13 - 18 October 2019
Leysin, Switzerland
Cancellation deadline:
01 October 2019
Academic: 600 CHF
For-profit: 1000 CHF
2 ECTS credits

No future instance of this course is planned yet

Application is now closed.

This course is organised by NBIS/SciLifeLab and the SIB PhD Training Network. Priority is given to their members, but is open to everyone.


Single-cell analysis of the various -omics makes possible to discover mechanisms, strains, expressions that would not be noticed when studying bulk cell populations. New developments lead more and more research groups to use this technology and this Autumn School will provide an overview of the various methods and fields of application through lectures and hands-on exercises.

Generally, the afternoons will be dedicated to practical exercises where you will be able to apply the theoretical concepts learned during the morning session. Sometimes there will be a mix of both.

One afternoon will be devoted to a social activity.

See the preliminary program below for more details...


This course is addressed to PhD students, postdocs and scientists starting to work with single cell technologies and analysis.

Learning objectives

The first objective of this school is to provide participants with a broad knowledge of single cell analysis that would enable them to understand its application in general. This would be achieved via the multiple lectures provided by our lecturers throughout the week.

The second objective is to enable participants to apply single cell analysis in their own research. This would be achieved by all the exercises that would follow the theoretical lectures.

The third objective is networking with the lecturers and also the other participants that will most likely share similar interests.


Knowledge / competencies

Students should

  • have intermediate to advanced R skills (able to read, understand and write R scripts),
  • know how to use common R/Bioconductor packages,
  • be familiar with the typical steps involved in a bulk RNA-seq (both experimental and data analysis parts).

Students should be able to bring their own laptop with R and RStudio installed. A list of required R-packages will be sent before the course and these should be installed prior to the course start.


  • ≈17-18h: arrival of the participants, check-in
  • Welcome and dinner
Monday: Transcriptomics
  • Introductory lecture: Vincent Gardeux, Laboratory of Systems and Genetics, EPFL / SIB, Lausanne, Switzerland.
  • Quantification, QC & Normalization: Davide Risso, Department of Statistical Sciences, University of Padova, Italy.
  • Dimensionality reduction: Paulo Czarnewski, NBIS, Uppsala University, SciLifeLab, Uppsala, Sweden.
Tuesday: Transcriptomics
  • Batch correction: Panagiotis Papasaikas, Computational Biology Group, Friedrich Miescher Institute for Biomedical Research / SIB, Basel. Switzerland.
  • Clustering - methods overview: Charlotte Soneson, Computational Biology Group, Friedrich Miescher Institute for Biomedical Research / SIB, Basel, Switzerland.
  • Cell fate mapping and trajectories: Wouter Saelens, VIB-UGent Center for Inflammation Research, Gent, Belgium.
Wednesday: Transcriptomics
  • Differential expression: Charlotte Soneson, Computational Biology, Friedrich Miescher Institute for Biomedical Research / SIB, Basel, Switzerland.
  • Afternoon: Team activity
  • Evening: Keynote lecture: Alejandro Sifrim, Laboratory of Reproductive Genomics, KU Leuwen, Belgium.
Thursday: Proteomics
  • Transcriptome + proteome: Johan Reimegård, Uppsala University, SciLifeLab, Uppsala, Sweden.
  • Differential abundance and differential state analysis of single cell cytometry data: Mark Robinson & Helena Crowell, Statistical Genomics, University of Zurich / SIB, Zurich, Switzerland.
Friday: Other omics and integration
  • Data integration methods: Sebastien Smallwood, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
  • Spatial mapping of scRNAseq: Lars Borm, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
  • Lineage tracing and scRNA: Maria Florescu, Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, Netherlands.

End of the event around 14h30.


Application is now closed.

Before applying, be sure your profile matches the prerequisites and do not forget to take this survey. If you do not take the survey, your application will not be taken into consideration. Please use the same email address for the application and the survey.

Registration fees are the following:

  • 250 Swiss Francs for members of the SIB PhD Training Network and for PhD students enrolled at a Swedish University,
  • 600 Swiss Francs for other academics,
  • 1200 Swiss Francs for for-profit institutions.

This includes full course fees, full board accommodation at the hotel and coffee breaks.

Deadline for free-of-charge cancellation is set is set to 31 August 2019. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.


At the end of the School, you will get a Certificate of Achivement in which the organizers recommend 2 ECTS credits.

Venue and Time

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

Arrival: Sunday before 18h

Departure: Friday around 14h30

Additional information

Coordination: Björn Nystedt (NBIS/SciLifeLab), Grégoire Rossier (SIB).

Scientific Committe: Åsa Björklund (NBIS/SciLifeLab), Michael Stadler & Charlotte Soneson (SIB and FMI Basel), Vincent Gardeux (EPFL).

For more information, please contact Grégoire Rossier.