Search result: Catalogue data in Autumn Semester 2016
Biology Master | ||||||
Elective Major Subject Areas | ||||||
Elective Major: Systems Biology | ||||||
Elective Compulsory Concept Courses See D-BIOL Master Studies Guide | ||||||
Number | Title | Type | ECTS | Hours | Lecturers | |
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551-0319-00L | Cellular Biochemistry (Part I) | W | 3 credits | 2V | U. Kutay, R. I. Enchev, B. Kornmann, M. Peter, I. Zemp, further lecturers | |
Abstract | Concepts and molecular mechanisms underlying the biochemistry of the cell, providing advanced insights into structure, function and regulation of individual cell components. Particular emphasis will be put on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes such as intracellular transport, cell division & growth, and cell migration. | |||||
Objective | The full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterisation of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry. The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain the integration of different molecules and signaling pathways into complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, cell division and cell growth. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer. | |||||
Content | Structural and functional details of individual cell components, regulation of their interactions, and various aspects of the regulation and compartmentalisation of biochemical processes. Topics include: biophysical and electrical properties of membranes; viral membranes; structural and functional insights into intracellular transport and targeting; vesicular trafficking and phagocytosis; post-transcriptional regulation of gene expression. | |||||
Lecture notes | Scripts and additional material will be provided during the semester. Please contact Dr. Alicia Smith for assistance with the learning materials. (Link) | |||||
Literature | Recommended supplementary literature (review articles and selected primary literature) will be provided during the course. | |||||
Prerequisites / Notice | To attend this course the students must have a solid basic knowledge in chemistry, biochemistry and general biology. The course will be taught in English. | |||||
551-0309-00L | Concepts in Modern Genetics | W | 6 credits | 4V | Y. Barral, D. Bopp, A. Hajnal, M. Stoffel, O. Voinnet | |
Abstract | Concepts of modern genetics and genomics, including principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference. | |||||
Objective | This course focuses on the concepts of classical and modern genetics and genomics. | |||||
Content | The topics include principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference. | |||||
Lecture notes | Scripts and additional material will be provided during the semester. | |||||
Prerequisites / Notice | This course is a co-production of the University of Zurich and ETH Zurich, and will be taught in English. The course takes place on Monday afternoon at ETH Hoenggerberg, and on Tuesday morning at UZH Irchel. | |||||
551-0313-00L | Microbiology (Part I) | W | 3 credits | 2V | W.‑D. Hardt, L. Eberl, H.‑M. Fischer, J. Piel, M. Pilhofer | |
Abstract | Advanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||
Objective | This concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||
Content | Advanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||
Lecture notes | Updated handouts will be provided during the class. | |||||
Literature | Current literature references will be provided during the lectures. | |||||
Prerequisites / Notice | English The lecture "Grundlagen der Biologie II: Mikrobiologie" is the basis for this advanced lecture. | |||||
551-1295-00L | Introduction to Bioinformatics: Concepts and Applications | W | 6 credits | 4G | W. Gruissem, K. Bärenfaller, A. Caflisch, G. Capitani, J. Fütterer, M. Robinson, A. Wagner | |
Abstract | Storage, handling and analysis of large datasets have become essential in biological research. The course will introduce students to a number of applications of bioinformatics in biology. Freely accessible software tools and databases will be explained and explored in theory and praxis. | |||||
