Courses

Course Academic Credits: 2 ECTS
Content: This course will cover the topics of the diversity of animal genomes, the mechanisms of their evolution, and methodology of analysis (phologenetic inference, phylogenomics, genome architecture evolution).
Time, Place and registration: u:find Univ. of Vienna
Course number: 300179 (Winter term)

Course Academic Credits: 3 ECTS
Content: Practical course on admixture genomics. We will use public data from modern and ancient genomes, filter and analyze this data using common tools, and find admixed fragments. This will involve the command line interface, bash scripting, visualization in R, application of command line tools. The goal will be an understanding of work flows to detect admixture in genomic data.
Time, Place and registration: u:find Univ. of Vienna
Course number: 300072

Course Academic Credits: 3

English or German, WS 2022/2023, weekly, Fr 8:00-9:30

Grading: only homework with some theoretical and some practical examples (R-programming) of varying difficulties, which are reflected in the obtainable points

Contents: Introduction to Bayesian statistics with biological examples. In detail: 1) introduction to Bayesian statistics with examples from genetics. 2) standard distributions and their conjugate prior distributions, also with examples from biology: binomial with beta prior, Poisson with gamma prior, exponential with gamma prior, normal with normal-inverse-chisquared prior; improper priors. 3) empirical Bayes method. 4) Bayesian networks, where the conditional dependencies can be described by a directed acyclic graph (DAG); hidden Markov model (as an example for a DAG) with the forward-backward algorithm (a dynamical programming method) to calculate probabilities numerically. 5) more complicated models, where dynamic programming is impossible (with many biological examples); numerical methods: Bayes and Markov chain Monte Carlo method (Metropolis, Metropolis-Hastings, Gibbs sampling) and expectation-maximization (EM) algorithms.

Literature:
- Durbin, R., Eddy, S., Krogh, A., and Mitchison, G. (1998). Biological sequence analysis. Cambridge University Press, Cambridge.
- Gelman, A., Carlin, J., Stern, H., and Rubin, D. (1995). Bayesian Data Analysis. Chapman & Hall.

Registration and details: https://ufind.univie.ac.at/en/course.html?lv=040775&semester=2022W

Course Academic Credits: 3 ECTS
Content: The course aims at giving a broad overview covering topics like historical background; theoretical basics and definitions; different approaches like maximum parsimony, distance methods, maximum likelihood and Bayesian and associated algorithms; tree search and tree rearrangements; models of sequence evolution and model selection; summarizing trees and branch support; tree topology testing; tracing phylogenetic signal and noise; phylogenomics, supertrees and partition models. The last two units will be hands-on exercises.

Time, Place and registration: https://ufind.univie.ac.at/en/course.html?lv=053522&semester=2022W

for registration after deadline send an email to heiko.schmidt@univie.ac.at

Course Academic Credits: 3 ECTS
Content: Introduction to concepts of computational methods in genomics. Basics of genomic data analysis, data types, databases, and modeling approaches. Fundamentals of population genomics, functional genomics. Insights into human evolutionary history from ancient and present-day genomic data.
Time, Place and registration: u:find Univ. of Vienna
Course number: 300075

Course Academic Credits: 3 ECTS
Content: This seminar will discuss recent papers published in the field of speciation genomics and related emerging topics largely circumscribed to evolutionary genomics. We will target recently published articles, independent of the study system or method addressed, according to the interest of students. The students and lecturers will take turns presenting one paper per meeting, which will be further discussed in detail together with the group. The topics may include comparative genomics, approaches to variation and adaptation, population genomics, ecological genomics (including speciation and hybridization) and population epigenomics.
Time and place: Weekly on Thursdays 14:00-15:30, ÜR3, Fakultätszentrum für Biodiversität, Rennweg 1.OG. Contact the lecturers for access.
Details and registration: https://ufind.univie.ac.at/en/course.html?lv=300164&semester=2022W

Course Academic Credits: 5 ECTS
Content: This seminar is a mandatory part of the Master Evolutionary Systems Biology (module MES2), but also open to other related Master programs. The language of the seminar is English. The students will get one or a few papers from the recent research in Molecular Evolution and Evolutionary Developmental Biology (EvoDevo). They are demanded to expand the literature research on this topic, present the topic in an oral seminar and write an 3-5 page essay summarizing the findings and the current status.

