# Jörg Stelling: Catalogue data in Autumn Semester 2016

Name | Prof. Dr. Jörg Stelling |

Field | Computational Systems Biology |

Address | Comput. Systems Biology, Stelling ETH Zürich, D-BSSE, BSA N 800 Mattenstrasse 26 4058 Basel SWITZERLAND |

Telephone | +41 61 387 31 94 |

joerg.stelling@bsse.ethz.ch | |

Department | Biosystems Science and Engineering |

Relationship | Full Professor |

Number | Title | ECTS | Hours | Lecturers | |
---|---|---|---|---|---|

626-0002-AAL | BioinformaticsEnrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | 4 credits | 9R | J. Stelling, N. Beerenwinkel | |

Abstract | The course introduces concepts of bioinformatics starting from first principles: DNA sequence alignment, phylogenetic tree inference, genome annotation, protein structure and function prediction. Key methods and algorithms are covered, including dynamic programming, Markov and Hidden Markov models, and molecular dynamics simulations. Practical applications and limitations are discussed. | ||||

Objective | The course aims at introducing the fundamental concepts and methods of bioinformatics. Emphasis is given to a deep understanding of the methods' foundations and limitations to enable critical evaluations and applications of bioinformatics tools in areas such as biotechnology and systems biology. | ||||

Content | From "Understanding Bioinformatics": Chapter 4: Producing and Analyzing Sequence Alignments Chapter 5: Pairwise Sequence Alignment and Database Searching Chapter 6: Patterns, Profiles, and Multiple Alignments Chapter 7: Recovering Evolutionary History Chapter 8: Building Phylogenetic Trees Chapter 9: Revealing Genome Features Chapter 10: Gene Detection and Genome Annotation Chapter 11: Obtaining Secondary Structure from Sequence Chapter 12: Predicting Secondary Structures Chapter 13: Modeling Protein Structure Chapter 14: Analyzing Structure-Function Relationships From "Biological Sequence Analysis": Sections 3.1, 3.2, 3.3, 4.1, 4.2, 4.4, 5.2, 5.3, 5.4, 6.5 (Markov Chains and Hidden Markov Models) From "A First Course in Systems Biology": Chapter 1: Biological Systems | ||||

Lecture notes | Course material will be made available at: http://www.csb.ethz.ch | ||||

Literature | Zvelebil M, Baum JO. Understanding Bioinformatics. Garland Science, 2008. Durbin R, Eddy S, Krogh A, Mitchinson G. Biological Sequence Analysis. Cambridge University Press, 2004. Voit EO. A First Course in Systems Biology. Garland Science, 2012. | ||||

Prerequisites / Notice | There will be two opportunities for tutorials during the semester http://www.csb.ethz.ch/teaching | ||||

636-0007-00L | Computational Systems Biology | 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 | https://www.ethz.ch/content/specialinterest/bsse/computational-systems-biology/en/education/lectures/csb/LectureMaterial.html | ||||

Literature | U. Alon, An introduction to systems biology. Chapman & Hall / CRC, 2006. Z. Szallasi et al. (eds.), System modeling in cellular biology. MIT Press, 2006. | ||||

636-0301-00L | Current Topics in Biosystems Science and Engineering | 2 credits | 1S | T. Stadler, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, D. J. Müller, S. Panke, P. Pantazis, R. Paro, R. Platt, S. Reddy, T. Schroeder, J. Stelling | |

Abstract | This seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology. | ||||

Objective | To provide an overview of current systems biology research. | ||||

Content | The final list of topics will be available at http://www.bsse.ethz.ch/education/. | ||||

636-0507-00L | Synthetic Biology II | 4 credits | 4A | S. Panke, Y. Benenson, J. Stelling | |

Abstract | 7 months biological design project, during which the students are required to give presentations on advanced topics in synthetic biology (specifically genetic circuit design) and then select their own biological system to design. The system is subsequently modeled, analyzed, and experimentally implemented. Results are presented at an international student competition at the MIT (Cambridge). | ||||

Objective | The students are supposed to acquire a deep understanding of the process of biological design including model representation of a biological system, its thorough analysis, and the subsequent experimental implementation of the system and the related problems. | ||||

Content | Presentations on advanced synthetic biology topics (eg genetic circuit design, adaptation of systems dynamics, analytical concepts, large scale de novo DNA synthesis), project selection, modeling of selected biological system, design space exploration, sensitivity analysis, conversion into DNA sequence, (DNA synthesis external,) implementation and analysis of design, summary of results in form of scientific presentation and poster, presentation of results at the iGEM international student competition (www.igem.org). | ||||

Lecture notes | Handouts during course | ||||

Prerequisites / Notice | The final presentation of the project is typically at the MIT (Cambridge, US). Other competing schools include regularly Imperial College, Cambridge University, Harvard University, UC Berkeley, Princeton Universtiy, CalTech, etc. This project takes place between end of Spring Semester and beginning of Autumn Semester. Registration in April. Please note that the number of ECTS credits and the actual work load are disconnected. |