Suchergebnis: Katalogdaten im Frühjahrssemester 2019

Biologie Master Information
Wahlvertiefungen
Wahlvertiefung: Systembiologie
Obligatorische Konzeptkurse
NummerTitelTypECTSUmfangDozierende
551-0324-00LSystems Biology Information O6 KP4VR. Aebersold, B. Christen, M. Claassen, U. Sauer
KurzbeschreibungIntroduction to experimental and computational methods of systems biology. By using baker’s yeast as a thread through the series, we focus on global methods for analysis of and interference with biological functions. Illustrative applications to other organisms will highlight medical and biotechnological aspects.
Lernziel- obtain an overview of global analytical methods
- obtain an overview of computational methods in systems biology
- understand the concepts of systems biology
InhaltOverview of global analytical methods (e.g. DNA arrays, proteomics, metabolomics, fluxes etc), global interference methods (siRNA, mutant libraries, synthetic lethality etc.) and imaging methods. Introduction to mass spectrometry and proteomics. Concepts of metabolism in microbes and higher cells. Systems biology of developmental processes. Concepts of mathematical modeling and applications of computational systems biology.
Skriptno script
LiteraturThe course is not taught by a particular book, but some books are suggested for further reading:

- Systems biology in Practice by Klipp, Herwig, Kowald, Wierling und Lehrach. Wiley-VCH 2005
Wahlpflicht Konzeptkurse
Siehe D-BIOL Master-Wegleitung
NummerTitelTypECTSUmfangDozierende
551-0320-00LCellular Biochemistry (Part II)W3 KP2VY. Barral, R. Kroschewski, A. E. Smith
KurzbeschreibungThis course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes.
LernzielThe 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 characterization 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 how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection.
InhaltSpatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection.
LiteraturRecommended supplementary literature (review articles and selected primary literature) will be provided during the course.
Voraussetzungen / BesonderesTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English.
In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform.
551-0314-00LMicrobiology (Part II)W3 KP2VW.‑D. Hardt, L. Eberl, H.‑M. Fischer, J. Piel, J. Vorholt-Zambelli
KurzbeschreibungAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
LernzielThis 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.
InhaltAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
SkriptUpdated handouts will be provided during the class.
LiteraturCurrent literature references will be provided during the lectures.
Voraussetzungen / BesonderesEnglish
Wahlpflicht Masterkurse I: Rechnergestütz
NummerTitelTypECTSUmfangDozierende
636-0702-00LStatistical Models in Computational BiologyW6 KP2V + 1U + 2AN. Beerenwinkel
KurzbeschreibungThe course offers an introduction to graphical models and their application to complex biological systems. Graphical models combine a statistical methodology with efficient algorithms for inference in settings of high dimension and uncertainty. The unifying graphical model framework is developed and used to examine several classical and topical computational biology methods.
LernzielThe goal of this course is to establish the common language of graphical models for applications in computational biology and to see this methodology at work for several real-world data sets.
InhaltGraphical models are a marriage between probability theory and graph theory. They combine the notion of probabilities with efficient algorithms for inference among many random variables. Graphical models play an important role in computational biology, because they explicitly address two features that are inherent to biological systems: complexity and uncertainty. We will develop the basic theory and the common underlying formalism of graphical models and discuss several computational biology applications. Topics covered include conditional independence, Bayesian networks, Markov random fields, Gaussian graphical models, EM algorithm, junction tree algorithm, model selection, Dirichlet process mixture, causality, the pair hidden Markov model for sequence alignment, probabilistic phylogenetic models, phylo-HMMs, microarray experiments and gene regulatory networks, protein interaction networks, learning from perturbation experiments, time series data and dynamic Bayesian networks. Some of the biological applications will be explored in small data analysis problems as part of the exercises.
Skriptno
Literatur- Airoldi EM (2007) Getting started in probabilistic graphical models. PLoS Comput Biol 3(12): e252. doi:10.1371/journal.pcbi.0030252
- Bishop CM. Pattern Recognition and Machine Learning. Springer, 2007.
- Durbin R, Eddy S, Krogh A, Mitchinson G. Biological Sequence Analysis. Cambridge university Press, 2004
401-0102-00LApplied Multivariate StatisticsW5 KP2V + 1UF. Sigrist
KurzbeschreibungMultivariate statistics analyzes data on several random variables simultaneously. This course introduces the basic concepts and provides an overview of classical and modern methods of multivariate statistics including visualization, dimension reduction, supervised and unsupervised learning for multivariate data. An emphasis is on applications and solving problems with the statistical software R.
LernzielAfter the course, you are able to:
- describe the various methods and the concepts behind them
- identify adequate methods for a given statistical problem
- use the statistical software R to efficiently apply these methods
- interpret the output of these methods
InhaltVisualization, multivariate outliers, the multivariate normal distribution, dimension reduction, principal component analysis, multidimensional scaling, factor analysis, cluster analysis, classification, multivariate tests and multiple testing
SkriptNone
Literatur1) "An Introduction to Applied Multivariate Analysis with R" (2011) by Everitt and Hothorn
2) "An Introduction to Statistical Learning: With Applications in R" (2013) by Gareth, Witten, Hastie and Tibshirani

Electronic versions (pdf) of both books can be downloaded for free from the ETH library.
Voraussetzungen / BesonderesThis course is targeted at students with a non-math background.

