Autumn Semester 2020 takes place in a mixed form of online and classroom teaching.
Please read the published information on the individual courses carefully.

Renato Paro: Catalogue data in Autumn Semester 2018

Name Prof. Dr. Renato Paro
Professur für Biosysteme
ETH Zürich, BSA N 814
Mattenstr. 26
4058 Basel
Telephone+41 61 387 31 20
Fax+41 61 387 39 96
DepartmentBiosystems Science and Engineering
RelationshipProfessor Emeritus

636-0102-00LAdvanced Bioengineering4 credits3SS. Panke, Y. Benenson, P. S. Dittrich, M. Fussenegger, A. Hierlemann, M. H. Khammash, D. J. Müller, R. Paro, R. Platt, T. Schroeder
AbstractThis course provides an overview of modern concepts of bioengineering across different levels of complexity, from single molecules to systems, microscaled reactors to production environments, and across different fields of applications
ObjectiveStudents will be able to recognize major developments in bioengineering across different organisms and levels of complexity and be able to relate it to major technological and conceptual advances in the underlying sciences.
ContentMolecular and cellular engineering; Synthetic biology: Engineering strategies in biology; from single molecules to systems; downscaling bioengineering; Bioengineering in chemistry, pharmaceutical sciences, and diagnostics, personalized medicine.
Lecture notesHandouts during class
LiteratureWill be announced during the course
636-0202-00LLab Course: Next-Generation Sequencing Restricted registration - show details
Does not take place this semester.
Only for Biotechnology MSc, Programme Regulations 2017.

Attention: this lab course will be offered again in Spring semester 2019.
2 credits5PR. 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 Engineering
For doctoral students only.
Master's students cannot receive credits for the seminar.
2 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