The spring semester 2021 will take place online until further notice. Exceptions: Courses that can only be carried out with on-site presence. Please note the information provided by the lecturers.

Tanja Stadler: Catalogue data in Autumn Semester 2016

Name Prof. Dr. Tanja Stadler
FieldComputational Evolution
Address
Computational Evolution
ETH Zürich, D-BSSE, BSD H 326
Mattenstrasse 26
4058 Basel
SWITZERLAND
Award: The Golden Owl
Telephone+41 61 387 34 10
E-mailtanja.stadler@bsse.ethz.ch
URLhttp://www.bsse.ethz.ch/cevo
DepartmentBiosystems Science and Engineering
RelationshipAssociate Professor

NumberTitleECTSHoursLecturers
636-0017-00LComputational Biology Information 4 credits3GT. Stadler, C. Magnus
AbstractThe aim of the course is to provide up-to-date knowledge on how we can study biological processes using genetic sequencing data. Computational algorithms extracting biological information from genetic sequence data are discussed, and statistical tools to understand this information in detail are introduced.
ObjectiveAttendees will learn which information is contained in genetic sequencing data and how to extract information from them using computational tools. The main concepts introduced are:
* stochastic models in molecular evolution
* phylogenetic & phylodynamic inference
* maximum likelihood and Bayesian statistics
Attendees will apply these concepts to a number of applications yielding biological insight into:
* epidemiology
* pathogen evolution
* macroevolution of species
ContentThe course consists of four parts. We first introduce modern genetic sequencing technology, and algorithms to obtain sequence alignments from the output of the sequencers. We then present methods to directly analyze this alignment (such as BLAST algorithm, GWAS approaches). Second, we introduce mechanisms and concepts of molecular evolution, i.e. we discuss how genetic sequences change over time. Third, we employ evolutionary concepts to infer ancestral relationships between organisms based on their genetic sequences, i.e. we discuss methods to infer genealogies and phylogenies. We finally introduce the field of phylodynamics. The aim of that field is to understand and quantify the population dynamic processes (such as transmission in epidemiology or speciation & extinction in macroevolution) based on a phylogeny. Throughout the class, the models and methods are illustrated on different datasets giving insight into the epidemiology and evolution of a range of infectious diseases (e.g. HIV, HCV, influenza, Ebola). Applications of the methods to the field of macroevolution provide insight into the evolution and ecology of different species clades. Students will be trained in the algorithms and their application both on paper and in silico as part of the exercises.
Lecture notesSlides of the lecture will be available online.
https://www.bsse.ethz.ch/cevo/education/cb-materials.html
LiteratureThe course is not based on any of the textbooks below, but they are excellent choices as accompanying material:
* Yang, Z. 2006. Computational Molecular Evolution.
* Felsenstein, J. 2004. Inferring Phylogenies.
* Semple, C. & Steel, M. 2003. Phylogenetics.
* Drummond, A. & Bouckaert, R. 2015. Bayesian evolutionary analysis with BEAST
Prerequisites / NoticeBasic knowledge in linear algebra, analysis, and statistics will be helpful. Some programming experience will be useful for the exercises, but is not required. Programming skills will not be tested in the examination.
636-0301-00LCurrent Topics in Biosystems Science and Engineering2 credits1ST. Stadler, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, D. J. Müller, S. Panke, P. Pantazis, R. Paro, R. Platt, S. Reddy, T. Schroeder, J. Stelling
AbstractThis seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology.
ObjectiveTo provide an overview of current systems biology research.
ContentThe final list of topics will be available at http://www.bsse.ethz.ch/education/.