Requirements:
==========
1) Introductory course in statistics (min: t-test, regression; ideal: conditional probability, multiple regression)
2) Good understanding of R (if you don't know R, it is recommended that you study chapters 1,2,3,4, and 5 of "Introductory Statistics with R" from Peter Dalgaard, which is freely available online from the ETH library)

An alternative course with more emphasis on theory is 401-6102-00L "Multivariate Statistics" (only every second year).

401-0102-00L and 401-6102-00L are mutually exclusive. You can register for only one of these two courses.
227-0396-00LEXCITE Interdisciplinary Summer School on Bio-Medical Imaging Information Belegung eingeschränkt - Details anzeigen
The school admits 60 MSc or PhD students with backgrounds in biology, chemistry, mathematics, physics, computer science or engineering based on a selection process.

Students have to apply for acceptance by April 22, 2019. To apply a curriculum vitae and an application letter need to be submitted. The notification of acceptance will be given by May 24, 2019. Further information can be found at: www.excite.ethz.ch.
W4 KP6GS. Kozerke, G. Csúcs, J. Klohs-Füchtemeier, S. F. Noerrelykke, M. P. Wolf
KurzbeschreibungTwo-week summer school organized by EXCITE (Center for EXperimental & Clinical Imaging TEchnologies Zurich) on biological and medical imaging. The course covers X-ray imaging, magnetic resonance imaging, nuclear imaging, ultrasound imaging, infrared and optical microscopy, electron microscopy, image processing and analysis.
LernzielStudents understand basic concepts and implementations of biological and medical imaging. Based on relative advantages and limitations of each method they can identify preferred procedures and applications. Common foundations and conceptual differences of the methods can be explained.
InhaltTwo-week summer school on biological and medical imaging. The course covers concepts and implementations of X-ray imaging, magnetic resonance imaging, nuclear imaging, ultrasound imaging, infrared and optical microscopy and electron microscopy. Multi-modal and multi-scale imaging and supporting technologies such as image analysis and modeling are discussed. Dedicated modules for physical and life scientists taking into account the various backgrounds are offered.
SkriptHand-outs, Web links
Voraussetzungen / BesonderesThe school admits 60 MSc or PhD students with backgrounds in biology, chemistry, mathematics, physics, computer science or engineering based on a selection process. To apply a curriculum vitae, a statement of purpose and applicants references need to be submitted. Further information can be found at: http://www.excite.ethz.ch/education/summer-school.html
Wahlpflicht Masterkurse II: Biologie
NummerTitelTypECTSUmfangDozierende
551-1310-00LA Problem-Based Approach to Cellular Biochemistry Belegung eingeschränkt - Details anzeigen
Number of participants limited to 15.
W6 KP2GM. Peter, E. Dultz, M. Gstaiger, V. Korkhov, V. Panse, A. E. Smith
KurzbeschreibungIndependent, guided acquisition of an overview over a defined area of research, identification of important open questions, development of an experimental strategy to address a defined question, and formulation of this strategy within the framework of a research grant.
LernzielThe students will learn to acquire independently an overview over a defined area of research, and to identify important open questions. In addition, they will learn to develop an experimental strategy to address a defined question, and to formulate this strategy within the framework of a research grant.
InhaltThe 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.
LiteraturThe identification of appropriate literature is a component of the course.
Voraussetzungen / BesonderesThis course will be taught in english, and requires extensive independent work.
551-0364-00LFunctional 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
W3 KP2VC. von Mering, C. Beyer, B. Bodenmiller, M. Gstaiger, H. Rehrauer, R. Schlapbach, K. Shimizu, N. Zamboni, weitere Dozierende
KurzbeschreibungFunctional 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.
LernzielFunctional 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.
InhaltThe 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 microarrays, 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.
Voraussetzungen / BesonderesThe Functional Genomics course will be taught in English.
551-0224-00LAdvanced Proteomics Belegung eingeschränkt - Details anzeigen
Für Masterstudierende ab 2. Semester, Doktorierende und Postdoktorierende
W4 KP6GR. Aebersold, L. Gillet, M. Gstaiger, A. Leitner, P. Pedrioli
KurzbeschreibungZiel dieses Kurses ist es, etablierte und neue Technologien der Protein- und Proteome-Analyse kennenzulernen in Bezug auf ihre Anwendung in Biologie, Biotechnologie und Medizin.
Format: Einführung durch Dozent mit anschliessender Diskussion, unterstützt durch Literaturarbeit und Übungen.
LernzielIm Kurs werden sowohl die bereits etablierten als auch die neuesten derzeit entstehenden Technologien und Methoden in der Protein- und Proteomanlayse diskutiert im Hinblick auf ihre Anwendung in der Biologie, Biotechnologie, Medizin und Systembiologie.
InhaltBlock course teaching current methods for the acquisition and processing of proteomic datasets.
Voraussetzungen / BesonderesNumber 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 http://www.rektorat.ethz.ch/students/admission/auditors/index_EN
701-1418-00LModelling Course in Population and Evolutionary Biology Information Belegung eingeschränkt - Details anzeigen
Number of participants limited to 20.

