Sysmedicine PhD Course 2020


Systems Biology of Human Metabolism and Gut Microbiome (3 ECTS)

View the Project on GitHub sysmedicine/phd2020

Systems Biology of Human Metabolism and Gut Microbiome

Welcome to the course! This webpage will be the main website for all informations and materials throughout the course. If you have any questions/requests, contact muhammad.arif [at]

Course Syllabus

If you need more information about the aim and expected outcome, also the syllabus in general, please refer to the course sylabus website.

Course Location

Air Room @ Science For Life Laboratory (SciLifeLab)

Closest Bus Stop: Karolinska Institutet Biomedicum

Google Maps: Tomtebodavägen 23a, 171 65 Solna

Pre-course Preparation

In order to ensure the smoothness of the workshop, please follow the instruction in this Workshop Preparation page. Please do this as soon as humanly possible and contact us if you find any problem during the preparation

On top of that, please do the preparation for GEM in MATLAB

OBS: This step might take a while to be completed, so please do it BEFORE the course.

Course Schedule

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Course Material

Topic Teacher Slide Workshop
Introduction to Systems Biology Adil Mardinoglu Part 1 Part 2 N/A
Proteomics Fredrik Edfors Link Link
Transcriptomics Muhammad Arif Link Link
Metabolomics Abdellah Tebani Link Link
Metagenomics Ozlem Altay Link Link
Genome Scale Metabolic Modelling Cheng Zhang Link Link
Transcript-centic and REOs analysis Xiangyu Li Link N/A
Multi-Omics Integration Rui Benfeitas Link HTML notebook

Mini Seminar

Topic Keynote Speaker Slide
Topic 1 Lukas Käll Link
Topic 2 Mathias Uhlén Link

Student Presentations

In this course, we will have students presentations. All group has 15 minutes to present one state-of-the-art paper from Systems Biology field, followed by 15 minutes Q&A. You will be given the group distribution by first day of the course and also you will have 90 minutes on Thursday to finish the presentation

Topic Link to paper
Group 1 Link
Group 2 Link
Group 3 Link
Group 4 Link
Group 5 Link