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Covert Systems Biology Lab

Publications

2014 | 2013 | 2012 | 2010 | 2009 | 2008 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000

2014
35.Bird SW, Maynard NM, Covert MW, Kirkegaard K. "Nonlytic viral spread enhanced by autophagy components" PNAS. 2014. 10.1073.1401437111 [html | pdf]
34.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]
33.Macklin DN, Ruggero NA, Covert MW. "The future of whole-cell modeling" Current Opinion in Biotechnology. 2014. 28: 111-115. [html | pdf]
32.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]
2013
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]
2012
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]
2010
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]
2009
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]
2008
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]
2005
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]
2004
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]
2003
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]
2002
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]
2001
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]
2000
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.