Search result: Catalogue data in Spring Semester 2021

Computational Biology and Bioinformatics Master Information
More informations at: https://www.cbb.ethz.ch
Advanced Courses
A total of 30 ECTS needs to be acquired in the Advanced Courses category. Thereof 18 ECTS in the Theory and 12 ECTS in the Biology category.
Note that some of the lectures are being recorded: https://video.ethz.ch/lectures.html
Biology
At least 12 ECTS need to be acquired in this category.
NumberTitleTypeECTSHoursLecturers
262-5110-00LProtein Crystallography and Electron Microscopy (University of Zurich)
No enrollment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BCH630

Mind the enrolment deadlines at UZH:
https://www.uzh.ch/cmsssl/en/studies/application/deadlines.html
W3 credits3GUniversity lecturers
AbstractThe lecture introduces two methods for the structure determination of
biological macromolecules and cellular components: X-ray crystallography and electron microscopy (EM).
ObjectiveTo understand the basic concepts of protein crystallography and electron microscopy in theory and practice.
ContentThe lecture introduces two methods for the structure determination of
biological macromolecules and cellular components: X-ray crystallography
and electron microscopy (EM). The lecture provides students with the
main concepts of protein structure determination by X-ray
crystallography (protein crystallization, crystal symmetry and
diffraction, data collection, phasing methods, refinement). The second
part of the lecture will deal with electron microscopy. The topics
include Transmission EM, Scanning EM, sample preparation, data
acquisition, 3D reconstruction, aberration, detectors.
551-0314-00LMicrobiology (Part II)W3 credits2VW.‑D. Hardt, L. Eberl, J. Piel, J. Vorholt-Zambelli
AbstractAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
ObjectiveThis 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.
ContentAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references will be provided during the lectures.
Prerequisites / NoticeEnglish
551-0318-00LImmunology IIW3 credits2VA. Oxenius, M. Kopf, S. R. Leibundgut, E. Wetter Slack, further lecturers
AbstractIntroduction into the cellular and molecular basis of the immune system and immune responses against diverse pathogens, tumors, transplants, and self (autoimmunity)
ObjectiveThe lectures will provide a detailed understanding:
- how innate and adaptive immune responses interact at the cellular and molecular level.
- how the immune system recognizes and fights against pathogenic microorganisms including viruses, bacteria, and parasites.
- why lymphocytes tolerate self molecules.
- about function and dysfunction the intestinal immune system.
- immunopathology and inflammatory diseases.
ContentThe aim of lecture is to understand:
> How pathogens are recognized by the innate immune system
> Immune defense against various pathogens
> Immunology of the skin, lung and intestines
> Tumor immunology
> Migration and homing of immune cells
> tolerance and autoimmunity
> T cell memory
Lecture notesPresentations of the lecturers are available at the Moodle link
LiteratureRecommended: Kuby Immunology (Freeman)
701-1708-00LInfectious Disease DynamicsW4 credits2VS. Bonhoeffer, R. D. Kouyos, R. R. Regös, T. Stadler
AbstractThis 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.
ObjectiveAttendees 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").
ContentAfter 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 notesSlides and script of the lecture will be available online.
LiteratureThe 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 / NoticeBasic knowledge of population dynamics and population genetics as well as linear algebra and analysis will be an advantage.
551-1404-00LRNA and Proteins: Post-Transcriptional Regulation of Gene Expression (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BCH252

Mind the enrolment deadlines at UZH:
https://www.uzh.ch/cmsssl/en/studies/application/deadlines.html
W3 credits2VUniversity lecturers
AbstractThe course introduces the cellular processes and molecular mechanisms involved in regulating genome expression at the post-transcriptional level.
Topics will include :
-RNA processing, and transport;
-protein synthesis and translational control, trafficking and degradation;
-RNA-guided regulation (RNA interference, microRNAs);
-molecular surveillance and quality control mechanisms
Objective-Outline the cellular processes
used by eukaryotic and prokaryotic cells
to control gene expression at the post-
transcriptional level.
-Describe the molecular mechanisms
underlying post-transcriptional gene
regulation
-Identify experimental approaches
used to study post-transcriptional gene
regulation and describe their strengths
and weaknesses.
636-0110-00LImmunoEngineering
Attention: This course was offered in previous semesters with the number: 636-0010-00L "Biomolecular Engineering and Immunotechnology". Students that already passed course 636-0010-00L cannot receive credits for course 636-0110-00L.
W4 credits3VS. Reddy, A. Yermanos
AbstractImmunoengineering is an emerging area of research that uses technology and engineering principles to understand and manipulate the immune system. This is a highly interdisciplinary field and thus the instructor will present an integrated view that will include basic immunology, systems immunology, and synthetic immunology.
ObjectiveThe objective of this course is to introduce the students to the basic principles and applications of Immunoengineering. There will be an emphasis directed towards applications directly relevant in immunotherapy and biotechnology. This course requires prerequisite knowledge of molecular biology, biochemistry, cell biology, and genetics; these subjects will only be reviewed briefly during the course.
ContentImmunoengineering will be divided into three primary sections: i) basic principles in immunology; ii) systems immunology; iii) synthetic immunology.

