ICTS

Santiago Elena

1. Lecture 1
   Title: A short introduction to Virology, viral quasispecies and virus population dynamics.
   1. Reading Material 1, 2, 3
2. Lecture 2
   Title: Evolutionary genetics of viral emergence. 
   1. Reading Material 1, 2, 3
3. Lecture 3
   Title: Systems Biology of virus-host interactions.
   1. Reading Material 1, 2, 3
4. Lecture 4
   Title: The arm race between host's resistance and virus' virulence.
   1. Reading Material 1, 2, 3
5. Lecture 5
   Title: Genome compactness and the evolution of genomic novelty in RNA viruses.
   1. Reading Material 1, 2, 3
       

1. ​Reading Material 1, 2, 3
    

1. ​Preparatory reading:
   

   Empirical fitness landscapes and the predictability of evolution
   J. Krug and J.A.G.M. de Visser
   Nature Reviews Genetics 15, 480-490 (2014)
   Link

   Lecture 1:
   Perspective: Sign epistasis and genetic constraint on evolutionary trajectories
   Daniel M. Weinreich, Richard A. Watson, Lin Chao
   Evolution 59(6):1165-1174 (2005)
   Link

   The Context-Dependence of Mutations: A Linkage of Formalisms
   Frank J. Poelwijk, Vinod Krishna and Rama Ranganathan
   PLoS Comput Biol 12(6): e1004771 (2016)
   Link

   Inferring genetic interactions from comparative fitness data
   Kristina Crona, Alex Gavryushkin, Devin Greene and Niko Beerenwinkel
   eLife 6:e28629 (2017)
   Link

   Lecture 2:
   Quantitative analyses of empirical fitness landscapes
   I.G. Szendro, M.F. Schenk, J. Franke, J. Krug and J.A.G.M. de Visser
   Journal of Statistical Mechanics: Theory and Experiment P01005 (2013)
   Link

   Patterns of Epistasis between Beneficial Mutations in an Antibiotic 
   Resistance Gene
   Martijn F. Schenk, Ivan G. Szendro, Merijn L.M. Salverda, Joachim Krug,
   J. Arjan G.M. de Visser
   Molecular Biology and Evolution 30:1779-1787 (2013)
   Link

   On the (un)predictability of a large intragenic fitness landscape
   Claudia Bank, Sebastian Matuszewski, Ryan T. Hietpas and Jeffrey D. Jensen
   PNAS 2016 December, 113 (49) 14085-14090.
   Link

   Lecture 3:
   Towards a general theory of adaptive walks on rugged landscapes
   Stuart Kauffman and Simon Levin
   Journal of Theoretical Biology
   Volume 128, Issue 1, 7 September 1987, Pages 11-45
   Link

   Evolutionary accessibility of mutational pathways
   J. Franke, A. Kloezer, J.A.G.M. de Visser and J. Krug
   PLoS Computational Biology 7, e1002134 (2011)
   Link

   Universality Classes of Interaction Structures for NK Fitness Landscapes
   Sungmin Hwang, Benjamin Schmiegelt, Luca Ferretti, Joachim Krug
   Journal of Statistical Physics, online first (2018)
   Link

   Lecture 4:
   The Utility of Fisher's Geometric Model in Evolutionary Genetics
   Olivier Tenaillon
   Annual Review of Ecology, Evolution, and Systematics 45:179-201 (2014)
   Link

   Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus
   Sijmen Schoustra, Sungmin Hwang, Joachim Krug, J. Arjan G. M. de Visser
   Proc. Roy. Soc. B Biol. Sc i. 283:20161376 (2016)
   Link

   Genotypic Complexity of Fisher's Geometric Model
   Sungmin Hwang, Su-Chan Park and Joachim Krug
   Genetics 206:1049-1079 (2017)
   Link

   Lecture 5:
   The population genetics of adaptation: The adaptation of DNA sequences
   H. Allen Orr
   Evolution 56(7):1317-1330 (2002)
   Link

   The Speed of Evolution in Large Asexual Populations
   Su-Chan Park, Damien Simon, Joachim Krug 
   Journal of Statistical Physics 138:381-410 (2010)
   Link

   Predictability of evolution depends nonmonotonically on population size
   Ivan G. Szendro, Jasper Franke, J. Arjan G. M. de Visser and Joachim Krug
   PNAS 2013 January, 110 (2) 571-576
   Link

2. Reading Material 1

   1. ​Problem Sheet
       

Ophelie Ronce

1. ​Reading Material 1, 2, 3, 4
    

Maria Orive

1. Lecture 1

2. Lecture 2

   1. Research Paper

3. Lecture 3

4. Lecture 4

5. Lecture 5

   1. Research talk paper

   2. Supplementary Material for the paper
       

Magnus Nordborg

1. ​Reading Material 1, 2, 3, 4, 5, 6, 7