Renato Paro: Catalogue data in Spring Semester 2019

Name Prof. em. Dr. Renato Paro
Professur für Biophysik
ETH Zürich, D-BSSE, BSA N 814
Mattenstrasse 26
4058 Basel
DepartmentBiosystems Science and Engineering
RelationshipProfessor emeritus

551-0140-00LEpigenetics4 credits2VA. Wutz, U. Grossniklaus, R. Paro, R. Santoro
AbstractEpigenetics 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.
ObjectiveThe 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.
- 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
636-0202-00LLab Course: Next-Generation Sequencing Restricted registration - show details
Only for Biotechnology MSc, Programme Regulations 2017.
2 credits5PC. Beisel, R. Paro, S. Reddy
AbstractThe Lab Course will take place Monday/Tuesday 9-17h, 10 days in total, start of this lab course is on Monday, September 25 2017.
ObjectiveStudents 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.
ContentIntroduction 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 notesMaterial will be provided during the course
LiteratureSara 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.
636-0301-00LCurrent Topics in Biosystems Science and Engineering2 credits1SR. 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
AbstractThis seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology.
ObjectiveTo provide an overview of current systems biology research.
ContentThe final list of topics will be available at
636-1005-AALBio 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 credits7RR. Paro
LiteraturePevsner, Bioinformatics and Functional Genomics, chapters: 1 – 7
636-1010-AALBio 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 credit3RR. Paro
Content“-omics” analyses in eukaryotic cells (sample preparation for and analysis of omics data)