Markus Covert

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Single-cell and population NF-κB dynamic responses depend on lipopolysaccharide preparation
    Miriam V Gutschow
    Department of Bioengineering, Stanford University, Stanford, California, United States of America
    PLoS ONE 8:e53222. 2013
  2. pmc WholeCellKB: model organism databases for comprehensive whole-cell models
    Jonathan R Karr
    Graduate Program in Biophysics, Stanford University, 318 Campus Drive West, Stanford, CA 94305, USA
    Nucleic Acids Res 41:D787-92. 2013
  3. pmc Determining host metabolic limitations on viral replication via integrated modeling and experimental perturbation
    Elsa W Birch
    Chemical Engineering, Stanford University, Stanford, CA, USA
    PLoS Comput Biol 8:e1002746. 2012
  4. pmc Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting
    Nathaniel D Maynard
    Department of Bioengineering, Stanford University, Stanford, CA, USA
    Mol Syst Biol 8:567. 2012
  5. pmc WholeCellViz: data visualization for whole-cell models
    Ruby Lee
    Department of Bioengineering, Stanford University, Stanford, CA 94025, USA
    BMC Bioinformatics 14:253. 2013
  6. pmc A dynamic network of transcription in LPS-treated human subjects
    Junhee Seok
    Department of Bioengineering, Stanford University, Stanford, California, USA
    BMC Syst Biol 3:78. 2009
  7. doi request reprint Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
    Markus W Covert
    Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305 5444, USA
    Bioinformatics 24:2044-50. 2008
  8. pmc Reconciling gene expression data with known genome-scale regulatory network structures
    Markus J Herrgard
    Department of Bioengineering, Bioinformatics Graduate Program, University of California, San Diego, La Jolla, California 92093 0412, USA
    Genome Res 13:2423-34. 2003
  9. ncbi request reprint Transcriptional regulation in constraints-based metabolic models of Escherichia coli
    Markus W Covert
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093 0412, USA
    J Biol Chem 277:28058-64. 2002
  10. ncbi request reprint Achieving stability of lipopolysaccharide-induced NF-kappaB activation
    Markus W Covert
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Science 309:1854-7. 2005

Collaborators

  • Junhee Seok
  • Bernhard Ø Palsson
  • Jonathan R Karr
  • Markus J Herrgard
  • Miriam V Gutschow
  • Ruby Lee
  • Nicholas A Ruggero
  • Derek N Macklin
  • Elsa W Birch
  • Nathaniel D Maynard
  • Bryce T Bajar
  • Sean D Valle
  • Abhishek Arora
  • Jayodita C Sanghvi
  • Jacob J Hughey
  • Karla Kirkegaard

Detail Information

Publications12

  1. pmc Single-cell and population NF-κB dynamic responses depend on lipopolysaccharide preparation
    Miriam V Gutschow
    Department of Bioengineering, Stanford University, Stanford, California, United States of America
    PLoS ONE 8:e53222. 2013
    ..The cellular response to lipopolysaccharide varies depending on the source and preparation of the ligand, however. Our goal was to compare single-cell NF-κB dynamics across multiple sources and concentrations of LPS...
  2. pmc WholeCellKB: model organism databases for comprehensive whole-cell models
    Jonathan R Karr
    Graduate Program in Biophysics, Stanford University, 318 Campus Drive West, Stanford, CA 94305, USA
    Nucleic Acids Res 41:D787-92. 2013
    ..WholeCellKB-MG is extensively cross-referenced to existing resources including BioCyc, KEGG and UniProt. WholeCellKB-MG is freely accessible through a web-based user interface as well as through a RESTful web service...
  3. pmc Determining host metabolic limitations on viral replication via integrated modeling and experimental perturbation
    Elsa W Birch
    Chemical Engineering, Stanford University, Stanford, CA, USA
    PLoS Comput Biol 8:e1002746. 2012
    ..Taken together, these results emphasize the importance of considering viral infections in the context of host metabolism...
  4. pmc Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting
    Nathaniel D Maynard
    Department of Bioengineering, Stanford University, Stanford, CA, USA
    Mol Syst Biol 8:567. 2012
    ..Based on the universality of many key components of this network, in both the host and the virus, we anticipate that these findings may have broad relevance to understanding other infections, including viral infection of humans...
  5. pmc WholeCellViz: data visualization for whole-cell models
    Ruby Lee
    Department of Bioengineering, Stanford University, Stanford, CA 94025, USA
    BMC Bioinformatics 14:253. 2013
    ..However, discovering new biology from whole-cell models and other high-throughput technologies requires novel tools for exploring and analyzing complex, high-dimensional data...
  6. pmc A dynamic network of transcription in LPS-treated human subjects
    Junhee Seok
    Department of Bioengineering, Stanford University, Stanford, California, USA
    BMC Syst Biol 3:78. 2009
    ..For example, Network Component Analysis (NCA) is an approach that can predict transcription factor activities over time as well as the relative regulatory influence of factors on each target gene...
  7. doi request reprint Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
    Markus W Covert
    Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305 5444, USA
    Bioinformatics 24:2044-50. 2008
    ..Of current interest is the integration of these approaches with detailed models based on ordinary differential equations (ODEs)...
  8. pmc Reconciling gene expression data with known genome-scale regulatory network structures
    Markus J Herrgard
    Department of Bioengineering, Bioinformatics Graduate Program, University of California, San Diego, La Jolla, California 92093 0412, USA
    Genome Res 13:2423-34. 2003
    ..The results suggest that targeted gene expression profiling data can be used to refine and expand particular subcomponents of known regulatory networks that are sufficiently decoupled from the rest of the network...
  9. ncbi request reprint Transcriptional regulation in constraints-based metabolic models of Escherichia coli
    Markus W Covert
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093 0412, USA
    J Biol Chem 277:28058-64. 2002
    ..This combined metabolic/regulatory model is thus an important step toward the goal of synthesizing genome-scale models that accurately represent E. coli behavior...
  10. ncbi request reprint Achieving stability of lipopolysaccharide-induced NF-kappaB activation
    Markus W Covert
    Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Science 309:1854-7. 2005
    ..The MyD88-independent pathway required Inferon regulatory factor 3-dependent expression of TNFalpha to activate NF-kappaB, and the time required for TNFalpha synthesis established the delay...
  11. ncbi request reprint Integrating high-throughput and computational data elucidates bacterial networks
    Markus W Covert
    Bioengineering Department, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093 0412, USA
    Nature 429:92-6. 2004
    ..We find that a systems biology approach that combines genome-scale experimentation and computation can systematically generate hypotheses on the basis of disparate data sources...
  12. ncbi request reprint Reconstruction of microbial transcriptional regulatory networks
    Markus J Herrgard
    Department of Bioengineering, Bioinformatics Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Curr Opin Biotechnol 15:70-7. 2004
    ..These models can further be combined with genome-scale metabolic models to build integrated models of cellular function including both metabolism and its regulation...

Research Grants3

  1. Combining Computational and Experimentation to Interrogate NF-kappaB Signaling
    Markus Covert; Fiscal Year: 2007
    ..We propose to use computer modeling and experiments to help us understand the NF-kappaB signaling network and its role in cancer development, particularly with regard to diffuse large B cell lymphomas. ..
  2. A Gene-Complete Computational Model of Yeast
    Markus Covert; Fiscal Year: 2009
    ..We anticipate that this could lead to a broad implementation of research which uses computational modeling and simulation to guide experimental programs and biological discovery. Public Health Relevance The broad goal of this res ..