Introduction to the concepts and methods of networks in evolutionary studies (sequence similarity networks, genome networks and multipartite graphs)
This free summer school will be held in Roscoff, France, between June 23rd 2019 (date of arrival) and June 29th (date of departure).
This school is designed in priority for biologists and bio-informaticians (completing a PhD degree or currently post-doctoral fellows, as well as researchers), who wish to learn the bases of network analyses.
The main notions (regarding various types of networks, the relevance of their analyses, and some bases in graph theory) will be introduced by short theoretical classes, followed by practical case-studies, introducing the basics in programming required to run such network analyses as well as to use the existing software/tools. Our goal is that, by the end of this summer school, all applicants will be qualified to perform network analyses of their own datasets.
More precisely, we will focus on the following concepts and methods:
- Introgressive evolution and large-scale diversity studies.
- Construction and analysis of sequence similarity networks (construction and sorting of connected components, definition of gene families, search for composite genes, implementation of centrality measures)
- Construction and analysis of genome networks (construction of weighted genome networks, implementation of their diameter, shortest paths, analyses of labeled nodes, etc.)
- Construction and analysis of gene-genome bipartite graphs (detection of connected components, and their articulation points, and twins)
In addition, 9 conferences on networks and evolution will be delivered by leading European and North American scientists during this school.
Confirmed speakers (complete list):
Pr. JP Gogarten (UConn, USA): Lateral Gene Transfer and Prokaryotic evolution
Pr. Robert Beiko (Dalhousie University, Canada) : Introduction to phylogenetic networks
Dr. Eric Bapteste (UPMC, France): Introduction to sequence similarity networks
Pr. Debashish Bhattacharya (U. Rutgers, USA): Reticulate evolution in eukaryotes
Pr. Eugene Koonin (NCBI, USA) : Viruses and networks
Pr. Michel Habib (LIAFA, France): Networks and centralities
Dr. Damien Eveillard (U. Nantes, France): Co-occurrence networks and the evolution of geochemical cycles in the environment
Pr. Daniel Huson (U Tuebingen, Germany): Network approaches in microbiome analysis
Pr. Marc-André Sélosse (MNHN, France): The living world as a network
This summer school is funded by ERC grant (FP7/2007-2013 Grant Agreement # 615274). Hence, registration is free, housing and food (breakfast, lunch) are also fully covered. Applicants will only need to fund their travel to Roscoff and their evening dinners.
10 places only are available, with a mandatory requirement: applicants must show basic computer skills (i.e. to be familiar with Linux environment and with at least one programming language, preferably Python).
Applications are to be submitted asap, and no later than February 15th 2019, by email to :
firstname.lastname@example.org , and contain a brief letter describing why this class will be of significant interest for the applicant and his/her future studies.
Applicants will be selected based on their motivation, and their resume, including the names of two scientific referees for PhD and postdoctoral fellows.
We are excited to meet you soon in Roscoff.
Eric Bapteste + Philippe Lopez + Eduardo Corel