J Goutsias

Summary

Affiliation: Johns Hopkins University
Country: USA

Publications

  1. ncbi request reprint Grayscale level connectivity: theory and applications
    Ulisses Braga-Neto
    Section of Clinical Cancer Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    IEEE Trans Image Process 13:1567-80. 2004
  2. pmc Intrinsic noise induces critical behavior in leaky markovian networks leading to avalanching
    Garrett Jenkinson
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS Comput Biol 10:e1003411. 2014
  3. pmc Numerical integration of the master equation in some models of stochastic epidemiology
    Garrett Jenkinson
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS ONE 7:e36160. 2012
  4. pmc Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems
    Garrett Jenkinson
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Bioinformatics 11:547. 2010
  5. pmc A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems
    Hong Xuan Zhang
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Bioinformatics 11:246. 2010
  6. pmc Thermodynamically consistent model calibration in chemical kinetics
    Garrett Jenkinson
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Syst Biol 5:64. 2011
  7. ncbi request reprint Computational and experimental approaches for modeling gene regulatory networks
    J Goutsias
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218, USA
    Curr Pharm Des 13:1415-36. 2007
  8. pmc Classical versus stochastic kinetics modeling of biochemical reaction systems
    John Goutsias
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland, USA
    Biophys J 92:2350-65. 2007
  9. ncbi request reprint A hidden Markov model for transcriptional regulation in single cells
    John Goutsias
    Whitaker Biomedical Engineering Institute, Clark Hall 308A, The Johns Hopkins University, Baltimore, MD 21218, USA
    IEEE/ACM Trans Comput Biol Bioinform 3:57-71. 2006
  10. ncbi request reprint Stochastic transcriptional regulatory systems with time delays: a mean-field approximation
    John Goutsias
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland 21218, USA
    J Comput Biol 13:1049-76. 2006

Collaborators

Detail Information

Publications14

  1. ncbi request reprint Grayscale level connectivity: theory and applications
    Ulisses Braga-Neto
    Section of Clinical Cancer Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    IEEE Trans Image Process 13:1567-80. 2004
    ..The use of grayscale level connectivity in image analysis applications, such as object extraction, image segmentation, object-based filtering, and hierarchical image representation, is discussed and illustrated...
  2. pmc Intrinsic noise induces critical behavior in leaky markovian networks leading to avalanching
    Garrett Jenkinson
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS Comput Biol 10:e1003411. 2014
    ..The general methods developed here can be used to study the emergence of avalanching (and other complex phenomena) in many biological, physical and man-made interaction networks. ..
  3. pmc Numerical integration of the master equation in some models of stochastic epidemiology
    Garrett Jenkinson
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland, United States of America
    PLoS ONE 7:e36160. 2012
    ..MATLAB software that implements the methods discussed in this paper is freely available as Supporting Information S1...
  4. pmc Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems
    Garrett Jenkinson
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Bioinformatics 11:547. 2010
    ..Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable...
  5. pmc A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems
    Hong Xuan Zhang
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Bioinformatics 11:246. 2010
    ....
  6. pmc Thermodynamically consistent model calibration in chemical kinetics
    Garrett Jenkinson
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218, USA
    BMC Syst Biol 5:64. 2011
    ..This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function...
  7. ncbi request reprint Computational and experimental approaches for modeling gene regulatory networks
    J Goutsias
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218, USA
    Curr Pharm Des 13:1415-36. 2007
    ..We conclude, by discussing a promising approach for inferring a transcriptional regulatory system from microarray data obtained by gene perturbations...
  8. pmc Classical versus stochastic kinetics modeling of biochemical reaction systems
    John Goutsias
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland, USA
    Biophys J 92:2350-65. 2007
    ....
  9. ncbi request reprint A hidden Markov model for transcriptional regulation in single cells
    John Goutsias
    Whitaker Biomedical Engineering Institute, Clark Hall 308A, The Johns Hopkins University, Baltimore, MD 21218, USA
    IEEE/ACM Trans Comput Biol Bioinform 3:57-71. 2006
    ..We employ simulations, based on a biologically relevant transcriptional regulatory system, to show the relative merits and limitations of various approximation techniques and provide general guidelines for their use...
  10. ncbi request reprint Stochastic transcriptional regulatory systems with time delays: a mean-field approximation
    John Goutsias
    Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland 21218, USA
    J Comput Biol 13:1049-76. 2006
    ..Moreover, it provides a rather simple and computationally attractive tool for rapid statistical characterization of the dynamic behavior of a nonlinear transcriptional regulatory system with time delays...
  11. ncbi request reprint Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems
    John Goutsias
    The Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA
    J Chem Phys 122:184102. 2005
    ..We present three examples which allow analytical calculations that clearly illustrate the mathematical steps underlying the proposed approximation and demonstrate the accuracy and effectiveness of our method...
  12. pmc A nonlinear discrete dynamical model for transcriptional regulation: construction and properties
    John Goutsias
    The Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, Maryland 21218, USA
    Biophys J 86:1922-45. 2004
    ....
  13. doi request reprint Probabilistic sensitivity analysis of biochemical reaction systems
    Hong Xuan Zhang
    The Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA
    J Chem Phys 131:094101. 2009
    ..The price to be paid, however, is a substantial increase in computational complexity over derivative-based techniques, which must be effectively addressed in order to make the proposed approach to sensitivity analysis more practical...
  14. ncbi request reprint Object-based image analysis using multiscale connectivity
    Ulisses Braga-Neto
    Virology and Experimental Therapy Laboratory of the Aggeu Magalhães Research Center CPqAM FIOCRUZ, Recife, PE Brazil
    IEEE Trans Pattern Anal Mach Intell 27:892-907. 2005
    ..Finally, we propose two object-based multiscale image summaries, reminiscent of the well-known (morphological) pattern spectrum, which can be useful in image analysis and image understanding applications...