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43.Van Valen D, Kudo T, Lane K, Macklin DN, Quach N, DeFelice M, Maayan I, Tanouchi Y, Ashley E, Covert MW, "'Deep learning automates the quantitative analysis of individual cells in live-cell imaging experiments" PLOS Computational Biology. November 4, 2016. doi: 10.1371/journal.pcbi.1005177 [html | pdf]
42.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]
41.Carrera J, Covert MW, "Why Build Whole-Cell Models?" Trends in Cell Biology. 2015. doi:10.1016/j.tcb.2015.09.004 [ html | pdf]
40.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]
39.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]
38.Hughey JJ*,Gutschow MV*, Bajar BT, Covert MW."Single-cell variation leads to population invariance in NF-κB signaling dynamics Molecular Biology of the Cell. 2014. doi: 10.1091/mbc.E14-08-1267 [html | pdf]
37.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]
36.Bird SW, Maynard NM, Covert MW, Kirkegaard K. "Nonlytic viral spread enhanced by autophagy components" PNAS. 2014. 10.1073.1401437111 [html | pdf]
35.Regot S, Hughey J, Bajar B, Carrasco Garcia S, Covert MW. "High-sensitivity measurements of multiple kinase activities in live single cells" Cell. 2014. 157(7): 1724-1734. [html | pdf]
34.Macklin DN*, Ruggero NA*, Covert MW. "The future of whole-cell modeling" Current Opinion in Biotechnology. 2014. 28: 111-115. [html | pdf]
33.Birch EW, Udell M, Covert MW. "Incorporationof flexible objectives and time-linked simulation with flux balance analysis" Journal of Theoretical Biology. 2014. 345: 12-21. [html | pdf]
32.Covert MW. "Simulating a Living Cell" Scientific American.2013.310(1):44-51. [html | pdf]
31.Sanghvi JC, Regot S, Carrasco Garcia S, Karr JR, Gutschow MV, Bolival B Jr, Covert MW. "Accelerated discovery via a whole-cell model" Nature Methods. 2013. 10(1038): nmeth.2724. [html | pdf]
30.Lee R*, Karr JR*, Covert MW. "WholeCellViz: data visualization for whole-cell models" BMC Bioinformatics. 2013. 14: 253. [html | pdf]
29.Purcell O., Jain B, Karr JR, Covert MW, Lu T. "Towards a whole-cell modeling approach for synthetic biology" Chaos. 2013. 23: 025112. [html | pdf]
28.Gutschow MV*, Hughey JJ*, Ruggero NA, Bajar BT, Valle SD, Covert MW. "Single-Cell and Population NF-κB Dynamic Responses Depend on Lipopolysaccharide Preparation" PLoS ONE. 2013. 8(1) : e53222. [html | pdf]
27.Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW. "WholeCellKB: model organism databases for comprehensive whole-cell models" Nucleic Acids Research. 2012. 41: Database issue. D787-92. [html | pdf]
26.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]
25.Birch EW, Ruggero 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]
24.Karr JR*, Sanghvi JC*, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW. "A Whole-Cell Computational Model Predicts Phenotype from Genotype" Cell. 2012. 150(2): 389-401. [html | pdf]
23.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]
22.Lee TK, Covert MW. "High-throughput, single-cell NF-κB dynamics" Current Opinion in Genetics & Development . 2010. 20(6): 677-83. [html | pdf]
21.Maynard ND, Gutschow MV, Birch EW, Covert MW. "The virus as metabolic engineer." Biotechnology Journal. 2010. 5(7): 686-94. [html | pdf]
20.Maynard ND, Birch EW, Sanghvi 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]
19.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]
18.Hughey JJ, Lee TK, Covert MW. "Computational modeling of mammalian signaling networks" Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2010. 2(2): 194 - 209. [html | pdf]
17.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]
16.Lee TK, Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW. "A noisy paracrine signal determines the cellular NF-κB response to lipopolysaccharide" Science Signaling. 2009. 2(93): ra65. [html | pdf]
15.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]
14.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]
13.Covert MW*, Leung TH*, Gaston JE, Baltimore D. "Achieving stability of lipopolysaccharide-induced NF-κB activation" Science. 2005. 309(5742): 1854-7. [html | pdf]
12.Covert MW. "Integrated regulatory and metabolic models" Computational Systems Biology. Academic Press, New York, 2005. [html | pdf]
11.Herrgård MJ, Covert MW, Palsson BØ. "Reconstruction of microbial transcriptional regulatory networks" Curr Opin Biotechnol. 2004. 15(1): 70-7. [html | pdf]
10.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]
9.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]
8.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]
7.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]
6.Edwards JS, Covert MW, Palsson BØ. "Metabolic modelling of microbes: the flux-balance approach" Environ Microbiol. 2002. 4(3): 133-40. [html | pdf]
5.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]
4.Covert MW, Palsson BØ. "Transcriptional regulation in constraints-based metabolic models of Escherichia coli" J Biol Chem. 2002. 277(31): 28058-64. [html | pdf]
3.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]
2.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]
1.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.