Berend Snijder: Catalogue data in Autumn Semester 2019

Name	Prof. Dr. Berend Snijder
Field	Molecular Systems Biology
Address	Inst. f. Molekulare Systembiologie ETH Zürich, HPM H 44 Otto-Stern-Weg 3 8093 Zürich SWITZERLAND
Telephone	+41 44 633 71 49
E-mail	snijder@imsb.biol.ethz.ch
URL	http://www.snijderlab.org
Department	Biology
Relationship	Assistant Professor

Number	Title	ECTS	Hours	Lecturers
551-1299-00L	Introduction to Bioinformatics	6 credits	4G	S. Sunagawa, M. Gstaiger, A. Kahles, G. Rätsch, B. Snijder, E. Vayena, C. von Mering, N. Zamboni
Abstract	This course introduces principle concepts, the state-of-the-art and methods used in some major fields of Bioinformatics. Topics include: genomics, metagenomics, network bioinformatics, and imaging. Lectures are accompanied by practical exercises that involve the use of common bioinformatic methods and basic programming.
Learning objective	The course will provide students with theoretical background in the area of genomics, metagenomics, network bioinformatics and imaging. In addition, students will acquire basic skills in applying modern methods that are used in these sub-disciplines of Bioinformatics. Students will be able to access and analyse DNA sequence information, construct and interpret networks that emerge though interactions of e.g. genes/proteins, and extract information based on computer-assisted image data analysis. Students will also be able to assess the ethical implications of access to and generation of new and large amounts of information as they relate to the identifiability of a person and the ownership of data.
Content	Ethics: Case studies to learn about applying ethical principles in human genomics research Genomics: Genetic variant calling Analysis and critical evaluation of genome wide association studies Metagenomics: Reconstruction of microbial genomes Microbial community compositional analysis Quantitative metagenomics Network bioinformatics: Inference of molecular networks Use of networks for interpretation of (gen)omics data Imaging: High throughput single cell imaging Image segmentation Automatic analysis of drug effects on single cell suspension (chemotyping)
Prerequisites / Notice	Course participants have already acquired basic programming skills in Python and R. Students will bring and work on their own laptop computers, preferentially running the latest versions of Windows or MacOSX.
551-1303-00L	Cellular Biochemistry of Health and Disease Number of participants limited to 20.	4 credits	2S	V. Korkhov, Y. Barral, J. Fernandes de Matos, T. Ishikawa, R. Kroschewski, M. Peter, P. Picotti, A. E. Smith, B. Snijder, K. Weis
Abstract	During this Masters level seminar style course, students will explore current research topics in cellular biochemistry focused on the structure, function and regulation of selected cell components, and the consequences of dysregulation for pathologies.
Learning objective	Students will work with experts toward a critical analysis of cutting-edge research in the domain of cellular biochemistry, with emphasis on normal cellular processes and the consequences of their dysregulation. At the end of the course, students will be able to introduce, present, evaluate, critically discuss and write about recent scientific articles in the research area of cellular biochemistry.
Content	Guided by an expert in the field, students will engage in classical round-table style discussions of current literature with occasional frontal presentations. Students will alternate as discussion leaders throughout the semester, with the student leader responsible to briefly summarize key general knowledge and context of the assigned primary research paper. Together with the faculty expert, all students will participate in discussion of the primary paper, including the foundation of the biological question, specific questions addressed, key methods, key results, remaining gaps and research implications.
Literature	The literature will be provided during the course
Prerequisites / Notice	The course will be taught in English.
551-1415-00L	Image-based Drug Screening in Human Blood for Personalized Medicine Number of participants limited to 5. The enrolment is done by the D-BIOL study administration.	6 credits	7G	B. Snijder, further lecturers
Abstract	Image based screening allows to measure in high throughput the phenotype of millions of individual cells to external perturbations. We have recently shown that image-based screening in human blood can help to find active treatments for patients with blood cancers. In this course we will take the students through the entire workflow (to the extent that biosafety regulations allow it).
Learning objective	Take the students through the entire workflow from experimental design, to screen, to imaging and analysis. -Learn to design an image-based screening experiment -Observe human blood sample handling -Perform immunofluorescence & automated confocal microscopy -Image analysis and result interpretation -Result presentation
Literature	-Relevant study: https://www.thelancet.com/journals/lanhae/article/PIIS2352-3026(17)30208-9/fulltext -Editorial commentary: https://www.thelancet.com/journals/lanhae/article/PIIS2352-3026(17)30213-2/fulltext