Search result: Catalogue data in Spring Semester 2021
Biology Master | ||||||
Elective Major Subject Areas | ||||||
Elective Major: Systems Biology | ||||||
Elective Compulsory Master Courses II: Biology | ||||||
Number | Title | Type | ECTS | Hours | Lecturers | |
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551-1310-00L | A Problem-Based Approach to Cellular Biochemistry Number of participants limited to 12. | W | 6 credits | 2G | M. Peter, V. Korkhov, G. Neurohr, V. Panse, A. E. Smith, F. van Drogen | |
Abstract | Independent, guided acquisition of a defined area of research, identification of key open questions, development of an experimental strategy to address a defined question, and formulation of this strategy within the framework of a research grant. | |||||
Objective | Working independently, students will acquire an overview of a defined research area, and identify important open questions. In addition, they will develop an experimental strategy to address a defined question, and to formulate this strategy within the framework of a research grant. | |||||
Content | The students will work in groups of two to three, in close contact with a tutor (ETH Prof or senior scientist). A research overview with open questions and a research grant will be developed independently by the students, with guidance from the tutor through regular mandatory meetings. The students will write both the research overview with open questions and the grant in short reports, and present them to their colleagues. | |||||
Literature | The identification of appropriate literature is a component of the course. | |||||
Prerequisites / Notice | This course will be taught in English, and requires extensive independent work. | |||||
551-0364-00L | Functional Genomics Information for UZH students: Enrolment to this course unit only possible at ETH. No enrolment to module BIO 254 at UZH. Please mind the ETH enrolment deadlines for UZH students: Link | W | 3 credits | 2V | C. von Mering, C. Beyer, B. Bodenmiller, M. Gstaiger, H. Rehrauer, R. Schlapbach, K. Shimizu, N. Zamboni, further lecturers | |
Abstract | Functional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. | |||||
Objective | Functional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. Such data provide the basis for systems biology efforts to elucidate the structure, dynamics and regulation of cellular networks. | |||||
Content | The curriculum of the Functional Genomics course emphasizes an in depth understanding of new technology platforms for modern genomics and advanced genetics, including the application of functional genomics approaches such as advanced sequencing, proteomics, metabolomics, clustering and classification. Students will learn quality controls and standards (benchmarking) that apply to the generation of quantitative data and will be able to analyze and interpret these data. The training obtained in the Functional Genomics course will be immediately applicable to experimental research and design of systems biology projects. | |||||
Prerequisites / Notice | The Functional Genomics course will be taught in English. | |||||
551-0224-00L | Advanced Proteomics For master students from the 2nd semester on, also doctoral candidates and post docs. | W | 4 credits | 6G | P. Picotti, L. Gillet, A. Leitner, P. Pedrioli | |
Abstract | Goal of the course is to analyze current and newly emerging technologies and approaches in protein and proteome analysis with regard to their application in biology, biotechnology and medicine. Format: Introduction by instructor followed by discussions stimulated by reading assignments and exercises. | |||||
Objective | To discuss current and newly emerging technologies and approaches in protein and proteome analysis with regard to their applications in biology, biotechnology, medicine and systems biology. | |||||
Content | Block course teaching current methods for the acquisition and processing of proteomic datasets. | |||||
Prerequisites / Notice | Number of people: Not exceeding 30. Students from ETHZ, Uni Zurich and University of Basel Non-ETH students must register at ETH Zurich as special students Link | |||||
701-1418-00L | Modelling Course in Population and Evolutionary Biology Number of participants limited to 20. Priority is given to MSc Biology and Environmental Sciences students. | W | 4 credits | 6P | S. Bonhoeffer, V. Müller | |
Abstract | This course provides a "hands-on" introduction into mathematical/computational modelling of biological processes with particular emphasis on evolutionary and population-biological questions. The models are developed using the Open Source software R. | |||||
Objective | The aim of this course is to provide a practical introduction into the modelling of fundamental biological questions. The participants will receive guidance to develop mathematical/computational models in small teams. The participants chose two modules with different levels of difficulty from a list of projects. The participant shall get a sense of the utility of modelling as a tool to investigate biological problems. The simpler modules are based mostly on examples from the earlier lecture "Ecology and evolution: populations" (script accessible at the course webpage). The advanced modules address topical research questions. Although being based on evolutionary and population biological methods and concepts, these modules also address topics from other areas of biology. | |||||
Content | see Link | |||||
Lecture notes | Detailed handouts describing both the modelling and the biological background are available to each module at the course website. In addition, the script of the earlier lecture "Ecology and evolution: populations" can also be downloaded, and contains further background information. | |||||
Prerequisites / Notice | The course is based on the open source software R. Experience with R is useful but not required for the course. Similarly, the course 701-1708-00L Infectious Disease Dynamics is useful but not required. | |||||
551-1126-00L | Technologies in Molecular Microbiology | W | 4 credits | 2V | B. Nguyen, W.‑D. Hardt, further lecturers | |
Abstract | The lecture course provides an advanced understanding of modern techniques used in molecular microbiology. Current technologies and research directions in molecular microbiology including applied aspects will be illustrated with paper discussions. The format is a lecture course enriched by group activities. | |||||
Objective | The lecture course aims at providing principles of modern techniques used in molecular microbiology. Emphasis is on genetic, biochemical, cellular, and community analysis . Discussion of a set of commonly applied technologies will assist students in evaluating current research in molecular microbiology and choosing appropriate methods for their own demands. | |||||
