From 2 November 2020, the autumn semester 2020 will take place online. Exceptions: Courses that can only be carried out with on-site presence.
Please note the information provided by the lecturers via e-mail.

Jörg Stelling: Catalogue data in Autumn Semester 2018

Name Prof. Dr. Jörg Stelling
FieldComputational Systems Biology
Address
Comput. Systems Biology, Stelling
ETH Zürich, D-BSSE, BSA N 800
Mattenstrasse 26
4058 Basel
SWITZERLAND
Telephone+41 61 387 31 94
E-mailjoerg.stelling@bsse.ethz.ch
DepartmentBiosystems Science and Engineering
RelationshipFull Professor

NumberTitleECTSHoursLecturers
636-0007-00LComputational Systems Biology Information 6 credits3V + 2UJ. Stelling
AbstractStudy of fundamental concepts, models and computational methods for the analysis of complex biological networks. Topics: Systems approaches in biology, biology and reaction network fundamentals, modeling and simulation approaches (topological, probabilistic, stoichiometric, qualitative, linear / nonlinear ODEs, stochastic), and systems analysis (complexity reduction, stability, identification).
ObjectiveThe aim of this course is to provide an introductory overview of mathematical and computational methods for the modeling, simulation and analysis of biological networks.
ContentBiology has witnessed an unprecedented increase in experimental data and, correspondingly, an increased need for computational methods to analyze this data. The explosion of sequenced genomes, and subsequently, of bioinformatics methods for the storage, analysis and comparison of genetic sequences provides a prominent example. Recently, however, an additional area of research, captured by the label "Systems Biology", focuses on how networks, which are more than the mere sum of their parts' properties, establish biological functions. This is essentially a task of reverse engineering. The aim of this course is to provide an introductory overview of corresponding computational methods for the modeling, simulation and analysis of biological networks. We will start with an introduction into the basic units, functions and design principles that are relevant for biology at the level of individual cells. Making extensive use of example systems, the course will then focus on methods and algorithms that allow for the investigation of biological networks with increasing detail. These include (i) graph theoretical approaches for revealing large-scale network organization, (ii) probabilistic (Bayesian) network representations, (iii) structural network analysis based on reaction stoichiometries, (iv) qualitative methods for dynamic modeling and simulation (Boolean and piece-wise linear approaches), (v) mechanistic modeling using ordinary differential equations (ODEs) and finally (vi) stochastic simulation methods.
Lecture noteshttp://www.csb.ethz.ch/education/lectures.html
LiteratureU. Alon, An introduction to systems biology. Chapman & Hall / CRC, 2006.

Z. Szallasi et al. (eds.), System modeling in cellular biology. MIT Press, 2010.

B. Ingalls, Mathematical modeling in systems biology: an introduction. MIT Press, 2013
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. Panke, R. Paro, S. Reddy, T. Schroeder, T. Stadler, 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 https://www.bsse.ethz.ch/news-and-events/seminar-series.html
636-0507-00LSynthetic Biology II Restricted registration - show details
Students in the MSc Programme Biotechnology (Programme Regulation 2017) may select Synthetic Biology II instead of the Research Project 1.
8 credits4AS. Panke, Y. Benenson, J. Stelling
Abstract7 months biological design project, during which the students are required to give presentations on advanced topics in synthetic biology (specifically genetic circuit design) and then select their own biological system to design. The system is subsequently modeled, analyzed, and experimentally implemented. Results are presented at an international student competition at the MIT (Cambridge).
ObjectiveThe students are supposed to acquire a deep understanding of the process of biological design including model representation of a biological system, its thorough analysis, and the subsequent experimental implementation of the system and the related problems.
ContentPresentations on advanced synthetic biology topics (eg genetic circuit design, adaptation of systems dynamics, analytical concepts, large scale de novo DNA synthesis), project selection, modeling of selected biological system, design space exploration, sensitivity analysis, conversion into DNA sequence, (DNA synthesis external,) implementation and analysis of design, summary of results in form of scientific presentation and poster, presentation of results at the iGEM international student competition (www.igem.org).
Lecture notesHandouts during course
Prerequisites / NoticeThe final presentation of the project is typically at the MIT (Cambridge, US). Other competing schools include regularly Imperial College, Cambridge University, Harvard University, UC Berkeley, Princeton Universtiy, CalTech, etc.

This project takes place between end of Spring Semester and beginning of Autumn Semester. Registration in April.

Please note that the number of ECTS credits and the actual work load are disconnected.
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.
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.