BIO4399 - Computational microbiome analysis
| Title | BIO-4399 - Vorlesung Advanced topics in bioinformatics - Computational microbiome analysis |
| Lecturers | Prof. Daniel Huson and Sina Beier |
| Venue | Thursdays, 8:15-10:00, Hörsaal 2, Sand 6/7 |
| Tutorials | Tuesdays, 12:15-14:00, C311, Sand 14 |
| Grading | Grades will be based on a written or oral exam. |
| Language | English |
| Links | Campus, Illias |
Prerequisites
Participants must have already taken "Grundlagen der Bioinformatik" or "Bioinformatics I", or an equivalent course.
Enrollment
Please use Ilias to enroll in this course and please use Ilias to submit assignments.
Tutorials
Weekly participation in the tutorials is mandatory.
Grading
Grades will be based on a written or oral exam.
To qualify for participation in the exam, you must attend all tutorials and must obtain at least 50% of all assignment points.
For each 10% of assignment points you obtain above 50%, your final grade will go up by 0.1.
Content
The aim of this course is to provide an overview of the main computational questions that arise in microbiome analysis and to discuss the algorithm details of the main approaches used to address them.
The lecture will focus on 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.
Script
A script is available here.
Schedule
(preliminary schedule, may change during course)
| Date | Topic | Assignment |
|---|---|---|
| 20.4. | 1. Introduction | Assignment 1 |
| 27.4. | 2. Community profiling using the 16S rRNA gene | Assignment 2 |
| 4.5.. | 3. Alpha- and beta-diversity, PCA analysis | Assignment 3 |
| 11.5. | continued | Assignment 4 |
| 18.5. | 4. Taxonomic analysis & functional analysis using homology | Assignment 5 |
| 1.6. | continued | Assignment 6 |
| 22.6. | 5. Other approaches to taxonomic analysis | Assignment 7 |
| 29.6... | 6. DNA extraction, library prep and sequencing (PD Dr. Silke Peter, UKT) | Assignment 8 |
| 6.7. | 7. Metagenomic assembly and binning | Assignment 9 |
| 13.7. | 8. Statistical analysis | Assignment 10 |
| 20.7. | 9. Long read analysis | |
| 27.7. | Oral exams according to schedule agreed upon in the lecture | |
Makeup exam:
Friday, September 22nd, 10:15-12:00, Hörsaal 2, Sand 6/7