Teaching

Spatial Omics Data Analysis (2025)

This course delves into the cutting-edge field of Spatial Omics, focusing on Spatially-Resolved Transcriptomics (SRT) technology which provides unprecedented insights into the spatial organization of gene expression within tissues. The rapid and recent advances in SRT technology are transforming our understanding of biological systems, and this course is designed to equip researchers with the tools to harness the power of SRT, adding significant value to biological knowledge and opening new avenues for scientific discovery.

This course was offered by ELIXIR and hosted by the SIB in Lausanne 21 - 24 January 2025.

Course organizers: Ahmed Mahfouz (LUMC), Diana Marek (SIB), Patricia Palagi (SIB), Eija Korpelainen (CSC).

For more information, please check the latest edition information here.

Single Cell Analysis (2019 - 2024)

This week-long course will cover the practicalities of single-cell sample prep and analysis with a particular focus on single-cell RNA-seq libraries. This course is aimed at both wet-lab researchers interested in learning how to analyze their own single-cell data sets, as well as bioinformaticians who are new to single-cell sequencing analysis. Basic knowledge of the programming language R is a prerequisite for participation in the course.

The course features a mix of lectures and practicals, and you will have the opportunity to perform hands-on analysis of scRNA-seq data in R. Topics to be covered in the course include (but not limited to): an overview of different single cell platforms, experimental design, preprocessing of scRNA-seq data, normalization, dimensionality reduction, clustering, batch correction, differential expression, trajectory inference. The fifth day of the course will be a mini-symposium featuring guest lectures from scientists using various single-cell techniques in their research.

This course is offered by the Medical Genetics Centre South-West Netherlands (MGC) and the Netherlands Bioinformatics and Systems Biology (BioSB) research schools.

Course organizers: Susan Kloet (LUMC), Miao-Ping Chien (Erasmus MC) and Ahmed Mahfouz (LUMC).

For more information, please check the latest edition information here.

Bioinformatics for Nanobiology (2016 - 2024)

In this course, the student will learn how to use computer methods as tools for biological research. An overview of core application software, databases and online applications will be provided, as well as in-depth knowledge on key algorithms and procedures to process and analyze sequence data and quantitative measurements. The course offers both theoretical insight and practical experience, in computer practicals and projects to be performed.

This is a second year bachelor course for the Nanobiology program, a joint program between TU Delft and Erasmus MC.

Course Lecturers: Jasmijn Baaijens (TU Delft), Ahmed Mahfouz (LUMC/TU Delft), and Stan Brouns (TU Delft)