I. Basic principles in immunology will cover the foundational concepts of innate and adaptive immunity. Topics include immunogenetics, pattern recognition receptors, lymphocyte receptors, humoral and T cell responses.

II. Systems immunology uses quantitative multiscale measurements and computational biology to describe and understand the complexity of the immune system. In this section we will cover high-throughput methods that are used to understand and profile immune responses.

III. Synthetic immunology is based on using methods in molecular and cellular engineering to control immune cell function and behavior. In this section students will learn about how immune receptors and cells are being engineered for applications such as cancer immunotherapy and precision and personalized medicine.
LiteratureReading material from Janeway's Immunobiology will be distributed, so students do not need to worry about purchasing or obtaining it. Supporting reading material from research articles will be provided to students.
Prerequisites / NoticeThis course requires prerequisite knowledge of molecular biology, biochemistry, cell biology, and genetics; these subjects will only be reviewed briefly during the course.
636-0518-00LMolecular Medicine IIW2 credits2Vexternal organisers
Abstract
Objective
636-0514-00LDynamics and Maintenance of the Genome: DNA Replication, Repair, Recombination
Does not take place this semester.
W2 credits2Vexternal organisers
Abstract
Objective
636-0516-00LTranscription, Regulation and Gene Expression in Eukaryotes
Does not take place this semester.
W2 credits2Vexternal organisers
Abstract
Objective
636-0536-00LChromatin and EpigeneticsW2 credits2Vexternal organisers
Abstract
Objective
262-6200-00LStem Cell Biology
Does not take place this semester.
W2 credits2Sexternal organisers
Abstract
Objective
262-6230-00LSignaling in the Nervous System
Does not take place this semester.
W2 credits2Vexternal organisers
Abstract
Objective
551-0338-00LCurrent Approaches in Single Cell Analysis (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BME327

Mind the enrolment deadlines at UZH:
https://www.uzh.ch/cmsssl/en/studies/application/deadlines.html
W2 credits2VB. Bodenmiller, University lecturers
AbstractIn this lecture, we will discuss the most important single cell
approaches, the questions they can address and current developments. We will cover single cell: genomics, transcriptomics, proteomics (CyTOF mass cytometry), metabolomics and highly multiplexed imaging. Finally, we will also discuss the latest approaches for the analysis of such generated highly multiplexed single cell data.
ObjectiveOn completion of this module the students should be able to:
- explain the basic principles of single cell analysis techniques
- identify and justify the limitations of the current single cell
technologies and suggest reasonable improvements
- know the basic challenges in data analysis imposed by the complex
multi parameter data.
Key skills:
On completion of this module the students should be able to:
- summarize and discuss the impact these technologies have on biology
and medicine
- design biological and biomedical experiments for which single cell
analysis is essential
ContentCurrently single cell analysis approaches revolutionize the way we study and understand biological systems. In all biological and biomedical settings, cell populations and tissues are highly heterogeneous; this heterogeneity plays a critical role in basic biological processes such as cell cycle, development and organismic function, but is also a major player in disease, e.g. for cancer development, diagnosis and treatment.
Currently, single cell analysis techniques are rapidly developing and
find broad application, as the single cell measurements not only enable
to study cell specific functions, but often reveal unexpected biological
mechanisms in so far (assumed) well understood biological processes.
In this lecture, we will discuss the most important single cell approaches, the questions they can address and current developments. We will cover single cell genomics, single cell transcriptomics, single cell proteomics (CyTOF mass cytometry), single cell metabolomics and highly multiplexed single cell imaging. Finally, we will also discuss the latest approaches for the analysis of such generated highly multiplexed single cell data.
262-5140-00LBiomedical Imaging and Scientific Visualization (University of Zurich)
No enrollment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: BIO219

