Renato Paro: Catalogue data in Spring Semester 2019 |
| Name | Prof. em. Dr. Renato Paro |
| Field | Biosysteme |
| Address | Professur für Biophysik ETH Zürich, D-BSSE, BSA N 814 Mattenstrasse 26 4058 Basel SWITZERLAND |
| renato.paro@bsse.ethz.ch | |
| Department | Biosystems Science and Engineering |
| Relationship | Professor emeritus |
| Number | Title | ECTS | Hours | Lecturers | |
|---|---|---|---|---|---|
| 551-0140-00L | Epigenetics | 4 credits | 2V | A. Wutz, U. Grossniklaus, R. Paro, R. Santoro | |
| Abstract | Epigenetics studies the inheritance of traits that cannot be attributed to changes in the DNA sequence. The lecture will present an overview of different epigenetic phenomena and provide detailed insight into the underlying molecular mechanisms. The role of epigenetic processes in the development of cancer and other disorders will be discussed. | ||||
| Objective | The aim of the course is to gain an understanding of epigenetic mechanisms and their impact on the development of organisms, regenerative processes or manifestation of disease. | ||||
| Content | Topics - historical overview, concepts and comparison Genetics vs. Epigenetics - Biology of chromatin: structure and function, organization in the nucleus and the role of histone modifications in processes like transcription and replication - DNA methylation as an epigenetic modification - Inheritance of epigenetic modifications during cell division: cellular memory - Stability and reversibility of epigenetic modifications: cellular plasticity and stem cells - Genomic imprinting in plants and mammals - X chromosome inactivation and dosis compensation - position effects, paramutations and transvection - RNA-induced gene silencing - The role of epigenetic processes in cancer development or cell aging | ||||
| 636-0202-00L | Lab Course: Next-Generation Sequencing  Only for Biotechnology MSc, Programme Regulations 2017. | 2 credits | 5P | C. Beisel, R. Paro, S. Reddy | |
| Abstract | The Lab Course will take place Monday/Tuesday 9-17h, 10 days in total, start of this lab course is on Monday, September 25 2017. | ||||
| Objective | Students shall obtain a basic understanding in NGS and its application in transcription profiling including theoretical considerations when starting an RNA-seq experiment and the practical hands-on work of library preparation and usage of bioinformatics tools for data analysis. | ||||
| Content | Introduction to NGS technologies and applications. Design of an RNA-seq transcription profiling experiment. Specific treatment of cells (+/- signal-induction) and RNA extraction. Handling and quality control of RNA samples. Sequencing library preparation starting with total RNA. Quality control and quantification of the libraries. Setup of an NGS run and sequencing of the prepared RNA-seq libraries using the NextSeq 500 system. Analysis of the generated sequence data: sequence data QC, criteria for run performance and quality of data; pre-processing of the raw data; mapping sequence reads to a reference sequence; quantification of transcript abundance and differential gene expression. | ||||
| Lecture notes | Material will be provided during the course | ||||
| Literature | Sara Goodwin, John D. McPherson & W. Richard McCombie. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics 17, 333-351 (2016) Zhong Wang, Mark Gerstein & Michael Snyder. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10, 57-63 (January 2009) Fatih Ozsolak & Patrice M. Milos. RNA sequencing: advances, challenges and opportunities. Nature Reviews Genetics 12, 87-98 (February 2011) Ana Conesa, Pedro Madrigal, Sonia Tarazona et al. A survey of best practices for RNA-seq data analysis. Genome Biology 2016 17:13. | ||||
| 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. | ||||
| 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/. | ||||
| 636-1005-AAL | Bio V: Bioinformatics Enrolment 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. | 5 credits | 7R | R. Paro | |
| Abstract | |||||
| Objective | |||||
| Literature | Pevsner, Bioinformatics and Functional Genomics, chapters: 1 – 7 | ||||
| 636-1010-AAL | Bio Lab V: Molecular Biology III Enrolment 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. | 1 credit | 3R | R. Paro | |
| Abstract | |||||
| Objective | |||||
| Content | “-omics” analyses in eukaryotic cells (sample preparation for and analysis of omics data) | ||||