Search result: Catalogue data in Autumn Semester 2018

Computational Biology and Bioinformatics Master Information
More informations at: Link
Master Studies (Programme Regulations 2011)
Advanced Courses and Methods of Computer Science
Advanced Courses
NumberTitleTypeECTSHoursLecturers
252-0025-00LDiscrete Mathematics Information W7 credits4V + 2UU. Maurer
AbstractContent: Mathematical reasoning and proofs, abstraction. Sets, relations (e.g. equivalence and order relations), functions, (un-)countability, number theory, algebra (groups, rings, fields, polynomials, subalgebras, morphisms), logic (propositional and predicate logic, proof calculi).
ObjectiveThe primary goals of this course are (1) to introduce the most important concepts of discrete mathematics, (2) to understand and appreciate the role of abstraction and mathematical proofs, and (3) to discuss a number of applications, e.g. in cryptography, coding theory, and algorithm theory.
ContentSee course description.
Lecture notesavailable (in english)
227-1033-00LNeuromorphic Engineering I Information Restricted registration - show details
Registration in this class requires the permission of the instructors. Class size will be limited to available lab spots.
Preference is given to students that require this class as part of their major.
W6 credits2V + 3UT. Delbrück, G. Indiveri, S.‑C. Liu
AbstractThis course covers analog circuits with emphasis on neuromorphic engineering: MOS transistors in CMOS technology, static circuits, dynamic circuits, systems (silicon neuron, silicon retina, silicon cochlea) with an introduction to multi-chip systems. The lectures are accompanied by weekly laboratory sessions.
ObjectiveUnderstanding of the characteristics of neuromorphic circuit elements.
ContentNeuromorphic circuits are inspired by the organizing principles of biological neural circuits. Their computational primitives are based on physics of semiconductor devices. Neuromorphic architectures often rely on collective computation in parallel networks. Adaptation, learning and memory are implemented locally within the individual computational elements. Transistors are often operated in weak inversion (below threshold), where they exhibit exponential I-V characteristics and low currents. These properties lead to the feasibility of high-density, low-power implementations of functions that are computationally intensive in other paradigms. Application domains of neuromorphic circuits include silicon retinas and cochleas for machine vision and audition, real-time emulations of networks of biological neurons, and the development of autonomous robotic systems. This course covers devices in CMOS technology (MOS transistor below and above threshold, floating-gate MOS transistor, phototransducers), static circuits (differential pair, current mirror, transconductance amplifiers, etc.), dynamic circuits (linear and nonlinear filters, adaptive circuits), systems (silicon neuron, silicon retina and cochlea) and an introduction to multi-chip systems that communicate events analogous to spikes. The lectures are accompanied by weekly laboratory sessions on the characterization of neuromorphic circuits, from elementary devices to systems.
LiteratureS.-C. Liu et al.: Analog VLSI Circuits and Principles; various publications.
Prerequisites / NoticeParticular: The course is highly recommended for those who intend to take the spring semester course 'Neuromorphic Engineering II', that teaches the conception, simulation, and physical layout of such circuits with chip design tools.

