Available Master's theses in the group
If you are interested in doing a master's thesis in our group, e.g. at the interface of machine learning and population genetics or microbial population dynamics, please contact me.
Currently, the following topics are available:
- Simulation of genotypes and prediction of phenotypes using machine learning in plant breeding programs (bioinfo)
(in collaboration with computomics)
- Visualization of ancestral CRISPR spacer array reconstructions (bioinfo)
- Improving most likelihood tree reconstruction based on CRISPR arrays
- Modeling CRISPR population dynamics (math)
- The ancestors of a microbial genome sequence (math)
- CNNs for lottery outcome prediction (really!)
- ... your own idea?
- ancestral gene presence/absence reconstruction (bioinfo -- no longer available)
- Simulating the mutation rate in fluctuating environments (comp bio or bioinfo) (in progress)
- Inferring and visualizing parental ancestry proportions (bioinfo) (in progress)
- Detecting oversampled strains in pathogen databases (bioinfo) (reserved)
Seminar Statistical Population Genetics SS 2023
FIRST MEETING at Seminarraum C215 at Sand at 19.04.23, 09:30-10:15
further meetings will be scheduled together at the first meeting.
I am providing a seminar "Statistical Population Genetics" where we will consider data-driven methods in population genetics that are based on statistical methods and stochastic processes relevant to a wide range of questions. Bioinformaticians, mathematicians, and methodologically interested biologists are invited to participate in the seminar. Topics will be assigned according to your background.
We will cover methods for the analysis of genomes in populations, including demographic inference, analysis of population structure, and detection of selection, using both model-based inference and simulation techniques.
Students get to know about advanced topics in population genetics theory and bioinformatics applications. They can reflect current research questions and investigate complex research topics. Students will be able to acquire knowledge about current findings through comprehensive literature search. They will know the importance of current topics in the area of bioinformatics and will be aware that there are still many open questions. Students will not only have improved their study, reading, and writing skills but will also have enhanced their capability of working independently. The teaching method in this seminar aims to boost the students’ confidence (oral presentation), enhance their communication skills, and enable them to accept criticism (discussion session and review of the written report following their presentation).
Preparation for a possible Master Thesis Project
If you are interested in one of the interesting and timely master thesis projects currently available in the group we can adjust your topic in this seminar to serve as an ideal preparation for the master thesis project. Please let me know in advance if you are interested in joining our group for your Master's thesis.
Yun S. Song, "Lecture Notes on Computational and Mathematical Population Genetics", github/popgenmethods/lecture_notes
Ewens and Grant, "Statistical Methods in Bioinformatics", Springer
Julien Y. Dutheil, "Statistical Population Genomics", Springer
You’ll be contacted later with more details. The course is limited to 12 people on a first come first serve basis.
Organization and Evaluation
Credits: 3 ECTS
Language: German or English
Dates & Room: The first meeting, including the distribution of topics among the participants, will be either at Wednesday, April 19th or Thursday, April 20th at a date where ideally all participants can attend.
We are aiming at in-person sessions but virtual, and hybrid sessions are possible if you prefer that e.g. due to childcare etc.
Evaluation: Presentation (55min + 5min Q&A), review of two other student papers (roughly 1 page each), written seminar paper (7-10 pages)
Only the final seminar paper (60%) and the presentation (40%) are graded.
The reviews and the first version of the paper have to be handed in on time to pass the course.
Tentative Course Plan
Dates & Room: The regular meeting dates will be chosen at the first meeting.
Week 1: Initial Meeting
Week 2 ff: Start of Individual Working Phase
Week 2: Introduction to Academic Writing and Presenting
Week 3 ff: joint reading sessions and individual Q&A sessions
19.06.23 Deadline First Hand-in Seminar paper
second half of the semester:
Presentations and Discussions including two exercises for non-presenters
31.08.23 Deadline Revised Seminar Paper