Content | Important genetic, biochemical, biophysical, and community analysis methods will be presented that are used to gain a deeper understanding of the molecular principles and mechanisms underlying basic physiological processes in prokaryotes. Applied aspects of molecular microbiology and current research in this area will also be covered. List of topics: - Analysis of genes, genomes and transcriptomes - Analysis of proteins, proteomes and microbial systems | |||||
Lecture notes | Updated handouts will be provided during the class. | |||||
Literature | Current literature references, relevant papers and handouts will be provided during the lectures. | |||||
Prerequisites / Notice | The following lecturers will contribute to the course: Dr. Alex Brachmann (ETH) Prof. Hans-Martin Fischer (ETH) Dr. Florian Freimoser (Agroscope) Dr. Jonas Grossmann (FGCZ) Annika Hausmann (ETH) Dr. Bidong Nguyen (ETH) Dr. Bernd Roschitzki (FGCZ) Dr. Roman Spörri (ETH) | |||||
701-1708-00L | Infectious Disease Dynamics | W | 4 credits | 2V | S. Bonhoeffer, R. D. Kouyos, R. R. Regös, T. Stadler | |
Abstract | This course introduces into current research on the population biology of infectious diseases. The course discusses the most important mathematical tools and their application to relevant diseases of human, natural or managed populations. | |||||
Objective | Attendees will learn about: * the impact of important infectious pathogens and their evolution on human, natural and managed populations * the population biological impact of interventions such as treatment or vaccination * the impact of population structure on disease transmission Attendees will learn how: * the emergence spread of infectious diseases is described mathematically * the impact of interventions can be predicted and optimized with mathematical models * population biological models are parameterized from empirical data * genetic information can be used to infer the population biology of the infectious disease The course will focus on how the formal methods ("how") can be used to derive biological insights about the host-pathogen system ("about"). | |||||
Content | After an introduction into the history of infectious diseases and epidemiology the course will discuss basic epidemiological models and the mathematical methods of their analysis. We will then discuss the population dynamical effects of intervention strategies such as vaccination and treatment. In the second part of the course we will introduce into more advanced topics such as the effect of spatial population structure, explicit contact structure, host heterogeneity, and stochasticity. In the final part of the course we will introduce basic concepts of phylogenetic analysis in the context of infectious diseases. | |||||
Lecture notes | Slides and script of the lecture will be available online. | |||||
Literature | The course is not based on any of the textbooks below, but they are excellent choices as accompanying material: * Keeling & Rohani, Modeling Infectious Diseases in Humans and Animals, Princeton Univ Press 2008 * Anderson & May, Infectious Diseases in Humans, Oxford Univ Press 1990 * Murray, Mathematical Biology, Springer 2002/3 * Nowak & May, Virus Dynamics, Oxford Univ Press 2000 * Holmes, The Evolution and Emergence of RNA Viruses, Oxford Univ Press 2009 | |||||
Prerequisites / Notice | Basic knowledge of population dynamics and population genetics as well as linear algebra and analysis will be an advantage. | |||||
636-0111-00L | Synthetic Biology I Attention: This course was offered in previous semesters with the number: 636-0002-00L "Synthetic Biology I". Students that already passed course 636-0002-00L cannot receive credits for course 636-0111-00L. | W | 4 credits | 3G | S. Panke, J. Stelling | |
Abstract | Theoretical & practical introduction into the design of dynamic biological systems at different levels of abstraction, ranging from biological fundamentals of systems design (introduction to bacterial gene regulation, elements of transcriptional & translational control, advanced genetic engineering) to engineering design principles (standards, abstractions) mathematical modelling & systems desig | |||||
Objective | After the course, students will be able to theoretically master the biological and engineering fundamentals required for biological design to be able to participate in the international iGEM competition (see Link). | |||||
Content | The overall goal of the course is to familiarize the students with the potential, the requirements and the problems of designing dynamic biological elements that are of central importance for manipulating biological systems, primarily (but not exclusively) prokaryotic systems. Next, the students will be taken through a number of successful examples of biological design, such as toggle switches, pulse generators, and oscillating systems, and apply the biological and engineering fundamentals to these examples, so that they get hands-on experience on how to integrate the various disciplines on their way to designing biological systems. | |||||
Lecture notes | Handouts during classes. | |||||
Literature | Mark Ptashne, A Genetic Switch (3rd ed), Cold Spring Haror Laboratory Press Uri Alon, An Introduction to Systems Biology, Chapman & Hall | |||||
Prerequisites / Notice | 1) Though we do not place a formal requirement for previous participation in particular courses, we expect all participants to be familiar with a certain level of biology and of mathematics. Specifically, there will be material for self study available on Link as of mid January, and everybody is expected to be fully familiar with this material BEFORE THE CLASS BEGINS to be able to follow the different lectures. Please contact Link for access to material 2) The course is also thought as a preparation for the participation in the international iGEM synthetic biology summer competition (Link, Link). This competition is also the contents of the course Synthetic Biology II. Link | |||||
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: Microbial Biochemistry and origin of life Methanogenesis and methylotrophy Anaerobic oxidation of methane Microbial autotrophy Complex: (Ligno-)Cellulose and in demand for bioenergy Challenging: Aromatics and hydrocarbons Living on a diet and the anaplerotic provocation 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 | |||||
Literature | Will be provided during the course. |
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