Dagmar Iber: Catalogue data in Autumn Semester 2024 |  |
| Name | Prof. Dr. Dagmar Iber |
| Field | Computational Biology |
| Address | Professur f. Computational Biology ETH Zürich, BSS G 11.1 Klingelbergstrasse 48 4056 Basel SWITZERLAND |
| Telephone | +41 61 387 32 10 |
| dagmar.iber@bsse.ethz.ch | |
| URL | http://www.bsse.ethz.ch/cobi |
| Department | Biosystems Science and Engineering |
| Relationship | Associate Professor |
| Number | Title | ECTS | Hours | Lecturers | ||||||||||||||||||||
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| 636-0117-00L | Mathematical Modelling for Bioengineering and Systems Biology  | 4 credits | 3G | D. Iber | ||||||||||||||||||||
| Abstract | Basic concepts and mathematical tools to explore biochemical reaction kinetics and biological network dynamics. | |||||||||||||||||||||||
| Learning objective | The course enables students to formulate, analyse, and simulate mathematical models of biochemical networks. To this end, the course covers basic mathematical concepts and tools to explore biochemical reaction dynamics as well as basic concepts from dynamical systems theory. The exercises serve to deepen the understanding of the presented concepts and the mathematical methods, and to train students to numerically solve and simulate mathematical models. | |||||||||||||||||||||||
| Content | Biochemical Reaction Modelling Basic Concepts from Linear Algebra & Differential Equations Mathematical Methods: Linear Stability Analysis, Phase Plane Analysis, Bifurcation Analysis Dynamical Systems: Switches, Oscillators, Adaptation Signal Propagation in Signalling Networks Parameter Estimation | |||||||||||||||||||||||
| Competencies |
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| 636-0704-00L | Computational Biology and Bioinformatics Seminar  Number of participants limited to 30. The seminar is addressed primarily at students enrolled in the MSc CBB programme. Students of other ETH study programmes interested in this course need to ask the lecturer for permission to enrol in the course. The Seminar will be offered in autumn semester in Basel (involving professors and lecturers from the University of Basel) and in spring semester in Zurich (involving professors and lecturers from the University of Zurich). Professors and lecturers from ETH Zurich are involved in both semesters. Uni Basel lecturers: Richard Neher, Attila Becskei, Mihaela Zavolan, Erik van Nimwegen | 2 credits | 2S | N. Beerenwinkel, D. Iber, T. Stadler | ||||||||||||||||||||
| 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. | |||||||||||||||||||||||
| Learning 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. | |||||||||||||||||||||||
| 636-0706-00L | Spatio-Temporal Modelling in Biology | 4 credits | 3G | D. Iber | ||||||||||||||||||||
| Abstract | This course focuses on modeling spatio-temporal problems in biology, in particular on the cell and tissue level. The main focus is on mechanisms and concepts, but mathematical and numerical techniques are introduced as required. Biological examples discussed in the course provide an introduction to key concepts in developmental biology. | |||||||||||||||||||||||
| Learning objective | Students will learn state-of-the-art approaches to modelling spatial effects in dynamical biological systems. The course provides an introduction to dynamical system, and covers the mathematical analysis of pattern formation in growing, developing systems, as well as the description of mechanical effects at the cell and tissue level. The course also provides an introduction to image-based modelling, i.e. the use of microscopy data for model development and testing. The course covers classic as well as current approaches and exposes students to open problems in the field. In this way, the course seeks to prepare students to conduct research in the field. The course prepares students for research in developmental biology, as well as for applications in tissue engineering, and for biomedical research. | |||||||||||||||||||||||
| Content | 1. Introduction to Modelling in Biology 2. Bioimage Analysis 3. Morphogen Gradients 4. Precision & Robustness of Patterning 5. Mathematical Description of Growing Biological Systems 6. Travelling Waves & Wave Pinning 7. Turing Patterns 8. Chemotaxis 9. Epithelial Organisation 10. Tissue Simulation Frameworks 11. Tissue Mechanics & Fluid Dynamics 12. Growth Control 13. Image-Based Modelling 14. Summary | |||||||||||||||||||||||
| Lecture notes | All lecture material will be made available online via Moodle. | |||||||||||||||||||||||
| Literature | The lecture course is not based on any textbook. The following textbooks are related to some of its content. The textbooks may be of interest for further reading, but are not necessary to follow the course: Murray, Mathematical Biology, Springer Forgacs and Newman, Biological Physics of the Developing Embryo, CUP Keener and Sneyd, Mathematical Physiology, Springer Fall et al, Computational Cell Biology, Springer Szallasi et al, System Modeling in Cellular Biology, MIT Press Wolkenhauer, Systems Biology Kreyszig, Engineering Mathematics, Wiley | |||||||||||||||||||||||
| Prerequisites / Notice | The course is self-contained. The course assumes no background in biology but a good foundation regarding mathematical and computational techniques. | |||||||||||||||||||||||