Mind the enrolment deadlines at UZH:
https://www.uzh.ch/cmsssl/en/studies/application/deadlines.html
W2 credits2VUniversity lecturers
Abstract
Objective
551-0307-01LMolecular and Structural Biology II: Molecular Machines and Cellular Assemblies
D-BIOL students are obliged to take part I and part II as a two-semester course.
W3 credits2VN. Ban, F. Allain, S. Jonas, M. Pilhofer
AbstractThis course on advanced topics in Molecular Biology and Biochemistry will cover the structure and function of cellular assemblies. General topics in basic biochemistry will be further developed with examples of the function of large cellular machines involved in DNA packaging, translation, virus architecture, RNA processing, cell-cell interactions, and the molecular basis of CRISPER systems.
ObjectiveStudents will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation.
ContentAdvanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies.
Lecture notesUpdated handouts will be provided during the class.
LiteratureThe lecture will be based on the latest literature. Additional suggested
literature:
Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed.
(1995). Garland, New York.
636-0113-00LGenome Engineering Restricted registration - show details W4 credits3VR. Platt
AbstractThis course is both an introduction to genome engineering and also a highly interactive practical training on effectively reading, writing, and presenting in an academic context.
ObjectiveThe objective of this course is to learn how gene editing technologies function at the molecular and cellular level and how they are applied in research and clinical settings. Students will be introduced to the history and motivation behind the discovery and development of transformative genome engineering technologies, and also gain insight into the ethical, safety, and regulatory facets shaping the field. This content will be explored by critically examining and discussing current literature in the field and devising a technology development plan.
ContentThe course content is comprised of lectures, discussions, and a project. Lectures in Genome Engineering will be technology-focused and incorporate: 1) historical context to motivate the need for developing the technology, 2) development of the technology from concept to robust tool, 3) methods to discover, characterize, and evaluate the technology, and 4) applications of the technology in basic and applied research. Primary research articles will be assigned each week, which will be followed by an in-class lecture and discussion. The course project will be team-based and entail devising a solution to a critical need in the field.

Main topics:
--Discovery and development of genome editing technologies
--The prokaryotic adaptive immune system CRISPR-Cas
--Genome engineering methods for generating genetically engineered model systems
--Genotype-phenotype linkage via genetic screens
--Massively paralleled perturbation and phenotyping
--Gene editing tools as molecular recording devices
--Gene editing tools as diagnostics and therapeutics
Lecture notesMade available through the course website.
LiteratureAssigned each week. Made available through the course website.
227-1034-00LComputational Vision (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: INI402

Mind the enrolment deadlines at UZH:
https://www.uzh.ch/cmsssl/en/studies/application/deadlines.html
W6 credits2V + 1UD. Kiper
AbstractThis course focuses on neural computations that underlie visual perception. We study how visual signals are processed in the retina, LGN and visual cortex. We study the morpholgy and functional architecture of cortical circuits responsible for pattern, motion, color, and three-dimensional vision.
ObjectiveThis course considers the operation of circuits in the process of neural computations. The evolution of neural systems will be considered to demonstrate how neural structures and mechanisms are optimised for energy capture, transduction, transmission and representation of information. Canonical brain circuits will be described as models for the analysis of sensory information. The concept of receptive fields will be introduced and their role in coding spatial and temporal information will be considered. The constraints of the bandwidth of neural channels and the mechanisms of normalization by neural circuits will be discussed.
The visual system will form the basis of case studies in the computation of form, depth, and motion. The role of multiple channels and collective computations for object recognition will
be considered. Coordinate transformations of space and time by cortical and subcortical mechanisms will be analysed. The means by which sensory and motor systems are integrated to allow for adaptive behaviour will be considered.
ContentThis course considers the operation of circuits in the process of neural computations. The evolution of neural systems will be considered to demonstrate how neural structures and mechanisms are optimised for energy capture, transduction, transmission and representation of information. Canonical brain circuits will be described as models for the analysis of sensory information. The concept of receptive fields will be introduced and their role in coding spatial and temporal information will be considered. The constraints of the bandwidth of neural channels and the mechanisms of normalization by neural circuits will be discussed.
The visual system will form the basis of case studies in the computation of form, depth, and motion. The role of multiple channels and collective computations for object recognition will
be considered. Coordinate transformations of space and time by cortical and subcortical mechanisms will be analysed. The means by which sensory and motor systems are integrated to allow for adaptive behaviour will be considered.
LiteratureBooks: (recommended references, not required)
1. An Introduction to Natural Computation, D. Ballard (Bradford Books, MIT Press) 1997.
2. The Handbook of Brain Theorie and Neural Networks, M. Arbib (editor), (MIT Press) 1995.
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