Objective | Introduction to Bioinformatics I: Concepts and Applications (formerly Bioinformatics I) will provide students with the theoretical background of approaches to store and retrieve information from large databases. Concepts will be developed how DNA sequence information can be used to understand phylogentic relationships, how RNA sequence relates to structure, and how protein sequence information can be used for genome annotation and to predict protein folding and structure. Students will be introduced to quantitative methods for measuring gene expression and how this information can be used to model gene networks. Methods will be discussed to construct protein interaction maps and how this information can be used to simulate dynamic molecular networks. In addition to the theoretical background, the students will develop hands-on experiences with the bioinformatics methods through guided exercises. The course provides students from different backgrounds with basic training in bioinformatics approaches that have impact on biological, chemical and physics experimentation. Bioinformatics approaches draw significant expertise from mathematics, statistics and computational science. Although "Intoduction to Bioinformatics I" will focus on theory and praxis of bioinformatics approaches, the course provides an important foundation for the course "Introduction to Bioinformatics II: Fundamentals of computer science, modeling and algorithms" that will be offered in the following semester. | |||||
Content | Bioinformatics I will cover the following topics: From genes to databases and information BLAST searches Prediction of gene function and regulation RNA structure prediction Gene expression analysis using microarrays Protein sequence and structure databases WWW for bioinformatics Protein sequence comparisons Proteomics and de novo protein sequencing Protein structure prediction Cellular and protein interaction networks Molecular dynamics simulation | |||||
Elective Compulsory Master Courses I: Computation | ||||||
Number | Title | Type | ECTS | Hours | Lecturers | |
636-0007-00L | Computational Systems Biology | W | 6 credits | 3V + 2U | J. Stelling | |
Abstract | Study 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). | |||||
Objective | The aim of this course is to provide an introductory overview of mathematical and computational methods for the modeling, simulation and analysis of biological networks. | |||||
Content | Biology 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 notes | Link | |||||
Literature | U. Alon, An introduction to systems biology. Chapman & Hall / CRC, 2006. Z. Szallasi et al. (eds.), System modeling in cellular biology. MIT Press, 2006. | |||||
636-0706-00L | Spatio-Temporal Modelling in Biology | W | 5 credits | 3G | D. Iber | |
Abstract | This course focuses on modeling spatio-temporal problems in biology, in particular on the cell and tissue level. A wide range of mathematical techniques will be presented as part of the course, including concepts from non-linear dynamics (ODE and PDE models), stochastic techniques (SDE, Master equations, Monte Carlo simulations), and thermodynamic descriptions. | |||||
Objective | The aim of the course is to introduce students to state-of-the-art mathematical modelling of spatio-temporal problems in biology. Students will learn how to chose from a wide range of modelling techniques and how to apply these to further our understanding of biological mechanisms. The course aims at equipping students with the tools and concepts to conduct successful research in this area; both classical as well as recent research work will be discussed. | |||||
Content | 1. Introduction to Modelling in Biology 2. Morphogen Gradients 3. Turing Pattern 4. Travelling Waves & Wave Pinning 5. Application Example 1: Dorso-ventral axis formation 6. Chemotaxis, Cell Adhesion & Migration 7. Introduction to Numerical Methods 8. Simulations on Growing Domains 9. Image-Based Modelling 10. Branching Processes 11. Cell-based Simulation Frameworks 12. Application Example 2: Limb Development 13. Summary | |||||
Lecture notes | All lecture material will be made available online Link | |||||
Literature | 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 builds on introductory courses in Computational Biology. The course assumes no background in biology but a good foundation regarding mathematical and computational techniques. | |||||
Elective Compulsory Master Courses II: Biology | ||||||
Number | Title | Type | ECTS | Hours | Lecturers | |
551-1103-00L | Microbial Biochemistry | W | 4 credits | 2V | J. Vorholt-Zambelli, J. Piel | |
Abstract | The lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms. Emphasis is on processes that are specific to bacteria and archaea and that contribute to the widespread occurrence of prokaryotes. Applied aspects of microbial biochemistry will be pointed out as well as research fields of current scientific interest. | |||||
Objective | The lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms. | |||||
Content | Important biochemical processes specific to bacteria and archaea will be presented that contribute to the widespread occurrence of prokaryotes. Applied aspects of microbial biochemistry will be pointed out as well as research fields of current scientific interest. Emphasis is on concepts of energy generation and assimilation. List of topics: Eating sugars and letting them in Challenging: Aromatics, xenobiotics, and oil Complex: (Ligno-)Cellulose and in demand for bioenergy Living on a diet and the anaplerotic provocation Of climate relevance: The microbial C1 cycle What are AMO and Anammox? 20 amino acids: the making of Extending the genetic code The 21st and 22nd amino acid Some exotic biochemistry: nucleotides, cofactors Ancient biochemistry? Iron-sulfur clusters, polymers Secondary metabolites: playground of evolution | |||||
