Videos of Talks by Thomas Schneider

If you are not familar with my work, it may be best to watch the videos in order.

Index:


  1. Evolution of binding sites. Mathematical Biosciences Institute Workshop, Autumn Quarter 2005, Workshop 2, Aspects of Self-Organization in Evolution (November 14-18, 2005). Ohio State University.
    • Abstracts, Lecture Materials, and Video
    • The talk, streaming from Ohio State University: Streaming Video: Real Media (requires a RealPlayer)
    • The talk, copy from this website: mbi-schneider-2005nov17.mov (can play in a browser)
      Posted with permission from MBI.
    • Title: Molecular Information Theory: From Clinical Applications To Binding Site Evolution

      Author: Thomas D. Schneider, National Institutes of Health, National Cancer Institute, Center for Cancer Research Nanobiology Program, Molecular Information Theory Group

      Molecular Information Theory: From Clinical Applications To Binding Site Evolution Thomas D. Schneider, National Institutes of Health, National Cancer Institute, Center for Cancer Research Nanobiology Program, Molecular Information Theory Group Video

      Abstract:

      Information theory was introduced by Claude Shannon in 1948 to precisely characterize data flows in communications systems. The same mathematics can also be fruitfully applied to molecular biology problems. We start with the problem of understanding how proteins interact with DNA at specific sequences called binding sites. Information theory allows us to make an average picture of the binding sites and this can be shown with a computer graphic called a sequence logo (http://schneider.ncifcrf.gov/glossary.html#sequence_logo).

      Sequence logos show how strongly parts of a binding site are conserved in bits of information. They have been used to study a variety of genetic control systems. More recently the same mathematics has been used to look at individual binding sites using another computer graphic called a sequence walker (http://schneider.ncifcrf.gov/glossary.html#sequence_walker). Sequence walkers are being used to predict whether changes in human genes cause mutations or are neutral polymorphisms. It may be possible to predict the degree of colon cancer by this method.

      How do genetic systems gain information by evolutionary processes? Information theory was used to observe information gain in the binding sites for an artificial `protein' in a computer model of evolution. The model begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. The transition is rapid, demonstrating that information gain can occur by punctuated equilibrium. (http://schneider.ncifcrf.gov/paper/ev).

    • related paper: http://schneider.ncifcrf.gov/paper/ev.

  2. Why is the Genetic Code Degenerate? by Tom Schneider at Bits <-> Biology 2014 May 1, Building E14, 6th floor, MIT

  3. Three Principles of Biological States: Ecology and Cancer by Tom Schneider 2014 Oct 29 Wednesday 09:04-10:13 at the meeting Biological and Bio-Inspired Information Theory (14w5170) at the Banff International Research Station (BIRS), Banff, Canada.

  4. Information Theory in Biology by Tom Schneider 2016 October 19 Wednesday at the meeting:
    100 claude Shannon 1916-2016

    The Department of Electrical Engineering
    at the Indian Institute of Technology, Kanpur India
    Celebrates Shannon Centenary
    • Abstract:
      Speaker: Thomas Schneider, National Institute of Health, USA

      In this talk I will sweep across the major ideas I have developed using information theory to understand biology (see https://alum.mit.edu/www/toms/). We will begin with measuring the information of protein or RNA binding sites on DNA or RNA (Rsequence, bits per site) using Claude Shannon's information theory. The resulting information curve can be displayed by the now-popular graphical method of sequence logos which we invented. The total information of binding sites (area under a logo) is predicted by the genome size and number of sites (Rfrequency, bits per site), and this leads to a model for the evolution of binding sites which you can run (https://alum.mit.edu/www/toms/papers/ev/). I will then introduce how to apply the same theory to individual binding sites, sequence walkers. An important question is the relationship between binding site information and the binding energy. This lead to my discovery that many molecular systems are 70% efficient. Surprisingly, the mathematics that explains 70% efficiency applies to all biological systems that have distinct states.
    • Video of the talk on YouTube.
    • Video of the talk on Tom's website.
    • Slides.

color bar Small icon for Theory of Molecular Machines: physics,
chemistry, biology, molecular biology, evolutionary theory,
genetic engineering, sequence logos, information theory,
electrical engineering, thermodynamics, statistical
mechanics, hypersphere packing, gumball machines, Maxwell's
Daemon, limits of computers


Schneider Lab

origin: 2014 Nov 03
updated: 2017 Dec 28: edit Kanpur
color bar
U.S. Department of Health and Human Services  |  National Institutes of Health  |  National Cancer Institute  |  USA.gov  | 
Policies  |  Viewing Files  |  Accessibility  |  FOIA