Name | Prof. Dr. Niko Beerenwinkel |

Field | Computational Biology |

Address | Professur f. Computational Biology ETH Zürich, BSS G 57.2 Klingelbergstrasse 48 4056 Basel SWITZERLAND |

Telephone | +41 61 387 31 69 |

niko.beerenwinkel@bsse.ethz.ch | |

URL | http://www.bsse.ethz.ch/cbg/people/nikob |

Department | Biosystems Science and Engineering |

Relationship | Full Professor |

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

636-0101-00L | Systems Genomics | 4 credits | 3G | N. Beerenwinkel, C. Beisel, S. Reddy | |

Abstract | This lecture course is an introduction to Systems Genomics. It addresses how fundamental questions in biological systems are studied and how the resulting data is statistically analyzed in order to derive predictive mathematical models. The focus is on viewing biology from a genomic perspective, which requires high-throughput experimental methods (e.g., RNA-seq, genome-scale screening, single-cell | ||||

Learning objective | The goal of this course is to learn how a detailed quantitative description of genome biology can be employed for a better understanding of molecular and cellular processes and function. Students will learn fundamental questions driving the field of Systems Genomics. They will also be introduced to traditional and advanced state-of-the-art technologies (e.g., CRISPR-Cas9 screening, droplet-microfluidic sequencing, cellular genetic barcoding) that are used to obtain quantitative data in Systems Genomics. They will learn how to use these data to develop mathematical models and efficient statistical inference algorithms to recognize patterns, molecular interrelationships, and systems behavior. Finally, students will gain a perspective of how Systems Genomics can be used for applied biological sciences (e.g., drug discovery and screening, bio-production, cell line engineering, biomarker discovery, and diagnostics). | ||||

Content | Lectures in Systems Genomics will alternate between lectures on (i) biological questions, experimental technologies, and applications, and (ii) statistical data analysis and mathematical modeling. Selected complex biological systems and the respective experimental tools for a quantitative analysis will be presented. Some specific examples are the use of RNA-sequencing to do quantitative gene expression profiling, CRISPR-Cas9 genome scale screening to identify genes responsible for drug resistance, single-cell measurements to identify novel cellular phenotypes, and genetic barcoding of cells to dissect development and lineage differentiation. Main Topics: -- Next-generation sequencing -- Transcriptomics -- Biological network analysis -- Functional and perturbation genomics -- Single-cell biology and analysis -- Genomic profiling of the immune system -- Genomic profiling of cancer -- Evolutionary genomics -- Genome-wide association studies Selected genomics datasets will be analyzed by students in the tutorials using the statistical programming language R and dedicated Bioconductor packages. | ||||

Lecture notes | The PowerPoint presentations of the lectures as well as other course material relevant for an active participation will be made available online. | ||||

Literature | -- Do K-A, Qin ZS & Vannucci M (2013) Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data, Cambridge University Press -- Klipp E. et al (2009) Systems Biology, Wiley-Blackwell -- Alon U (2007) An Introduction to Systems Biology, Chapman & Hall -- Zvelebil M & Baum JO (2008) Understanding Bioinformatics, Garland Science | ||||

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

Learning 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/. | ||||

636-0702-00L | Statistical Models in Computational Biology | 6 credits | 2V + 1U + 2A | N. Beerenwinkel | |

Abstract | The 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. | ||||

Learning objective | The 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. | ||||

Content | Graphical 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. | ||||

Lecture notes | no | ||||

Literature | - 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 |