/single-cell_sib_scilifelab

SIB/Scilifelab autumn school in single cell omics 2019.

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Joint SIB and NBIS/SciLifeLab Autumn School

Single Cell Analysis Course

13 - 18 October 2019 - Leysin, Switzerland


Date

13.10.2019 - 18.10.2019


Location

Hotel Central Residence & Spa, Leysin, Switzerland.

Arrival: Sunday before 18h

Departure: Friday around 14h30


Programme

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

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

  • 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.