Topic outline

  • General

    SIB PhD Training Network Retreat

    24-26 June 2019, Fribourg


    The annual retreats are exclusively reserved to the Training Network (TN) members and combine, in a relaxed atmosphere, interactive sessions in which the students can both present their work as well as network with their peers and with a speaker/tutor, usually a Group Leader from a Swiss University. Furthermore, we organize a social/fun activity.
    This year we are very happy to invite Dr Frédéric Schütz, co-group leader of SIB Bioinformatics Core Facility, Lausanne.


  • Location

    Hotel NH, Fribourg

    Grand Places 14, 1700 Fribourg

    tel: 026 351 91 91

    • Presentations

      This year, the event will be a soft skill exercise in order to improve data visualization in presentations and the students' presentations should have the following format:

      • 1 Title slide
      • 5 content slides: 1 Introduction slide; 3 different types of data on 3 different slides; 1 conclusion slide.

      List:

      1. Mariia Bilous - A network-based approach for visualization and simplification of single-cell RNA sequencing data (5:50 / 4:20)
      2. Nastassia Gobet - A systems genetics approach to uncover recovery of sleep loss (5:48 / 5:04)
      3.  Erblin Asllanaj - Mapping the 3D space of drug resistance in Mycobacterium tuberculosis: an overview over the resistome (5:10 / 5:50)
      4. Madeleine Suffiotti - Combined anomaly detection and unsupervised clustering to identify disease associated rare cell populations in CyTOF data (4:50 / 4:17)
      5. Alejandro V. Cano - Mutation bias in empirical genotype-phenotype landscapes (6:34 / 5:55)
      6. Anna Marcionetti - Diversification of clownfishes: Insights from the akallopisos group (6:00 / 5:20)
      7. Alexis Loetscher - A diversity study of the Epstein-Barr virus in patients from the Swiss-HIV cohort (7:07 / 6:38)
      8. Paula Carrio Cordo - Assessing tumor heterogeneity among cancer types (6:20 / 4:47)
      9. Alexandre Gouy - On the scent of rodent speciation (6:35 / 5:22)

      10. Marija Dmitrijeva - Strain-resolved dynamics of the lung microbiome in patient with cystic fibrosis (7:10 / 6:30)
      11. Simon Eggenschwiler - Pan-specific predictors for HLA-I ligands (5:40 / 4:30)
      12. Sara Heim - Clownfish and sea anemone metabolomics: understanding the mechanisms behind this mutualism (5:50 / 5:25)
      13. Francisco Brito - A number of (metagenomics) plots that might need fixing (6:00 / 4:55)
      14. Annika Gable - Hierarchical clustering of the STRING protein interaction network (6:50 / 5:05)
      15. Diana Ivette Cruz Dávalos - Ancient Brazilian genomics (8:40 / 6:50)
      16. Oluwaseun Oyewole - Discovery of a newly evolved pneumococcal Serotype 6F in Switzerland (6:35 / 4:57)
      17. Mathieu Seppey - A benchmarking platform for metagenomics classifiers (6:25 / 4:30)
      18. Ilektra Schulz - Ancient sequencing data (6:55 / 6:10)
      19. Deepak Tanwar - Computational analysis of multi-omics Spermatogonial Cells data across stages of development (5:20 / 5:20)
      20. Almut Luetge - Batch effects in scRNA-seq: What do they look like? (5:35 / 6:00)
      21. Stephany Orjuela León- DAMEfinder : A method to detect differential allele-specific methylation (6:25 / 3:53)
      • Detailed Program

        The schedule is indicative and might vary slightly

        Day 1:
        10:00 Welcome and introduction
        10:30 Students' presentation
        11:00 Coffee Break
        11:15 Students' presentation
        12:45 Lunch
        13:45 Students' presentation
        15:45 Coffee break
        16:00 Students' presentation

        Evening: Dinner

        Day 2:
        09:00 Last 3 presentations
        10:00 Tutor's lectures and tips about data visualization presentations
        10:45 Coffee break
        11:15 Participants freely work on their slides
        12:30 Lunch
        16:15 Departure to City Play meeting point (Place Georges Python)
        19:00 End of the team activity
        19:30 Dinner at the hotel


        Day 3:
        09:00 Presentation of the modified slides (part 1)
        10:30 Check out + coffee break
        11:00 Presentation of the modified slides (part 2)
        12:30 Lunch
        14:00 Presentation of the modified slides (part 3)
        Conclusion