Joint SIB and NBIS/SciLifeLab Autumn School

Single Cell Analysis Course

13 - 18 October 2019 - Leysin, Switzerland

Date

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13.10.2019 - 18.10.2019

Location

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Hotel Central Residence & Spa, Leysin, Switzerland.

Arrival: Sunday before 18h

Departure: Friday around 14h30

Programme

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For the full schedule, please go to: Schedule

Sunday

• ≈17-18h: arrival of the participants, check-in
• Welcome and dinner

Monday: Transcriptomics

• Introductory lecture (Vincent Gardeux)
• Quantification, QC & Normalization (Davide Risso)
• Dimensionality reduction (Paulo Czarnewski)

Tuesday: Transcriptomics

• Batch correction (Panagiotis Papasaikas)
• Clustering - methods overview (Charlotte Soneson)
• Cell fate mapping and trajectories (Wouter Saelens)

Wednesday: Transcriptomics

• Differential expression (Charlotte Soneson)
• Afternoon: Team activity
• Evening: Keynote lecture: Alejandro Sifrim, Laboratory of Reproductive Genomics, KU Leuwen, Belgium.

Thursday: Proteomics

• Transcriptome + proteome (Johan Reimegård)
• Differential abundance and differential state analysis of single cell cytometry data (Mark Robinson & Helena Crowell)

Friday: Other omics and integration

• Data integration methods (Sebastien Smallwood)
• Spatial mapping of scRNAseq (Lars Borm)
• Lineage tracing and scRNA (Maria Florescu)

Learning objectives

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After this course you will be able to:

• use a range of bioinformatics tools to analyze single cell RNA-seq data
• discuss a variety of aspects of single cell RNA-seq data analysis
• understand the advantages and limitations of single cell RNA-seq data analysis

Lecturers

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• Alejandro Sifrim, Laboratory of Reproductive Genomics, KU Leuwen, Belgium
• Åsa Björklund, NBIS, Uppsala University, SciLifeLab, Uppsala, Sweden
• Charlotte Soneson, Computational Biology Group, Friedrich Miescher Institute for Biomedical Research / SIB, Basel, Switzerland
• Davide Risso, Department of Statistical Sciences, University of Padova, Italy
• Helena Crowell, Statistical Genomics, University of Zurich / SIB, Zurich, Switzerland
• Johan Reimegård, NBIS, Uppsala University, SciLifeLab, Uppsala, Sweden
• Lars Borm, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
• Maria Florescu, Hubrecht Institute, Developmental Biology and Stem Cell Research, Utrecht, Netherlands
• Mark Robinson, Statistical Genomics, University of Zurich / SIB, Zurich, Switzerland
• Nadine Zangger, Bioinformatics Core Facility, SIB, Lausanne, Switzerland
• Panagiotis Papasaikas, Computational Biology Group, Friedrich Miescher Institute for Biomedical Research / SIB, Basel, Switzerland
• Paulo Czarnewski, NBIS, Stockholm University, SciLifeLab, Stockholm, Sweden
• Sebastien Smallwood, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
• Vincent Gardeux, Laboratory of Systems and Genetics, EPFL / SIB, Lausanne, Switzerland
• Wouter Saelens, VIB-UGent Center for Inflammation Research, Gent, Belgium

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.