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Advanced Immunology course

Enrollment is Closed

About This Course

We will give a short introduction into the IonTorrent bioinformatics workflow, what to consider when designing an experiment. You will learn about important file formats, get a short introduction to R and RStudio, learn how to deal with data in R, and run the differential expression pipeline from SARTools.

Depending on time and interest we can explore how to compare different gene sets using Venn diagrams, go into detail about more complex experimental designs, or perform basic gene set enrichment analyses (GSEA).


There are no special requirements

Course Staff

Course Staff Image #1

Bernd Jagla


Bernd Jagla received his PhD in bioinformatics (department of Biology, Chemistry, and Pharmacy) from the Free University in Berlin, Germany in 1999. Before joining the Institut Pasteur, he worked for almost ten years in New York City, including as an associate research scientist in the Joint Centers for System Biology (Columbia University) and at the Columbia University Screening Center led by Dr J.E. Rothman. He joined the Institut Pasteur in 2009 to take charge of the bioinformatic needs at the Transcriptome et Epigenome platform, focusing on Next Generation Sequencing. As of 2016 he is member of the C3BI – HUB Team detached to the Human immunology center (CIH) and provides support for cytometry, next generation sequencing, and microarray data analysis. His areas of interest include the quality assurance and data analysis and visualization at the facility. He also has strong expertise in developing algorithms for function prediction from sequence data, image analysis, analysis of mass spectrometry data, workflow management systems.

Frequently Asked Questions

Do I need to follow the EdX and take the final examen?

No, you don't have to follow the EdX, but there is a quiz/final examen that you should take. This will be part of your final evaluation for the whole course. If you don't want to follow the course, please contact the instructor.

Where can I take notes?

Good question. Why not use the discussion forum. There should be a discussion section at the end of each column/section. After the course you will get a print-out. We decided to give out the printout after the course because otherwise we want to promote the EdX course.