Topic outline

  • General

    Joint SIB / SciLifeLab Autumn School Single Cell Analysis

    13 - 18 October 2019 - Leysin, Switzerland


    This page is addressed to registered participants. To access course description and application form, please click here.

    For any assistance, please contact training@sib.swiss.


    • Practical information

      • Location: Hotel Central Residence & Spa, Leysin, Switzerland

      • Travel:

        • By plane: arrival at Geneva-Airport. Trains 1x / hour every xx:20 direction Brig, change at Aigle. Travel time 2h10. Detailed timetable below.

        • By train only: wherever your starting point, the last (small) train will be from Aigle to Leysin-Feydey, then a few minutes walk

        • Detailed timetable on https://www.sbb.ch/en/home.html

        • By car: Hotel address: route du Belvédère 20, CH-1854 Leysin

      • Social activity & free time: if weather is not too bad we will go for hiking on Wednesday afternoon, so please bring good walking shoes and warm clothes. The hotel is equipped with a small spa, don't forget your swimsuit.


      • Program (might be slightly modified)

        Usual schedule:

        Start: 9:00

        End: between 17:00 and 18:00

        Lunch break: around 1h30

        Coffee breaks: usually 2x per day

        Dinner: around 20:00
        Free time / swimming pool: 18-20:00 (open from 8 to 21)


        Sunday
        • Until 18h: arrival of the participants, check-in

        • 18:45 Welcome drink and dinner


        Monday: Transcriptomics
        • 9:00 - 10:00 Introductory lecture: Vincent Gardeux, Laboratory of Systems and Genetics, EPFL / SIB, Lausanne, Switzerland.

        • 10:00 - 11:00 Quantification, QC & Normalization: Davide Risso, Department of Statistical Sciences, University of Padova, Italy.

        • 11:00 - 11:30 Coffee break

        • 11:30 - 12:30 Dimensionality reduction: Paulo Czarnewski, NBIS, Stockholm University, SciLifeLab, Stockholm, Sweden.

        • 12:30 - 14:00 Lunch break

        • 14:00 - 18:00 hands-on including a coffee break (David + Paulo)

        • 18:00 - 20:00 free time / spa 

        • 20:00 Dinner


        Tuesday: Transcriptomics
        • 9:00 - 10:00 Batch correction: Panagiotis Papasaikas, Computational Biology Group, Friedrich Miescher Institute for Biomedical Research / SIB, Basel. Switzerland.

        • 10:00 - 11:00 Clustering - methods overview: Charlotte Soneson, Computational Biology Group, Friedrich Miescher Institute for Biomedical Research / SIB, Basel, Switzerland.

        • 11:00 - 11:30 Coffee break

        • 11:30 - 12:30 Cell fate mapping and trajectories: Wouter Saelens, VIB-UGent Center for Inflammation Research, Gent, Belgium.

        • 12:30 - 14:00 Lunch break

        • 14:00 - 18:00 hands-on including a coffee break (Panagiotis, Charlotte, Wouter)

        • 18:00 - 20:00 free time / spa 

        • 20:00: special dinner - Cheese fondue


        Wednesday: Transcriptomics
        • 9:00 - Differential expression: Charlotte Soneson, Computational Biology, Friedrich Miescher Institute for Biomedical Research / SIB, Basel, Switzerland + short hands-on session.

        • ~12:30 Lunch break

        • Afternoon: Team activity

        • 18:30 - 19:30 Keynote lecture: Alejandro Sifrim, Laboratory of Reproductive Genomics, KU Leuven, Belgium.

        • 20:00 Dinner


        Thursday: Proteomics
        • 9:00 - 10:30 Transcriptome + proteome: Johan Reimegård, Uppsala University, SciLifeLab, Uppsala, Sweden.

        • 10:30 - 11:00 Coffee break

        • 11:00 - 12:30 Differential abundance and differential state analysis of single cell cytometry data, Mark Robinson & Helena Crowell, Statistical Genomics, University of Zurich / SIB, Zurich, Switzerland.

        • 12:30 - 14:00 Lunch break

        • 14:00-15:45 hands-on part 1

        • 15:45-16:15 coffee break

        • 16:15:18:00 hands-on part 2 (Mark, Helena, Johan)

        • 18:45 Dinner

        • <20:00 - 22:00 Special late opening of the spa


        Friday: Other omics and integration
        • 9:00 - 10:00 Data integration methods: Sebastien Smallwood, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

        • 10:00 - 11:00 Spatial mapping of scRNAseq: Lars Borm, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

        • 11:00 - 11:30 Coffee break

        • 11:30 - 12:30 Lineage tracing and scRNA: Maria Florescu, Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, Netherlands.

        • 12:30 - 14:00 Lunch break

        • 14:00 - 14:20 Conclusion and wrap up

        • 14:20 End of the event

        • 14:58 Train from Leysin-Feydey station


        • Software install

          Software packages installation will be communicated Wednesday