JS, Covert MW, Palsson BØ. "Metabolic modelling of microbes: the flux-balance approach" Environ Microbiol. 2002. 4(3): 133-40. [html | pdf]

  • Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BØ. "Genome-scale metabolic model of Helicobacter pylori 26695" J Bacteriol. 2002. 184(16): 4582-93. [html | pdf]

  • Covert MW, Palsson BØ. "Transcriptional regulation in constraints-based metabolic models of Escherichia coli" J Biol Chem. 2002. 277(31): 28058-64. [html | pdf]

  • Covert MW, Schilling CH, Palsson BØ. "Regulation of gene expression in flux balance models of metabolism" J Theor Biol. 2001. 213(1): 73-88. [html | pdf]

  • Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BØ. "Metabolic modeling of microbial strains in silico" Trends Biochem Sci. 2001. 26(3): 179-86. [html | pdf]

  • Edwards JS, Schilling CH, Covert MW, Smith SJ, Palsson BØ. "Genomic Engineering of Bacterial Metabolism" Encyclopedia of Microbiology. Academic Press, New York, 2000. [html]

*These authors contributed equally to this work.

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