Seminar Stochastic Processes in Biological Systems WS 2021/2022
I am providing a seminar "Stochastic Processes in Biological Systems" where we will consider stochastic methods and processes in evolutionary bioinformatics.
Bioinformaticians, mathematicians, and methodologically interested biologists are invited to participate in the seminar. Topics will be assigned according to your background.
At the end of the seminar, you will know about stochastic processes, including the Poisson process, Markov chains, and branching processes with multiple types, as well as hidden Markov models. We will also explore the role of these processes in applications. This includes models of nucleotide substitution, Gene Finding methods, phylogenetic tree estimation, and models of gene amplification. In addition, the genealogies of branching processes and their applications will be considered.
Kimmel and Axelrod, "Branching Processes in Biology", Springer
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.
Organisation 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 Thursday, October 28th or Friday, October 29th at a date where ideally all participants can attend.
Virtual, in-person, and hybrid sessions are possible.
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 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 2: Initial Meeting
Week 3 ff: Start of Individual Working Phase
Week 3: Introduction to Academic Writing and Presenting
Week 4 ff: joint reading sessions and individual Q&A sessions
20.12.21 Deadline First Hand-in Seminar paper
second half of the semester:
Presentations and Discussions including two exercises for non-presenters
20.03.22 Deadline Revised Seminar Paper
Possible master thesis in the group
Feel free to contact me if you are interested in doing a master thesis in mathematics or bioinformatics in our group, e.g. at the interface of machine learning and population genetics or microbial population dynamics.
Currently, the following topics are available:
- Simulating the mutation rate in fluctuating environments (comp bio or bioinfo)
- Modeling CRISPR population dynamics (math)
- The ancestors of a microbial genome sequence (math)
- ancestral gene presence/absence reconstruction (bioinfo -- no longer available)
- Inferring and visualizing parental ancestry proportions (bioinfo)
- Detecting oversampled strains in pathogen databases (bioinfo)
- CNNs for lottery outcome prediction (really!)
- ... your own idea?