Algorithmen der Bioinformatik

BIOINF4399 - Microbiome analysis

Title BIOINF4399 - Vorlesung Advanced topics in bioinformatics - Microbiome analysis
Lecturers Prof. Daniel Huson and Prof. Ruth Ley
Teaching assistant Caner Bagci
Time and place Thursdays, 8:15-10:00, A301, Sand 14
Tutorials Wednesdays, 8:15-10, A302 (first tutorial: Oct 31st)
Grading Grades will be based on a written or oral exam.
Language English
Links CampusIllias


Participants must have already taken "Grundlagen der Bioinformatik" , "Sequence Bioinformatics", "Bioinformatics I", or an equivalent course.


Please use Ilias to enroll in this course and please use Ilias to submit assignments.

Assignments and weekly tutorials

We will hand out weekly assignments for you to work on. Some of the assignment sheets will be part of a multi-part project. Your solutions will be graded and you will be asked to present them in the tutorials (Übungsgruppen). Participation in the tutorial is mandatory, if you miss two or more sessions, then you cannot take the exam. You may work on and hand in assignments in groups of two people.


Grades will be based on a written exam. To qualify for participation in the exam, you must attend all tutorials and must obtain at least 50% of all assignment points. If you achieve 70%, 80% or 90% of all points, then your

final grade will go up by 1/3, 2/3 or 1, respectively.


The aim of this course is to provide an overview of the main questions that arise in microbiome analysis and to 

discuss the algorithmic details of the main approaches used to address them.

The lecture will focus on microbiome challenges and the conceptual and algorithmic aspects of different approaches, whereas the tutorials will focus on the application of different methods to different types of questions and datasets.


A script (for parts of the course) will be made available on Ilias. 


This currently reflect last year's content. This year, the course will be taught together with Prof. Ruth Ley (Director of Microbiome Research at the Max-Planck Institute for Developmental Biology) and so the schedule will be revised. To plan to alternate between presenting microbiome research questions and studying the methods that are used to address them.


Date Topic Assignment
18.10 1. Introduction Assign. 1
25.10.- 2. Community profiling using the 16S rRNA gene Assign. 2
1.11.. Public holiday - no lecture  
8.11.- 3. Alpha- and beta-diversity, PCA analysis Assign. 3
15.11. 4. The reality of 16S community profiling (Prof. Ruth Ley) Assign. 4
22.11.- 5. Ordination using PCA and PCoA Assign. 5
29.11. 6. Practical 16S analysis using QIIME (Dr. Tony Walters) Assign. 6
(mini project 16S)
6.12. 7. Taxonomic analysis & functional analysis using homology  
13.12. 8. Stories from metagenomics (Prof. Ruth Ley) Assign. 7
20.12. 9. Other approaches to taxonomic analysis Assign. 8
(mini project metagenomics)
10.1. 10. Metagenomic assembly and binning  
17.1. 11. Long read analysis Assign. 9
(mini project long reads)
24.1.- continued  
31.1. 12. Hypothesis testing in microbiome analysis Practice exam
7.2.  Exam  

Makeup exam: 

Friday, March 22nd, 10:15-12:00, C311, Sand 14