Winter School on Quantitative Systems Biology
Reading Material

  1. Michael Lynch

    1. The population-genetic environment.
      Lynch, M., M. Ackerman, J.-F. Gout, H. Long, W. Sung, W. K. Thomas, and P. L. Foster. 2016. Genetic drift, selection, and evolution of the mutation rate. Nature Rev. Genetics 17: 704-714.
       
    2. Population genomics.
      Lynch, M. 2008. Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects. Mol. Biol. Evol. 25: 2421-2431.
      Maruki, T., and M. Lynch. 2015. Genotype-frequency estimation from high-throughput sequencing data. Genetics 201: 473-486.
      Lynch, M., M. Ackerman, K. Spitze, Z. Ye, and T. Maruki. 2017. Population genomics of Daphnia pulex. Genetics 206: 315-332.           
       
    3. The detailed-balance view of evolution: evolution of multimeric proteins, and transcription-factor binding sites.
      Lynch, M. 2013. Evolutionary diversification of the multimeric states of proteins. Proc. Natl. Acad. Sci. USA 110: E2821-E2828.
      Lynch, M., and K. Hagner. 2014. Evolutionary meandering of intermolecular interactions along the drift barrier. Proc. Natl. Acad. Sci. USA 112: E30-E38.
       

    https://biodesign.asu.edu/michael-lynch/publications
     

  2. Matteo Marsili

    For reading material, I’m going to use chapter 6 and 7 of the book Networks, Crowds, and Markets: Reasoning about a Highly Connected World by David Easley and Jon Kleinberg.

    Link
     

  3. Sergey Gavrilets
    ​
    The general topic of my lectures will be "Models of speciation".
    A tentative course outline is:

    1. Introduction
    2. Fitness landscapes
    3. Speciation on rugged fitness landscapes
    4. Speciation on holey fitness landscapes
    5. Disruptive selection and nonrandom mating
    6. Sympatric speciation
       

    The course will be loosely based on my book: Link

    I also attached 2 review papers which should be a good introduction. Prerequisites are basic knowledge of population ecology, genetics and evolution, calculus, ordinary differential/difference equations and matrices.

    1. Review Paper 1
    2. Review Paper 2
       
  4. Richard Neher

    ​

    Reviews on population genetic theory that might be helpful:
     
    1. Annual Reviews
    2. Journals
    3. Review Paper
    4. Lecture 1 & 2 Notes
       
  5. Vidyanand Nanjundiah
    ​
    1. Review Paper
    2. Talk Slides  
       
  6. Luca Peliti
    ​
    Lecture Notes
    Reading Material 1
    Reading Material 2
    Reading Material 3

     

  7. Vijaykumar Krishnamurthy

    Reading Material
     

  8. John Reinitz

    Lecture Notes

     

  9. Erik van Nimwegen
     
    1. Regarding the first topic, this is a good review: (Link), Review Paper 1, Talk Slides
    2. For the second topic, the most relevant paper is: (Link) Review Paper 2  
    3. Review Paper 3
    4. For the fourth topic, the relevant paper to read is: (Link), Review Paper

     

  10. Harmit Malik

    Reading Material
     

  11. Kavita Jain
     
    1. Lecture Notes
    2. Review Paper

       

  12. Lucy Colwell​
     
    1. Reading Material 1
    2. Reading Material 2
    3. Reading Material 3
    4. Reading Material 4
    5. Talk Slide

       

  13. Paul Sneigowski
     
    1. Talk slide Link 1, Link 2, Link 3
    2. Review Paper 1
    3. Review Paper 2
    4. Review Paper 3
    5. Review Paper 4

       

  14. Jeff Gore
     
    1. Reading Material 1
    2. Reading Material 2
    3. Reading Material 3