The first meeting will take place on October 6, 2022 at 13:15-14:45 at SR1.2 of the UBB. In this meeting we will distribute the topics to the students and agree on blocked seminar dates in the last month of the semester.

Time, Place and registration: https://ufind.univie.ac.at/en/course.html?lv=300186&semester=2022W

Course Academic Credits: 3 ECTS
Content: In the first part of the lecture the theoretical foundations, scientific questions, and research domains of EvoDevo will be presented, and the general relation between genetic and phenotypic evolution will be discussed. Iin the second part specific examples of recent experimental approaches to fundamental questions in EvoDevo will be presented: conservation and diversification of molecular systems and developmental processes in axis evolution, evolution of new limb and appendage structures, changes in cis-regulation and protein-coding parts, etc.
Time, Place and registration: https://ufind.univie.ac.at/en/course.html?lv=300685&semester=2022W

Course Academic Credits: 2 ECTS
Time and Place: every Tuesday, 17:00-18:00 Vetmeduni Vienna hybrid seminar
Content: Seminar series with invited international and national speakers covering current advances in population genetics, genome research,bioinformatics and evolutionary biology.
Program: Vienna Graduate School of Population Genetics
Details and registration: here
Course number: 094013 (Summer & Winter term)

Course Academic Credits: 1 ECTS
Content: The lectures will take place on Tuesdays from 13:15 -14:45 in HS1. The precise dates and speakers will be announced on posters and sent out by email during the first week of the semester.

Time, Place and registration: https://ufind.univie.ac.at/en/course.html?lv=300114&semester=2022W

Course Academic Credits: 3 ECTS
Content: Students learn essential concepts in evolutionary and population genomics from next-generation sequencing data including genome assembly, detecting Single Nucleotide Polymorphisms (SNPs) and Copy Number Variants (CNV´s), genomic investigation procedures to trace natural selection during adaptation and speciation, Genome Wide Association Scanning (GWAS) in wild species, genomic and geographic clines and the impact of hybridization and gene flow on genomes, structural and functional aspects of genomes, and gene-environment interactions.
Time and place: Course takes place Mondays between Oct 3th and Nov 28th 17:30-19:30
Details and registration: https://ufind.univie.ac.at/en/course.html?lv=300127&semester=2022W

Course Academic Credits: 4 ECTS
Content: In this seminar (called the “Journal Club”), recent papers in theoretical population genetics are discussed. Knowledge of the basic population genetics theory is required. The papers to be discussed are distributed in advance by email. Participants are expected to have read the paper because the seminar focuses on discussions. Current and prospective PhD students are advised to attend this seminar.

Time and Place: tba
Details and registration: https://ufind.univie.ac.at/en/course.html?lv=250097&semester=2022W

Course Academic Credits: 2 ECTS
Time and Place: every Friday, 16:00-17:00, Institut für Populationsgenetik (building HA, 4th floor), Vetmeduni Vienna.
Content: Supervised introduction and discussion of recent publications, selected by the students themselves. In this format the students learn and discuss the latest research developments and practice their presentation and discussion skills.
Details and registration: here
Course number: 094013 (Summer & Winter term)

Time and place: Sept. 02 - Oct 03, 2024 Vetmeduni Vienna
An intense Population Genetics Introductory Course for PhD students will be organised by the Vienna Graduate School of Population Genetics.
Schedule and details are available here

Course Academic Credits: 2 ECTS
Time and Place: every Wednesday, 16:00-17:00, Institut für Populationsgenetik (building HA, 4th floor), Vetmeduni Vienna. Currently run as Webinar
Content: Students defend their research plan as well as the obtained results. Students actively discuss research plans and results covering the following research disciplines: population genetics, genome research, bioinformatics, evolutionary biology.
Details and registration: here
Course number: 094013 (Summer & Winter term)