Niko Beerenwinkel: Catalogue data in Autumn Semester 2019

Award: The Golden Owl
Name Prof. Dr. Niko Beerenwinkel
FieldComputational Biology
Address
Professur f. Computational Biology
ETH Zürich, BSS G 57.2
Klingelbergstrasse 48
4056 Basel
SWITZERLAND
Telephone+41 61 387 31 69
E-mailniko.beerenwinkel@bsse.ethz.ch
URLhttp://www.bsse.ethz.ch/cbg/people/nikob
DepartmentBiosystems Science and Engineering
RelationshipFull Professor

NumberTitleECTSHoursLecturers
636-0009-00LEvolutionary Dynamics6 credits2V + 1U + 2AN. Beerenwinkel
AbstractEvolutionary dynamics is concerned with the mathematical principles according to which life has evolved. This course offers an introduction to mathematical modeling of evolution, including deterministic and stochastic models.
Learning objectiveThe goal of this course is to understand and to appreciate mathematical models and computational methods that provide insight into the evolutionary process.
ContentEvolution is the one theory that encompasses all of biology. It provides a single, unifying concept to understand the living systems that we observe today. We will introduce several types of mathematical models of evolution to describe gene frequency changes over time in the context of different biological systems, focusing on asexual populations. Viruses and cancer cells provide the most prominent examples of such systems and they are at the same time of great biomedical interest. The course will cover some classical mathematical population genetics and population dynamics, and also introduce several new approaches. This is reflected in a diverse set of mathematical concepts which make their appearance throughout the course, all of which are introduced from scratch. Topics covered include the quasispecies equation, evolution of HIV, evolutionary game theory, birth-death processes, evolutionary stability, evolutionary graph theory, somatic evolution of cancer, stochastic tunneling, cell differentiation, hematopoietic tumor stem cells, genetic progression of cancer and the speed of adaptation, diffusion theory, fitness landscapes, neutral networks, branching processes, evolutionary escape, and epistasis.
Lecture notesNo.
Literature- Evolutionary Dynamics. Martin A. Nowak. The Belknap Press of Harvard University Press, 2006.
- Evolutionary Theory: Mathematical and Conceptual Foundations. Sean H. Rice. Sinauer Associates, Inc., 2004.
Prerequisites / NoticePrerequisites: Basic mathematics (linear algebra, calculus, probability)
636-0301-00LCurrent Topics in Biosystems Science and Engineering
For doctoral students only.
Master's students cannot receive credits for the seminar.
2 credits1SR. Platt, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, D. J. Müller, S. Reddy, T. Schroeder, T. Stadler, J. Stelling, B. Treutlein
AbstractThis seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology.
Learning objectiveTo provide an overview of current systems biology research.
ContentThe final list of topics will be available at https://www.bsse.ethz.ch/news-and-events/seminar-series.html
636-0704-00LComputational Biology and Bioinformatics Seminar
The Seminar will be offered in autumn semester in Basel and in spring semester in Zürich.
2 credits2SN. Beerenwinkel, M. Claassen, D. Iber, T. Stadler, J. Stelling
AbstractComputational 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.
Learning objectiveStudying 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.
ContentComputational 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.
LiteratureOriginal papers to be presented by the students will be provided in the first week of the seminar.