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2010 Topics in Computational and Systems biology

    Table of contents
    1. 1. Rules
    2. 2. Ideas for topics

    Open to the public!  This seminar covers a broad range of topics in computational and systems biology.  While many of the students are biologically oriented, some come from primarily experimental backgrounds; presentations are therefore a mix of computational and experimental topics.  Our primary goal is to learn interesting new ideas in this dynamic research area.  Each talk focuses on a small group of papers and provides a survey of past work and highlights of current research, not all of which may be covered in the provided papers.  The balance, naturally, varies from topic to topic.  The presentations are followed by a discussion session; while this is intended for the student participants, feel free to attend.

    Please contact Michael Gribskov, x46933,  for information

    Student Participants:  Clayton Collings, Patrick Dolan, Subhangi Ghosh, Aditi Gupta, Jim Hengenius, Kejie Li, Prasad Siddavatam, Qiong Wu, Greg Ziegler, Reazur Rahman

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    1. Each session will be two hours.  The first hour will be a presentation and the second a discussion of the talk.
    2. Each presentation should provide a survey of the topic, related the topic to important biological questions, and introduce research questions that are currently being addressed.  Your own ideas on what is important or interesting, whether or not someone is doing it, are highly valued. 
    3. You may not choose a topic that overlaps your personal research to the extent that you would have to do no work to make a presentation; a topic that significantly extends your personal research is acceptable.
    4. the presenter will post, no later than a week in advance, two to four papers that provide background/thinking material for the talk.  Failure to do so can affect your grade.  Review articles may me included but should not be onerously long, and must be accompanied by research article(s). 
    5. Student participants must read the papers!
    6. During the discussion, everyone will be expected to contribute by making insightful comments or asking intelligent questions. 


     Date  Presenter  Topic
     1 February
     Gribskov Petri Nets: Qualitative models of Biological Systems
     8 February
     Kejie Li Protein Dynamics Network Analysis
     15 February
     James Hengenius
    Evolutionary Dynamics on Graphs
     22 February
     Qiong Wu
    Ontology Engineering
     1 March
     Greg Ziegler
    Circadian Clocks: Systems and Synthetic Biology
     8 March
    Subhangi Ghosh A Study in Protein Evolution
     15 March
     Spring Break

     22 March
     Patrick Dolan
    Systems Virology
     29 March
     Clayton Collings
    Genomic DNA methylation (epigenetics)
     5 April

     12 April
     Reazur Rahman
    Translation Efficiency
     19 April
     Prasad Siddavatam Use(fullness) of network topological characteristics in understanding biological systems
     26 April
     Aditi Gupta Mutational Pathways in HIV

    Ideas for topics

    feel free to add your own

    • Summer 2009 seminar - has examples of previous topics
    • Role of neutral vs adaptive change
    • Use(fullness) of network topological characteristics in understanding biological systems
    • Network evolution
    • Structural genomics
    • Lattice folding models of protein structure
    • Protein disorder
    • Microbial community analysis/dynamics

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