Priority is given to MSc Biology and Environmental Sciences students.
W4 KP6PS. Bonhoeffer, V. Müller
KurzbeschreibungDieser Kurs ist eine praktische Einfuehrung in die mathematische/computerorientierte Modellierung biologischer Prozesse mit Schwerpunkt auf evolutionsbiologischen und populationsbiologischen Fragestellungen. Die Modelle werden in der Open Source software R entwickelt.
LernzielDen Teilnehmern soll der Nutzen der Modellierung als ein Hilfsmittel zur Untersuchung biologischer Fragestellungen vermittelt werden. Die einfacheren Module orientieren sich mehrheitlich an Beispielen aus der ehemaligen Vorlesung "Oekologie und Evolution: Populationen" (Skript von der Kurswebseite zugaenglich). Die fortgeschrittenen Module orientieren sich an aktuellen Forschungsthemen. Hierbei werden auch Fragestellungen untersucht, die zwar konzeptionell und methodisch auf Evolutions- und Populations-biologischen Ansaetzen beruhen, aber sich mit anderen Bereichen der Biologie befassen.
Inhaltsiehe www.tb.ethz.ch/education/learningmaterials/modelingcourse.html
SkriptDetaillierte Handouts für alle Module sind an der Webseite des Kurses zu finden. Zusaetzlich ist das Skript für die frühere Vorlesung "Oekologie und Evolution: Populationen" auch zugaenglich, und enthaelt weitere relevante Informationen.
Voraussetzungen / BesonderesDer Kurs basiert auf der Open Source Software R. Programmiererfahrung in R ist nuetzlich, aber keine Voraussetzung. Ebenso ist der Kurs 701-1708-00L Infectious Disease Dynamics nützlich, aber keine Voraussetzung.
551-1126-00LTechnologies in Molecular MicrobiologyW4 KP2VH.‑M. Fischer, B. Christen, M. Christen, weitere Dozierende
KurzbeschreibungThe 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.
LernzielThe lecture course aims at providing principles of modern techniques used in molecular microbiology. Emphasis is on genetic, biochemical, and cellular analysis including also bioinformatics aspects. 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.
InhaltImportant genetic, biochemical, biophysical, bioinformatic and structural 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
- Synthetic biology
SkriptUpdated handouts will be provided during the class.
LiteraturCurrent literature references, relevant papers and handouts will be provided during the lectures.
Voraussetzungen / BesonderesThe following lecturers will contribute to the course:

Prof. Beat Christen (ETH)
Dr. Matthias Christen (ETH)
Prof. Hans-Martin Fischer (ETH)
Dr. Jonas Grossmann (FGCZ)
Dr. Florian Freimoser (Agroscope)
Dr. Bernd Roschitzki (FGCZ)
Dr. Roman Spörri (ETH)
701-1708-00LInfectious Disease DynamicsW4 KP2VS. Bonhoeffer, R. D. Kouyos, R. R. Regös, T. Stadler
KurzbeschreibungThis 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.
LernzielAttendees 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").
InhaltAfter 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.
SkriptSlides and script of the lecture will be available online.
LiteraturThe 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
Voraussetzungen / BesonderesBasic knowledge of population dynamics and population genetics as well as linear algebra and analysis will be an advantage.
636-0111-00LSynthetic 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.
W4 KP3GS. Panke, J. Stelling
KurzbeschreibungTheoretical & 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
LernzielAfter 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 www.syntheticbiology.ethz.ch).
InhaltThe 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.
SkriptHandouts during classes.
LiteraturMark Ptashne, A Genetic Switch (3rd ed), Cold Spring Haror Laboratory Press
Uri Alon, An Introduction to Systems Biology, Chapman & Hall
Voraussetzungen / Besonderes1) 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 http://www.bsse.ethz.ch/bpl/education/index 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 sven.panke@bsse.ethz.ch for access to material
2) The course is also thought as a preparation for the participation in the international iGEM synthetic biology summer competition (www.syntheticbiology.ethz.ch, http://www.igem.org). This competition is also the contents of the course Synthetic Biology II. http://www.bsse.ethz.ch/bpl/education/index
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