Tanja Stadler: Catalogue data in Autumn Semester 2018
|Name||Prof. Dr. Tanja Stadler|
ETH Zürich, D-BSSE, BSD H 326
|Telephone||+41 61 387 34 10|
|Department||Biosystems Science and Engineering|
|636-0017-00L||Computational Biology||6 credits||3G + 2A||T. Stadler, C. Magnus, T. Vaughan|
|Abstract||The 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.|
|Objective||Attendees will learn which information is contained in genetic sequencing data and how to extract information from this data 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:
* pathogen evolution
* macroevolution of species
|Content||The 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 for direct alignment analysis using approaches such as BLAST and GWAS. 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. Lastly, we introduce the field of phylodynamics, the aim of which is to understand and quantify 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 notes||Lecture slides will be available on moodle.|
|Literature||The 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 / Notice||Basic knowledge in linear algebra, analysis, and statistics will be helpful. Programming in R will be required for the project work (compulsory continuous performance assessments). We provide an R tutorial and help sessions during the first two weeks of class to learn the required skills. However, in case you do not have any previous experience with R, we strongly recommend to get familiar with R prior to the semester start. For the D-BSSE students, we highly recommend the voluntary course „Introduction to Programming“, which takes place at D-BSSE from Wednesday, September 12 to Friday, September 14, i.e. BEFORE the official semester starting date http://www.cbb.ethz.ch/news-events.html |
For the Zurich-based students without R experience, we recommend the R course http://www.vvz.ethz.ch/Vorlesungsverzeichnis/lerneinheit.view?semkez=2018W&ansicht=KATALOGDATEN&lerneinheitId=123546&lang=de, or working through the script provided as part of this R course.
|636-0301-00L||Current Topics in Biosystems Science and Engineering|
For doctoral students only.
Master's students cannot receive credits for the seminar.
|2 credits||1S||R. Platt, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, D. J. Müller, S. Panke, R. Paro, S. Reddy, T. Schroeder, T. Stadler, J. Stelling|
|Abstract||This seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology.|
|Objective||To provide an overview of current systems biology research.|
|Content||The final list of topics will be available at https://www.bsse.ethz.ch/news-and-events/seminar-series.html|
|636-0704-00L||Computational Biology and Bioinformatics Seminar|
The Seminar will be offered in autumn semester in Basel and in spring semester in Zürich.
|2 credits||2S||N. Beerenwinkel, M. Claassen, D. Iber, T. Stadler, J. Stelling|
|Abstract||Computational biology and bioinformatics aim at an understanding of living systems through computation. The seminar combines student presentations and current research project presentations to review the rapidly developing field from a computer science perspective. Areas: DNA sequence analysis, proteomics, optimization and bio-inspired computing, and systems modeling, simulation and analysis.|
|Objective||Studying and presenting fundamental papers of Computational Biology and Bioinformatics. Learning how to make a scientific presentation and how classical methods are used or further developed in current research.|
|Content||Computational biology and bioinformatics aim at advancing the understanding of living systems through computation. The complexity of these systems, however, provides challenges for software and algorithms, and often requires entirely novel approaches in computer science. The aim of the seminar is to give an overview of this rapidly developing field from a computer science perspective. In particular, it will focus on the areas of (i) DNA sequence analysis, sequence comparison and reconstruction of phylogenetic trees, (ii) protein identification from experimental data, (iii) optimization and bio-inspired computing, and (iv) systems analysis of complex biological networks. The seminar combines the discussion of selected research papers with a major impact in their domain by the students with the presentation of current active research projects / open challenges in computational biology and bioinformatics by the lecturers. Each week, the seminar will focus on a different topic related to ongoing research projects at ETHZ, University of Basel and University of Zurich, thus giving the students the opportunity of obtaining knowledge about the basic research approaches and problems as well as of gaining insight into (and getting excited about) the latest developments in the field.|
|Literature||Original papers to be presented by the students will be provided in the first week of the seminar.|