# Search result: Catalogue data in Autumn Semester 2020

Mathematics Master | ||||||

Application Area Only necessary and eligible for the Master degree in Applied Mathematics. One of the application areas specified must be selected for the category Application Area for the Master degree in Applied Mathematics. At least 8 credits are required in the chosen application area. | ||||||

Biology | ||||||

Number | Title | Type | ECTS | Hours | Lecturers | |
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551-0015-00L | Biology I | W | 2 credits | 2V | E. Hafen, E. Dufresne | |

Abstract | The lecture Biology I, together with the lecture Biology II in the following summer semester, is a basic, introductory course into Biology for Students of Materials Sciences and other students with biology as subsidiary subject. | |||||

Objective | The goal of this course is to give the students a basic understanding of the molecules that build a cell and make it function, and the basic principles of metabolism and molecular genetics. | |||||

Content | Die folgenden Kapitelnummern beziehen sich auf das der Vorlesung zugrundeliegende Lehrbuch "Biology" (Campbell & Rees, 10th edition, 2015) Kapitel 1-4 des Lehrbuchs werden als Grundwissen vorausgesetzt 1. Aufbau der Zelle Kapitel 5: Struktur und Funktion biologischer Makromoleküle Kapitel 6: Eine Tour durch die Zelle Kaptiel 7: Membranstruktur und-funktion Kapitel 8: Einführung in den Stoffwechsel Kapitel 9: Zelluläre Atmung und Speicherung chemischer Energie Kapitel 10: Photosynthese Kapitel 12: Der Zellzyklus Kapitel 17: Vom Gen zum Protein 2. Allgemeine Genetik Kapitel 13: Meiose und Reproduktionszyklen Kapitel 14: Mendel'sche Genetik Kapitel 15: Die chromosomale Basis der Vererbung Kapitel 16: Die molekulare Grundlage der Vererbung Kapitel 18: Genetik von Bakterien und Viren Kapitel 46: Tierische Reproduktion Grundlagen des Stoffwechsels und eines Überblicks über molekulare Genetik | |||||

Lecture notes | Der Vorlesungsstoff ist sehr nahe am Lehrbuch gehalten, Skripte werden ggf. durch die Dozenten zur Verfügung gestellt. | |||||

Literature | Das folgende Lehrbuch ist Grundlage für die Vorlesungen Biologie I und II: „Biology“, Campbell and Rees, 10th Edition, 2015, Pearson/Benjamin Cummings, ISBN 978-3-8632-6725-4 | |||||

Prerequisites / Notice | Zur Vorlesung Biologie I gibt es während der Prüfungssessionen eine einstündige, schriftliche Prüfung. Die Vorlesung Biologie II wird separat geprüft. | |||||

636-0017-00L | Computational Biology | W | 6 credits | 3G + 2A | T. Stadler, T. Vaughan | |

Abstract | The aim of the course is to provide up-to-date knowledge on how we can study biological processes using genetic sequencing data. Computational algorithms extracting biological information from genetic sequence data are discussed, and statistical tools to understand this information in detail are introduced. | |||||

Objective | Attendees will learn which information is contained in genetic sequencing data and how to extract information from this data using computational tools. The main concepts introduced are: * stochastic models in molecular evolution * phylogenetic & phylodynamic inference * maximum likelihood and Bayesian statistics Attendees will apply these concepts to a number of applications yielding biological insight into: * epidemiology * pathogen evolution * macroevolution of species | |||||

Content | The course consists of four parts. We first introduce modern genetic sequencing technology, and algorithms to obtain sequence alignments from the output of the sequencers. We then present methods for direct alignment analysis using approaches such as BLAST and GWAS. Second, we introduce mechanisms and concepts of molecular evolution, i.e. we discuss how genetic sequences change over time. Third, we employ evolutionary concepts to infer ancestral relationships between organisms based on their genetic sequences, i.e. we discuss methods to infer genealogies and phylogenies. Lastly, we introduce the field of phylodynamics, the aim of which is to understand and quantify population dynamic processes (such as transmission in epidemiology or speciation & extinction in macroevolution) based on a phylogeny. Throughout the class, the models and methods are illustrated on different datasets giving insight into the epidemiology and evolution of a range of infectious diseases (e.g. HIV, HCV, influenza, Ebola). Applications of the methods to the field of macroevolution provide insight into the evolution and ecology of different species clades. Students will be trained in the algorithms and their application both on paper and in silico as part of the exercises. | |||||

Lecture notes | Lecture slides will be available on moodle. | |||||

Literature | The course is not based on any of the textbooks below, but they are excellent choices as accompanying material: * Yang, Z. 2006. Computational Molecular Evolution. * Felsenstein, J. 2004. Inferring Phylogenies. * Semple, C. & Steel, M. 2003. Phylogenetics. * Drummond, A. & Bouckaert, R. 2015. Bayesian evolutionary analysis with BEAST. | |||||

Prerequisites / Notice | Basic knowledge in linear algebra, analysis, and statistics will be helpful. Programming in R will be required for the project work (compulsory continuous performance assessments). We provide an R tutorial and help sessions during the first two weeks of class to learn the required skills. However, in case you do not have any previous experience with R, we strongly recommend to get familiar with R prior to the semester start. For the D-BSSE students, we highly recommend the voluntary course „Introduction to Programming“, which takes place at D-BSSE from Wednesday, September 12 to Friday, September 14, i.e. BEFORE the official semester starting date Link For the Zurich-based students without R experience, we recommend the R course Link, or working through the script provided as part of this R course. | |||||

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, 2010. B. Ingalls, Mathematical modeling in systems biology: an introduction. MIT Press, 2013 | |||||

636-0009-00L | Evolutionary Dynamics | W | 6 credits | 2V + 1U + 2A | 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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