Markus Covert

Honors and Awards

• Robert Black Postdoctoral Fellow, Damon Runyon Cancer Research Foundation (2004-2006)
• First Graduate of the Bioinformatics Program, University of California, San Diego (2003)
• Ezra Taft Benson Presidential Scholar, Brigham Young University (1991-1997)

Professional Education

• Ph.D., UCSD Bioengineering/ Bioinformatics (2003)
• M.S., UCSD Bioengineering (2002)
• B.S., Brigham Young University Chemical Engineering (1997)

Postdoctoral Advisees

• Nathaniel Maynard

Graduate & Fellowship Program Affiliations

• Bioengineering

Web Site Links

• Lab Website

Research Interests

Our focus is on building computational models of complex biological processes, and using these models to guide an experimental program. Such an approach leads to a relatively rapid identification and validation of previously unknown components and interactions. Biological systems of interest include metabolic, regulatory and signaling networks as well as cell-cell interactions. Current research involves the dynamic behavior of NF-kappaB, an important family of transcription factors whose aberrant activity has been linked to oncogenesis, tumor progression, and resistance to chemotherapy.

Publications

• A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide. Lee TK,  Denny EM, Sanghvi JC, Gaston JE, Maynard ND, Hughey JJ, Covert MW.  Sci Signal.  2009; 2 (93): ra65
• Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Covert MW,  Xiao N, Chen TJ, Karr JR.  Bioinformatics.  2008; 24 (18): 2044-50
• Achieving stability of lipopolysaccharide-induced NF-kappaB activation. Covert MW,  Leung TH, Gaston JE, Baltimore D.  Science.  2005; 309 (5742): 1854-7
• Integrated regulatory and metabolic models Covert, M.W.,  Computational Systems Biology, Academic Press, New York.  2005;
• Reconstruction of microbial transcriptional regulatory networks. Herrgård MJ,  Covert MW, Palsson BØ.  Curr Opin Biotechnol.  2004; 15 (1): 70-7
• Integrating high-throughput and computational data elucidates bacterial networks. Covert MW,  Knight EM, Reed JL, Herrgard MJ, Palsson BO.  Nature.  2004; 429 (6987): 92-6
• Constraints-based models: regulation of gene expression reduces the steady-state solution space. Covert MW,  Palsson BO.  J Theor Biol.  2003; 221 (3): 309-25
• Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Covert MW,  Famili I, Palsson BO.  Biotechnol Bioeng.  2003; 84 (7): 763-72
• Reconciling gene expression data with known genome-scale regulatory network structures. Herrgård MJ,  Covert MW, Palsson BØ.  Genome Res.  2003; 13 (11): 2423-34
• Transcriptional regulation in constraints-based metabolic models of Escherichia coli. Covert MW,  Palsson BØ.  J Biol Chem.  2002; 277 (31): 28058-64
• Genome-scale metabolic model of Helicobacter pylori 26695. Schilling CH,  Covert MW, Famili I, Church GM, Edwards JS, Palsson BO.  J Bacteriol.  2002; 184 (16): 4582-93
• Regulation of gene expression in flux balance models of metabolism. Covert MW,  Schilling CH, Palsson B.  J Theor Biol.  2001; 213 (1): 73-88
• Metabolic modeling of microbial strains in silico. Covert MW,  Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO.  Trends Biochem Sci.  2001; 26 (3): 179-86