The spring semester 2021 will take place online until further notice. Exceptions: Courses that can only be carried out with on-site presence. Please note the information provided by the lecturers.

Mark Robinson: Catalogue data in Autumn Semester 2016

Name Prof. Dr. Mark Robinson
(Professor Universität Zürich (UZH))
Universität Zürich
Winterthurerstrasse 190
Inst. Molecular Life Sciences
8057 Zürich
Telephone044 635 48 48

401-5640-00LZüKoSt: Seminar on Applied Statistics Information 0 credits1KM. Kalisch, P. L. Bühlmann, R. Furrer, L. Held, T. Hothorn, M. H. Maathuis, M. Mächler, L. Meier, N. Meinshausen, M. Robinson, C. Strobl
AbstractAbout 5 talks on applied statistics.
ObjectiveSee how statistical methods are applied in practice.
ContentThere will be about 5 talks on how statistical methods are applied in practice.
Prerequisites / NoticeThis is no lecture. There is no exam and no credit points will be awarded. The current program can be found on the web:
Course language is English or German and may depend on the speaker.
401-6282-00LStatistical Analysis of High-Throughput Genomic and Transcriptomic Data (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: STA426

Mind the enrolment deadlines at UZH:
5 credits3GH. Rehrauer, M. Robinson
AbstractA range of topics will be covered, including basic molecular biology, genomics technologies and in particular, a wide range of statistical and computational methods that have been used in the analysis of DNA microarray and high throughput sequencing experiments.
Objective-Understand the fundamental "scientific process" in the field of Statistical Bioinformatics
-Be equipped with the skills/tools to preprocess genomic data (Unix, Bioconductor, mapping, etc.) and ensure reproducible research (Sweave)
-Have a general knowledge of the types of data and biological applications encountered with microarray and sequencing data
-Have the general knowledge of the range of statistical methods that get used with microarray and sequencing data
-Gain the ability to apply statistical methods/knowledge/software to a collaborative biological project
-Gain the ability to critical assess the statistical bioinformatics literature
-Write a coherent summary of a bioinformatics problem and its solution in statistical terms
ContentLectures will include: microarray preprocessing; normalization; exploratory data analysis techniques such as clustering, PCA and multidimensional scaling; Controlling error rates of statistical tests (FPR versus FDR versus FWER); limma (linear models for microarray analysis); mapping algorithms (for RNA/ChIP-seq); RNA-seq quantification; statistical analyses for differential count data; isoform switching; epigenomics data including DNA methylation; gene set analyses; classification
Lecture notesLecture notes, published manuscripts
Prerequisites / NoticePrerequisites: Basic knowlegde of the programming language R, sufficient knowledge in statistics

Former course title: Statistical Methods for the Analysis of Microarray and Short-Read Sequencing Data
551-1295-00LIntroduction to Bioinformatics: Concepts and Applications Information 6 credits4GW. Gruissem, K. Bärenfaller, A. Caflisch, G. Capitani, J. Fütterer, M. Robinson, A. Wagner
AbstractStorage, handling and analysis of large datasets have become essential in biological research. The course will introduce students to a number of applications of bioinformatics in biology. Freely accessible software tools and databases will be explained and explored in theory and praxis.
ObjectiveIntroduction to Bioinformatics I: Concepts and Applications (formerly Bioinformatics I) will provide students with the theoretical background of approaches to store and retrieve information from large databases. Concepts will be developed how DNA sequence information can be used to understand phylogentic relationships, how RNA sequence relates to structure, and how protein sequence information can be used for genome annotation and to predict protein folding and structure. Students will be introduced to quantitative methods for measuring gene expression and how this information can be used to model gene networks. Methods will be discussed to construct protein interaction maps and how this information can be used to simulate dynamic molecular networks.

In addition to the theoretical background, the students will develop hands-on experiences with the bioinformatics methods through guided exercises. The course provides students from different backgrounds with basic training in bioinformatics approaches that have impact on biological, chemical and physics experimentation. Bioinformatics approaches draw significant expertise from mathematics, statistics and computational science.

Although "Intoduction to Bioinformatics I" will focus on theory and praxis of bioinformatics approaches, the course provides an important foundation for the course "Introduction to Bioinformatics II: Fundamentals of computer science, modeling and algorithms" that will be offered in the following semester.
ContentBioinformatics I will cover the following topics:

From genes to databases and information
BLAST searches
Prediction of gene function and regulation
RNA structure prediction
Gene expression analysis using microarrays
Protein sequence and structure databases
WWW for bioinformatics
Protein sequence comparisons
Proteomics and de novo protein sequencing
Protein structure prediction
Cellular and protein interaction networks
Molecular dynamics simulation