MBI Videos

Videos by Workshop 6: Algebraic Methods in Systems and Evolutionary Biology

  • Transcriptional Regulatory Networks from the Bottom Down
    Ilya Shmulevich
    Regulatory networks of biomolecular interactions in cells govern virtually all cellular behaviors and functions. Modern measurement technologies are being used to generateinformation on many types of interactions, involving transcriptional and microRNA regulatory networks, signaling networks, and cytokine networks. Temporal measurements of gene and protein expression level...
  • A stochastic model for the evolution of metabolic network using neighbor dependence
    Aziz Mithani

    The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions) or complex (incorporating dep...

  • Coloured Petri Nets for Multiscale Systems Biology
    Monika Heiner
    This talk reports on our investigations to explore appropriate modelling and analysis techniques for processes evolving simultaneously over time and space, applied to biological systems. Current challenges for modelling in Systems Biology include those associated with issues of complexity and representing systems with multi-scale attributes. A drawback of current modelling...
  • Chemical reaction systems with toric steady states
    Anne Shiu
    Chemical reaction networks taken with mass-action kinetics are dynamical systems governed by polynomial differential equations that arise in systems biology. In general, establishing the existence of (multiple) steady states is challenging, as it requires the solution of a large system of polynomials with unknown coefficients. If, however, the steady state ideal of the sys...
  • Logical modelling of regulatory networks, results and challenges
    Elisabeth Remy
    The logical method proved useful for the modelling of regulatory networks and the analysis of their dynamical properties. It relies on two directed graphs: the regulatory graph, which represents the interactions between regulatory components, each associated with discrete levels of expression (or activity), and the state transition graph, which represents the discrete dyna...
  • Non-parametric analysis of mass action models and data
    Heather Harrington
    How cells make decisions can be investigated using mathematical models. We describe a procedure to decide whether a model is compatible with steady-state data. This method requires no parameter values-- it is based on techniques from algebraic geometry, linear algebra, and optimization. Cellular decisions also depend on where they occur in the cell (e.g., nucleus or cytopl...
  • Cancer Therapy Design Based on Pathway Logic
    Aniruddha Datta
    Cancer encompasses various diseases associated with loss of cell-cycle control, leading to uncontrolled cell proliferation and/or reduced apoptosis. Cancer is usually caused by malfunction(s) in the cellular signaling pathways. Malfunctions occur in different ways and at different locations in a pathway. Consequently, therapy design should first identify the location and t...
  • Avenues toward simplified Boolean modeling of signal transduction networks
    Reka Albert
    Over the past five years my group, in collaboration with wet-bench biologists, developed and validated asynchronous Boolean models of several signal transduction networks. Along the way we have encountered obstacles related to the lack of timing knowledge and the large size of the state space. In this talk I will present three methodologies we developed to overcome these o...

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