Prerequisites: Background in basics of semiconductor physics helpful, but not required.
227-1037-00LIntroduction to Neuroinformatics Information W6 credits2V + 1UV. Mante, M. Cook, B. Grewe, G. Indiveri, D. Kiper, W. von der Behrens
AbstractThe course provides an introduction to the functional properties of neurons. Particularly the description of membrane electrical properties (action potentials, channels), neuronal anatomy, synaptic structures, and neuronal networks. Simple models of computation, learning, and behavior will be explained. Some artificial systems (robot, chip) are presented.
ObjectiveUnderstanding computation by neurons and neuronal circuits is one of the great challenges of science. Many different disciplines can contribute their tools and concepts to solving mysteries of neural computation. The goal of this introductory course is to introduce the monocultures of physics, maths, computer science, engineering, biology, psychology, and even philosophy and history, to discover the enchantments and challenges that we all face in taking on this major 21st century problem and how each discipline can contribute to discovering solutions.
ContentThis course considers the structure and function of biological neural networks at different levels. The function of neural networks lies fundamentally in their wiring and in the electro-chemical properties of nerve cell membranes. Thus, the biological structure of the nerve cell needs to be understood if biologically-realistic models are to be constructed. These simpler models are used to estimate the electrical current flow through dendritic cables and explore how a more complex geometry of neurons influences this current flow. The active properties of nerves are studied to understand both sensory transduction and the generation and transmission of nerve impulses along axons. The concept of local neuronal circuits arises in the context of the rules governing the formation of nerve connections and topographic projections within the nervous system. Communication between neurons in the network can be thought of as information flow across synapses, which can be modified by experience. We need an understanding of the action of inhibitory and excitatory neurotransmitters and neuromodulators, so that the dynamics and logic of synapses can be interpreted. Finally, the neural architectures of feedforward and recurrent networks will be discussed in the context of co-ordination, control, and integration of sensory and motor information in neural networks.
529-0004-01LComputer Simulation in Chemistry, Biology and Physics Information W6 credits4GP. H. Hünenberger
AbstractMolecular models, Force fields, Boundary conditions, Electrostatic interactions, Molecular dynamics, Analysis of trajectories, Quantum-mechanical simulation, Structure refinement, Application to real systems. Exercises: Analysis of papers on computer simulation, Molecular simulation in practice, Validation of molecular dynamics simulation.
ObjectiveIntroduction to computer simulation of (bio)molecular systems, development of skills to carry out and interpret computer simulations of biomolecular systems.
ContentMolecular models, Force fields, Spatial boundary conditions, Calculation of Coulomb forces, Molecular dynamics, Analysis of trajectories, Quantum-mechanical simulation, Structure refinement, Application to real systems. Exercises: Analysis of papers on computer simulation, Molecular simulation in practice, Validation of molecular dynamics simulation.
Lecture notesAvailable (copies of powerpoint slides distributed before each lecture)
LiteratureSee: Link
Prerequisites / NoticeSince the exercises on the computer do convey and test essentially different skills as those being conveyed during the lectures and tested at the oral exam, the results of the exercises are taken into account when evaluating the results of the exam (learning component, possible bonus of up to 0.25 points on the exam mark).

For more information about the lecture: Link
529-0733-01LEnzymesW6 credits3GD. Hilvert
AbstractPrinciples of enzymatic catalysis, enzyme kinetics, mechanisms of enzyme-catalyzed reactions (group transfer reactions, carbon-carbon bond formation, eliminations, isomerisations and rearrangements), cofactor chemistry, enzymes in organic synthesis and the biosynthesis of natural products, catalytic antibodies.
ObjectiveOverview of enzymes, enzyme-catalyzed reactions and metabolic processes.
ContentPrinciples of enzymatic catalysis, enzyme kinetics, mechanisms of enzyme catalyzed reactions (group transfer reactions, carbon-carbon bond formation, eliminations, isomerisations and rearrangements), cofactor chemistry, enzymes in organic synthesis and the biosynthesis of natural products, catalytic antibodies.
Lecture notesA script will not be handed out.
LiteratureGeneral:
T. Bugg, An Introduction to Enzyme and Coenzyme Chemistry, Blackwell Science Ltd., Oxford, 1997.

In addition, citations from the original literature relevant to the individual lectures will be assigned weekly.
535-0810-00LGene Technology Information W2 credits2GD. Neri
AbstractThe course will provide a solid overview of the science and issues in gene technology and its pharmaceutical applications.
ObjectiveThe aim of the lecture course is to provide a solid overview of gene technology, with a special focus on drug development. Topics: Antibody phage technology, DNA-encoded chemistry, protein modification technology, genome sequencing, transcriptomics, proteomics, functional genomics, principle of drug discovery. The course is suited for advanced undergraduate and early graduate students in pharmaceutical sciences or related fields.
Content1. Antibody phage technology
The antibody molecule
V genes, CDRs, basics of antibody engineering
Principles of phage display
Phagemid and phage vectors
Antibody libraries
Phage display selection methodologies
Other phage libraries (peptides, globular proteins, enzymes)
Alternative screening/selection methodologies
DNA-encoded chemical libraries

2. Proteins: chemical modification and detection of biomolecular interactions
Homo- and hetero-dimerization of proteins
Chemical modifications of proteins
Antibody-drug conjugates
Radioactive labeling of proteins
Kinetic association and dissociation constants
Affinity constant: definition and its experimental measurement

