|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.|
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.
|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)
|31.1.||12. Hypothesis testing in microbiome analysis||Practice exam|
Friday, March 22nd, 10:15-12:00, C311, Sand 14