These summer school were held in Roscoff, France, and were designed in priority for biologists and bio-informaticians (completing a PhD degree or currently post-doctoral fellows, as well as researchers), who wished 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) were 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 was that, by the end of these summer schools, all applicants were qualified to perform network analyses of their own datasets.
More precisely, we focused 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)
2016 July 4th – 7th : EVOLUNET 1st Summer School On Networks In Roscoff (France)
Invited speakers :
Pr. Fernando Baquero, Val Fernández-Lanza (Group of Biology and Evolution of Microorganisms, IRYCIS, Department of Microbiology, Ramón y Cajal University Hospital, CIBERESP, Spain): “Reticulate Nested Evolution in the Clinical Bacterial World”
Pr. Robert G. Beiko (Faculty of Computer Science, Dalhousie University): “Lateral gene transfer: how many stories can a network tell?”
Pr. Marc-André Sélosse (Institut de Systématique, Évolution, Biodiversité (ISYEB – UMR 7205 – CNRS, MNHN, UPMC, EPHE), Muséum national d’Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP50, 75005, Paris, France): “The evolution of interdependency by neutral evolution in holobionts”
Dr. E. Bapteste (CNRS, UPMC, France): “Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution”
Dr. Marco Fondi (Dep. of Biology, University of Florence): “Microbial sequence similarity networks: deciphering the role of plasmids in microbial evolution and ecology.”
Pr. François-Joseph Lapointe (Département de sciences biologiques, Université de Montréal): “A statistical framework to assess and compare complex biological networks”
Dr. Mattis List (CRLAO and UPMC, France): “ Non-Tree-Like Processes in Language Evolution”
Dr. Philippe Huneman (IHPST, France): “Network analysis and the philosophy of scientific explanations.”
Pr. Michel Habib (LIAFA, INRIA, France): “Modeling with graphs, from success stories to quicksands”
2018 June 25th – 29th: EVOLUNET 2nd Summer School On Networks In Roscoff (France)
Invited speakers :
Monday June 25th:
Pr. James McInerney (U. Manchester, UK): Networks and public goods : reticulate evolution in prokaryotes
Dr. Philippe Gambette (U. Marne, France): The different types of networks used in evolutionary study : how they are made and what they are useful for
Dr. Eric Bapteste (UPMC, France): Introduction to sequence similarity networks
Tuesday June 26th:
Pr. Debashish Bhattacharya (U. Rutgers, USA): Reticulate evolution in eukaryotes
Pr. Michel Habib (U. Paris 7, France): Graph centralities and graph comparisons
Dr. Damien Eveillard (U. Nantes, France): Co-occurrence networks and the evolution of geochemical cycles in the environment
Friday June 29th:
Pr. Tal Dagan (U. kiel, Germany): Directed bipartite graphs and LGT mediated by phages
Dr. Mehdi Layeghifard (U. Toronto, Canada): Metagenomic networks
Marc-André Sélosse (MNHN, France): The living world as a network
2019 June 24th – 29th: EVOLUNET 3rd Summer School On Networks In Roscoff (France)
Invited speakers
Monday 24th
Pr. J. Peter Gogarten (Board of Trustees Distinguished Professor, Molecular and Cell Biology, University of Connecticut, USA): Lateral gene transfer and prokaryotic evolution
Pr. Robert Beiko (Faculty of Computer Science, Dalhousie University, Canada): Introduction to phylogenetic networks
Dr. Eric Bapteste (CNRS, UPMC, MNHN): Introduction to sequence similarity networks
Tuesday 25th
Pr. Debashish Bhattacharya (Department of Biochemistry and Microbiology, Rutgers University, USA): Lateral gene transfer and eukaryotic evolution: the case of red algae
Pr. Michel Habib (Liafa, France): Networks and centralities
Pr. Eugene Koonin (National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA): Bipartite network analysis to reveal biological modules
Friday 28th
Prof. Dr. Daniel Huson (Algorithms in Bioinformatics, University of Tübingen, Germany): Network approaches in microbiome analysis
Dr. Marko Budinich (Département Informatique, UMR 6004 Laboratoire des Sciences du Numérique de Nantes, Université de Nantes, France): Metabolic networks and ecosystems
Pr. Marc-André Sélosse (Professeur du Muséum national d’Histoire naturelle, ISYEB UMR7205, France) : Nature as networks