Jose M G Vilar

Summary

Affiliation: Memorial Sloan-Kettering Cancer Center
Country: USA

Publications

  1. ncbi request reprint DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise
    Jose M G Vilar
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, 307 East 63rd Street, New York, NY 10021, USA
    Curr Opin Genet Dev 15:136-44. 2005
  2. pmc Signal processing in the TGF-beta superfamily ligand-receptor network
    Jose M G Vilar
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS Comput Biol 2:e3. 2006
  3. ncbi request reprint Multiprotein DNA looping
    Jose M G Vilar
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Phys Rev Lett 96:238103. 2006
  4. pmc Ab initio thermodynamic modeling of distal multisite transcription regulation
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Nucleic Acids Res 36:726-31. 2008
  5. ncbi request reprint DNA looping and physical constraints on transcription regulation
    Jose M G Vilar
    The Rockefeller University, 1230 York Avenue, Box 34, New York, NY 10021, USA
    J Mol Biol 331:981-9. 2003
  6. pmc Inferring the in vivo looping properties of DNA
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, 307 East 63rd Street, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 102:17642-5. 2005
  7. pmc Multilevel deconstruction of the In vivo behavior of looped DNA-protein complexes
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS ONE 2:e355. 2007
  8. pmc Stochastic dynamics of macromolecular-assembly networks
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Mol Syst Biol 2:2006.0024. 2006
  9. ncbi request reprint DNA looping: the consequences and its control
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10021, USA
    Curr Opin Struct Biol 16:344-50. 2006
  10. pmc Synthetic cooperation in engineered yeast populations
    Wenying Shou
    Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 104:1877-82. 2007

Detail Information

Publications12

  1. ncbi request reprint DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise
    Jose M G Vilar
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, 307 East 63rd Street, New York, NY 10021, USA
    Curr Opin Genet Dev 15:136-44. 2005
    ..Recent developments indicate that DNA looping can also lead to the suppression of cell-to-cell variability, the control of transcriptional noise, and the activation of cooperative interactions on demand...
  2. pmc Signal processing in the TGF-beta superfamily ligand-receptor network
    Jose M G Vilar
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS Comput Biol 2:e3. 2006
    ..Our computational approach unifies seemingly disparate experimental observations and suggests specific changes in receptor trafficking patterns that can lead to phenotypes that favor tumor progression...
  3. ncbi request reprint Multiprotein DNA looping
    Jose M G Vilar
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Phys Rev Lett 96:238103. 2006
    ..Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance...
  4. pmc Ab initio thermodynamic modeling of distal multisite transcription regulation
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Nucleic Acids Res 36:726-31. 2008
    ..Our results provide new insights into the detailed functioning of the lac operon and reveal an efficient avenue to incorporate the required underlying molecular complexity into fully predictive models of gene regulation...
  5. ncbi request reprint DNA looping and physical constraints on transcription regulation
    Jose M G Vilar
    The Rockefeller University, 1230 York Avenue, Box 34, New York, NY 10021, USA
    J Mol Biol 331:981-9. 2003
    ..Looping is thus able to circumvent some of the constraints inherent to mechanisms based solely on binding to a single operator site and provides a mechanism to regulate the average properties of transcription and its fluctuations...
  6. pmc Inferring the in vivo looping properties of DNA
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, 307 East 63rd Street, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 102:17642-5. 2005
    ..These unexpected results can confer to the physical properties of DNA a more prominent role at shaping the properties of gene regulation than previously thought...
  7. pmc Multilevel deconstruction of the In vivo behavior of looped DNA-protein complexes
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS ONE 2:e355. 2007
    ..Incorporation of all this molecular information into gene-regulation models reveals an unprecedented versatility of looped DNA-protein complexes at shaping the properties of gene expression...
  8. pmc Stochastic dynamics of macromolecular-assembly networks
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Mol Syst Biol 2:2006.0024. 2006
    ..This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes...
  9. ncbi request reprint DNA looping: the consequences and its control
    Leonor Saiz
    Integrative Biological Modeling Laboratory, Computational Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10021, USA
    Curr Opin Struct Biol 16:344-50. 2006
    ....
  10. pmc Synthetic cooperation in engineered yeast populations
    Wenying Shou
    Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 104:1877-82. 2007
    ....
  11. pmc Modeling network dynamics: the lac operon, a case study
    Jose M G Vilar
    The Rockefeller University, 1230 York Avenue, Box 34, New York, NY 10021, USA
    J Cell Biol 161:471-6. 2003
    ..We integrate three different levels of description (molecular, cellular, and that of cell population) into a single model, which seems to capture many experimental aspects of the system...
  12. pmc Modularizing gene regulation
    Jose M G Vilar
    Mol Syst Biol 2:2006.0016. 2006