Lecture notes | A script will be provided during the course. | |||||
551-1153-00L | Systems Biology of Metabolism Number of participants limited to 15. | W | 4 credits | 2V | U. Sauer, N. Zamboni, M. Zampieri | |
Abstract | Starting from contemporary biological problems related to metabolism, the course focuses on systems biological approaches to address them. In a problem-oriented, this-is-how-it-is-done manner, we thereby teach modern methods and concepts. | |||||
Objective | Develop a deeper understanding of how relevant biological problems can be solved, thereby providing advanced insights to key experimental and computational methods in systems biology. | |||||
Content | The course will be given as a mixture of lectures, studies of original research and guided discussions that focus on current research topics. For each particular problem studied, we will work out how the various methods work and what their capabilities/limits are. The problem areas range from microbial metabolism to cancer cell metabolism and from metabolic networks to regulation networks in populations and single cells. Key methods to be covered are various modeling approaches, metabolic flux analyses, metabolomics and other omics. | |||||
Lecture notes | Script and original publications will be supplied during the course. | |||||
Prerequisites / Notice | The course extends many of the generally introduced concepts and methods of the Concept Course in Systems Biology. It requires a good knowledge of biochemistry and basics of mathematics and chemistry. | |||||
636-0001-00L | Separations in Biotechnology and Bioprocess Economy | W | 6 credits | 3G | S. Panke | |
Abstract | Separations play an integral part of any biotechnological process. This course aims at enabling students specifically with a chemistry/biology background to select & roughly design suitable separation processes for typical biotechnological products such as monoclonal antibodies, antibiotics, and fine chemicals and at providing a basic set of purification operations & judge on process economy. | |||||
Objective | Students should be able to select for a given biotechnological product a suitable set of purification operations and judge on process economy. | |||||
Content | Introduction – membrane operations – adsorption and chromatography – crystallization – overall process economics – | |||||
Lecture notes | Handouts during course | |||||
636-0507-00L | Synthetic Biology II | W | 4 credits | 4A | S. Panke, Y. Benenson, J. Stelling | |
Abstract | 7 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). | |||||
Objective | The 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. | |||||
Content | Presentations 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 (Link). | |||||
Lecture notes | Handouts during course | |||||
Prerequisites / Notice | The 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. | |||||
551-0571-00L | From DNA to Diversity (University of Zurich) No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH. UZH Module Code: BIO336 Mind the enrolment deadlines at UZH: Link | W | 2 credits | 2V | A. Hajnal, D. Bopp, E. Hafen | |
Abstract | The evolution of the various body-plans is investigated by means of comparison of developmentally essential control genes of molecularly analysed model organisms. | |||||
Objective | By the end of this module, each student should be able to - recognize the universal principles underlying the development of different animal body plans. - explain how the genes encoding the molecular toolkit have evolved to create animal diversity. - relate changes in gene structure or function to evolutionary changes in animal development. Key skills: By the end of this module, each student should be able to - present and discuss a relevant evolutionary topic in an oral presentation - select and integrate key concepts in animal evolution from primary literature - participate in discussions on topics presented by others | |||||
636-0009-00L | Evolutionary Dynamics | W | 5 credits | 2V + 1U | N. Beerenwinkel | |
Abstract | Evolutionary 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. | |||||
Objective | The goal of this course is to understand and to appreciate mathematical models and computational methods that provide insight into the evolutionary process. | |||||
Content | Evolution 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 notes | No. | |||||
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 / Notice | Prerequisites: Basic mathematics (linear algebra, calculus, probability) |
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