3. Genomics: Applications to Human Biology
Protein cloning and expression
DNA sequencing
Some foundations of genetic analysis
Knock-out technologies
Transcriptomics
Proteomics
Recombinant vaccines

4: Pharmaceuticals: Focus on Discovery
Ligand Discovery
Half-life extension
Cancer therapy
Gene therapy
Lecture notesSkript "Gene Technology" by Prof. Dario Neri and slides of the lecture
551-0307-00LMolecular and Structural Biology I: Protein Structure and Function Information
D-BIOL students are obliged to take part I and part II (next semester) as a two-semester course
W3 credits2VR. Glockshuber, K. Locher, E. Weber-Ban
AbstractBiophysics of protein folding, membrane proteins and biophysics of membranes, enzymatic catalysis, catalytic RNA and RNAi, current topics in protein biophysics and structural biology.
ObjectiveUnderstanding of structure-function relationships in proteins and in protein folding, detailed understanding of biophysics and physical methods as well as modern methods for protein purification and microanalytics.
Lecture notesScripts on the individual topics can be found under Link.
LiteratureBasics:
- Creighton, T.E., Proteins, Freeman, (1993)
- Fersht, A., Enzyme, Structure and Mechanism in Protein Science (1999), Freeman.
- Berg, Tymoczko, Stryer: Biochemistry (5th edition), Freeman (2001).

Current topics: References will be given during the lectures.

.
551-0309-00LConcepts in Modern GeneticsW6 credits4VY. Barral, D. Bopp, A. Hajnal, M. Stoffel, O. Voinnet
AbstractConcepts 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.
ObjectiveThis course focuses on the concepts of classical and modern genetics and genomics.
ContentThe 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 notesScripts and additional material will be provided during the semester.
551-0313-00LMicrobiology (Part I)W3 credits2VW.‑D. Hardt, L. Eberl, H.‑M. Fischer, J. Piel, M. Pilhofer
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
The lecture "Grundlagen der Biologie II: Mikrobiologie" is the basis for this advanced lecture.
551-0317-00LImmunology IW3 credits2VM. Kopf, A. Oxenius
AbstractIntroduction into structural and functional aspects of the immune system.
Basic knowledge of the mechanisms and the regulation of an immune response.
ObjectiveIntroduction into structural and functional aspects of the immune system.
Basic knowledge of the mechanisms and the regulation of an immune response.
Content- Introduction and historical background
- Innate and adaptive immunity, Cells and organs of the immune system
- B cells and antibodies
- Generation of diversity
- Antigen presentation and Major Histoincompatibility (MHC) antigens
- Thymus and T cell selection
- Autoimmunity
- Cytotoxic T cells and NK cells
- Th1 and Th2 cells, regulatory T cells
- Allergies
- Hypersensitivities
- Vaccines, immune-therapeutic interventions
Lecture notesElectronic access to the documentation will be provided. The link can be found at "Lernmaterialien"
Literature- Kuby, Immunology, 7th edition, Freemen + Co., New York, 2009
Prerequisites / NoticeImmunology I (WS) and Immunology II (SS) will be examined as one learning entity in a "Sessionsprüfung".
401-0647-00LIntroduction to Mathematical OptimizationW5 credits2V + 1UD. Adjiashvili
AbstractIntroduction to basic techniques and problems in mathematical optimization, and their applications to a variety of problems in engineering.
ObjectiveThe goal of the course is to obtain a good understanding of some of the most fundamental mathematical optimization techniques used to solve linear programs and basic combinatorial optimization problems. The students will also practice applying the learned models to problems in engineering.
ContentTopics covered in this course include:
- Linear programming (simplex method, duality theory, shadow prices, ...).
- Basic combinatorial optimization problems (spanning trees, shortest paths, network flows, ...).
- Modelling with mathematical optimization: applications of mathematical programming in engineering.
LiteratureInformation about relevant literature will be given in the lecture.
Prerequisites / NoticeThis course is meant for students who did not already attend the course "Mathematical Optimization", which is a more advance lecture covering similar topics. Compared to "Mathematical Optimization", this course has a stronger focus on modeling and applications.
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