Systems Biology (2014)

Systems Biology (2014)

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Introduction to cellular and population-level systems biology with an emphasis on synthetic biology, modeling of genetic networks, cell-cell interactions, and evolutionary dynamics.

Jeff Gore


    • Jul 17, 2015 LATEST EPISODE
    • infrequent NEW EPISODES
    • 1h 19m AVG DURATION
    • 24 EPISODES


    Search for episodes from Systems Biology (2014) with a specific topic:

    Latest episodes from Systems Biology (2014)

    Interspecies interactions

    Play Episode Listen Later Jul 17, 2015 81:03


    This lecture by Prof. Jeff Gore covers models and experiments of predator-prey interactions and oscillations. He begins with the Lokta-Volterra model, which has been called both "bad" (mathematically speaking) and "profoundly important."

    Dynamics of populations in space

    Play Episode Listen Later Jul 17, 2015 80:46


    In this lecture, Prof. Jeff Gore finishes the discussion of the Lotka-Volterra competition model. He then moves on to the topic of non-transitive interactions, what he calls rock-paper-scissor interactions.

    Ecosystem stability, critical transitions, and biodiversity

    Play Episode Listen Later Jul 17, 2015 80:04


    In this lecture, Prof. Jeff Gore discusses the stability, resilience, and diversity of populations at a systems level. He begins by considering a single population, and then moves on to a simple model of interactions between species.

    The neutral theory of ecology

    Play Episode Listen Later Jul 17, 2015 77:45


    In this lecture, Prof. Jeff Gore asks why are some species abundant and others rare? Are there universal patterns at play? And what lead to these patterns?

    Microbial evolution experiments and optimal gene circuit design

    Play Episode Listen Later Jul 17, 2015 79:40


    In this lecture, Prof. Jeff Gore discusses the Nature article "Optimality and evolutionary tuning of the expression level of a protein," with emphasis on the connection between theory, prediction, and experiment.

    Clonal interference and the distribution of beneficial mutations

    Play Episode Listen Later Jul 17, 2015 81:04


    In this lecture, Prof. Jeff Gore covers the principles of the scientific article "An equivalence principle for the incorporation of favorable mutations in asexual populations."

    Fitness landscapes and sequence spaces

    Play Episode Listen Later Jul 17, 2015 78:45


    In this lecture, Prof. Jeff Gore continues his discussion of clonal interference (CI) and the equivalence principle. He discussed CI and the rate of evolution. And finally he thinks about evolution from the perspective of rugged fitness landscapes.

    Evolutionary games

    Play Episode Listen Later Jul 17, 2015 80:41


    In this lecture, Prof. Jeff Gore begins with a review problem on rugged landscaped. He then moved on to the main subject: evolutionary game theory. This includes the Nash equilibrium, the prisoner's dilemma, and the hawk-dove game.

    Survival in fluctuating environments

    Play Episode Listen Later Jul 17, 2015 78:26


    In this lecture, Prof. Jeff Gore discusses the regulation of genes in response to changing environments. He discusses a few theories for phenotypic heterogeneity and examples from biology.

    Parasites, the evolution of virulence and sex

    Play Episode Listen Later Jul 17, 2015 78:44


    This lecture by Prof. Jeff Gore covers two topics. The first is the evolution of virulence, and how to model host-parasite interactions. The second is the evolutionary benefit of sex.

    Evolution in finite populations

    Play Episode Listen Later Jul 17, 2015 80:56


    This lecture by Prof. Jeff Gore is on the topic of evolution in finite populations. Several aspects are covered, including the Moran process, neutral and non-neutral evolution, and stochastic extinction of beneficial mutants.

    Robustness in development and pattern formation

    Play Episode Listen Later Jul 17, 2015 81:18


    This lecture by Prof. Jeff Gore is about the mechanisms of biological pattern formation. One mechanism discussed is diffusion.

    Robustness and bacterial chemotaxis

    Play Episode Listen Later Jul 17, 2015 78:41


    In this lecture, Prof. Jeff Gore continues his discussion of bacterial chemotaxis, or how bacteria find food. The principle is a biased random walk of runs and tumbles, and is a shown to display perfect adaptation.

    Life at low Reynold’s number

    Play Episode Listen Later Jul 17, 2015 79:12


    In this lecture, Prof. Jeff Gore asks, and answers, questions like how do bacteria find food? How do they know which direction to swim, and how do they swim? All of these questions relate to the low Reynold's number regime in which bacteria live.

    Feed-forward loop network motif

    Play Episode Listen Later Jul 17, 2015 81:29


    In this lecture, Prof. Jeff Gore discusses the feed-forward loop (FFL) network motif. He covers coherent type 1 (C1) and the incoherent type 1 (I1) FFL motifs. This discussion of network motifs is extended to larger structures.

    Stochastic modeling

    Play Episode Listen Later Jul 17, 2015 81:51


    Prof. Jeff Gore discusses modeling stochastic systems. The discussion of the master equation continues. Then he talks about the Gillespie algorithm, an exact way to simulate stochastic systems. He then moves on to the Fokker-Planck equation.

    Causes and consequences of stochastic gene expression

    Play Episode Listen Later Jul 17, 2015 80:42


    In this lecture, the class analyzes a simple model of gene expression, first to understand the deterministic behavior of the model, and then to look at the stochastic behavior of the model.

    Introduction to stochastic gene expression

    Play Episode Listen Later Jul 17, 2015 80:34


    This lecture by Prof. Jeff Gore centers on discussion of one of his favorite scientific papers: "Probing gene expression in live cells, one protein molecule at a time," by Yu et al. http://dx.doi.org/10.1126/science.1119623

    Graph properties of transcription networks

    Play Episode Listen Later Jul 17, 2015 81:29


    Prof. Jeff Gore continues the discussion of oscillators, including alternative designs for oscillators. He then discusses the article Emergence of scaling in random networks, by Barabási & Albert. The final topic is network motifs.

    Synthetic biology and stability analysis in the toggle switch

    Play Episode Listen Later Jul 17, 2015 79:57


    In this lecture, Prof. Jeff Gore discusses the toggle switch, or two genes that repress each other. He then moves on to dimensionless equations and stability analysis.

    Oscillatory genetic networks

    Play Episode Listen Later Jul 17, 2015 81:11


    Prof. Jeff Gore introduces oscillatory genetic networks. He asks why oscillations are useful, and why might we want to design an oscillator. Central to the lecture is a Nature article: A synthetic oscillatory network of transcriptional regulators.

    Autoregulation, feedback and bistability

    Play Episode Listen Later Jul 17, 2015 78:40


    Prof. Jeff Gore continues his discussion of gene expression, this time with a focus on autoregulation (when a gene regulates its own expression). He begins by discussing the network motif, then moves on to both negative and positive autoregulation.

    Input function, Michaelis-Menten kinetics, and cooperativity

    Play Episode Listen Later Jul 17, 2015 77:45


    Prof. Jeff Gore discusses the kinetics of gene expression. Simple input-output relationships and chemical/enzyme kinetics. Response time for stable proteins. Ultrasensitivity: cooperative binding or multimer molecular titration.

    Introduction to the class and overview of topics

    Play Episode Listen Later Jul 17, 2015 67:19


    In this lecture, Prof. Jeff Gore introduces the topics of the course, which broadly include gene networks and cellular decision-making, evolutionary systems biology, and ecological systems biology.

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