Markus W Covert

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. 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
  2. pmc Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing
    Savaş Tay
    Department of Bioengineering, Stanford University, Stanford, California 94305, USA
    Nature 466:267-71. 2010
  3. 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
  4. pmc A forward-genetic screen and dynamic analysis of lambda phage host-dependencies reveals an extensive interaction network and a new anti-viral strategy
    Nathaniel D Maynard
    Department of Bioengineering, Stanford University, Palo Alto, California, United States of America
    PLoS Genet 6:e1001017. 2010
  5. pmc A whole-cell computational model predicts phenotype from genotype
    Jonathan R Karr
    Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA
    Cell 150:389-401. 2012
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

  • Bernhard Ø Palsson
  • Markus J Herrgard
  • Junhee Seok
  • Nathaniel D Maynard
  • Timothy K Lee
  • Jonathan R Karr
  • Miriam V Gutschow
  • Jacob J Hughey
  • Elsa W Birch
  • Jayodita C Sanghvi
  • Derek N Macklin
  • Ruby Lee
  • Nicholas A Ruggero
  • Savaş Tay
  • Bryce T Bajar
  • Sean D Valle
  • Abhishek Arora
  • Nacyra Assad-Garcia
  • John I Glass
  • Benjamin Bolival
  • Jared M Jacobs
  • Karla Kirkegaard
  • Stephen R Quake
  • Lu Chen
  • Tomasz Lipniacki
  • Elissa M Denny
  • Jahlionais E Gaston

Detail Information

Publications20

  1. 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)...
  2. pmc Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing
    Savaş Tay
    Department of Bioengineering, Stanford University, Stanford, California 94305, USA
    Nature 466:267-71. 2010
    ..These results highlight the value of high-throughput quantitative measurements with single-cell resolution in understanding how biological systems operate...
  3. 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...
  4. pmc A forward-genetic screen and dynamic analysis of lambda phage host-dependencies reveals an extensive interaction network and a new anti-viral strategy
    Nathaniel D Maynard
    Department of Bioengineering, Stanford University, Palo Alto, California, United States of America
    PLoS Genet 6:e1001017. 2010
    ..Based on our data, it appears that 2-thiouridine modification of tRNAGlu, tRNAGln, and tRNALys is particularly important for the efficient production of infectious lambda phage particles...
  5. pmc A whole-cell computational model predicts phenotype from genotype
    Jonathan R Karr
    Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA
    Cell 150:389-401. 2012
    ..We conclude that comprehensive whole-cell models can be used to facilitate biological discovery...
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. 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...
  11. pmc Computational modeling of mammalian signaling networks
    Jacob J Hughey
    Department of Bioengineering, Stanford University, Stanford, CA, USA
    Wiley Interdiscip Rev Syst Biol Med 2:194-209. 2010
    ..Finally, we focus on three specific instances of 'model-driven discovery': cases in which computational modeling of a signaling network has led to new insights that have been verified experimentally...
  12. pmc High-throughput, single-cell NF-κB dynamics
    Timothy K Lee
    Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, United States
    Curr Opin Genet Dev 20:677-83. 2010
    ..We highlight the major aspects of increasing throughput and describe a current system that can monitor, image and analyze the NF-κB activation of thousands of single cells in parallel...
  13. 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...
  14. 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...
  15. pmc The virus as metabolic engineer
    Nathaniel D Maynard
    Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
    Biotechnol J 5:686-94. 2010
    ..As a result, metabolic engineers have a unique perspective that could lead to novel and effective methods to combat viral infection...
  16. pmc A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide
    Timothy K Lee
    Bioengineering Department, Stanford University, 318 Campus Drive West, Stanford, CA 94305 5444, USA
    Sci Signal 2:ra65. 2009
    ..Our findings show that mammalian cells can create "noisy" environments to produce diversified responses to stimuli...
  17. 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...
  18. ncbi request reprint Constraints-based models: regulation of gene expression reduces the steady-state solution space
    Markus W Covert
    Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    J Theor Biol 221:309-25. 2003
    ..5 and 97.5%. The method developed here provides a way to interpret how regulatory mechanisms are used to constrain network functions and produce a small range of physiologically meaningful behaviors from all allowable network functions...
  19. 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...
  20. 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...