Topic outline

  • General

    Next Generation Comparative Phylogenomics

    Geneva, 2-6 June 2014


    The species classification is based on synapomorphies observed in comparative life science studies, including morphology, anatomy, cell biology, developmental biology. In this course, evolutionary concepts and biological findings will be linked to associated alterations at the molecular level.

    This event will be composed of

    • a 4-day course (limited to 20 registered participants, priority to PhD students members of StarOmics doctoral program)
    • a mini symposium, open to all (4th of June)


    The purpose of this course is to explore efficient ways of moving from molecular phylogenetics to comparative phylogenomics. Theoretical sessions will introduce concepts of genome evolution, phylogenomic data resources and methods suitable to large-scale analysis. The practicals will cover a wide range of tasks essential to next generation comparative phylogenomics. Course days will be an alternance of lectures and practicals. At the mini-symposium, international experts will present studies on improving the quality of large-scale analysis and application of comparative phylogenomics.


    • Skills: Basics in evolutionary biology, phylogenetics and bioinformatics (recommended, but not mandatory).
    • Please bring your own laptop with WIFI activated


    Application is now closed.


    Centre Médical Universitaire (CMU), Geneva

    Course: Room S3
    Mini symposium: auditorium C150

    Additional information

    We will recommend 1 ECTS credit for the course and an additional ECTS credit for an optional project (participants will be contacted before the course starts).

    • Schedule

      Monday, June 2: Evolution of life, genomes, proteomes, proteins
      Group Xenarios. Brigitte Boeckmann, Emmanuel Boutet
      Theoretical: Evolution of life; Model organisms; Reference proteomes; Protein evolution; Protein architectures.
      Practical: Prediction of remote protein family members (Similarity vs homology); Comparison of domain architectures; Domain orthology; Concepts of phylogenomic databases.

      Tuesday, June 3: Comparative genomics
      Group Zdobnov. Evgenia Kriventseva, Thomas Petty, Thomas Junier
      Theoretical: Comparative genomics, Orthology, Handling Phylogenetic trees (introduction of Newick utilities), Metagenomics.

      Practicals: OrthoDB, Newick utilities, Metagenomics tools.

      Wednesday, June 4: mini-SYMPOSIUM (schedule)

      Thursday, June 5: Comparative phylogenomics
      Group Milinkovitch. Djordje Grbic, Michel Milinkovitch, Athanasia Tzika, Asier Ullate
      Theoretical: Multi-species genome comparisons, phylogeny inference

      Practicals: MANTiS, MetaPIGA, FigTree.

      Friday, June 6: Gene and genome duplication
      Group Robinson-Rechavi. Nadezda Kryuchkova, Sacha Laurent, Marc Robinson-Rechavi
      Duplication is responsible for a large part of the diversity of genes present in genomes. We will study how gene or genome duplications are detected and characterized bioinformatically; discuss examples of whole genome duplication; study the models of evolution for duplicate genes; examine methods and types of data to test these models; and finally discuss recent results from my lab concerning the evolution of orthologs and paralogs.
      The day will be an alternance of lectures and practical use of web-based bioinformatics resources.

      projects: contact Marc Robinson-Rechavi



      4-June-2014, UNIGE-CMU, Auditorium C150

      Program (pdf)

      Ioannis Xenarios

      Swiss Institute of Bioinformatics (SIB), Switzerland

      Session I: Methods for Phylogenomics

      Chair: Evgeny Zdobnov

      Des Higgins
      Conway Institute, University College Dublin, Ireland
      "Making accurate multiple sequence alignments of very large numbers of protein sequences"

      Eyal Privmann
      Institute of Evolution, University of Haifa, Israel
      "Alignment reliability, alignment filtering, and their effect on downstream evolutionary analyses"

      11:10-11:40 Coffee break

      Maria Anisimova
      Institute of Applied Simulations, Zurich University of Applied Sciences (ZHAW), and Computer Science Department, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
      "Current standards in phylogenomics as applied to sequences with tandem repeats”"

      12:25-13:45 Lunch break

      Session II: Applied Phylogenomics

      Chair: Michel Milinkovitch

      Vincent Daubin
      Biometry and Evolutionary Biology laboratory (LBBE), National Center for Scientific Research (CNRS), Lyon 1, France
      "Genomes as documents of evolutionary history"

      Shinichi Sunagawa
      European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
      "Quantitative metagenomics of the human gut and ocean microbiome"

      15:15-15:45 Coffee break

      Margarida Cardoso Moreira
      Center for Integrative Genomics, University of Lausanne, Switzerland
      "Functional evolution of mammalian genomes”"

      Panel discussion
      Moderator: Marc Robinson-Rechavi
      "Thousands of phylogenies with thousands of species, then what?"