Teaching

The URPP Evolution teaching efforts aim at allowing PhD students to become researchers with a comprehensive understanding of the fields of evolutionary biology, genomics, bioinformatics, population genetics, and ecology.

 

The following courses are organized and taught by the URPP Evolution bioinformaticians and / or members of the URPP Evolution:

Tutorials in Practical Bioinformatics

Biology is constantly making use of new technologies that allow the acquisition of genomic and expression data (i.e. genomes, transcriptomes, methylomes). The goal of the tutorials is to teach students the skills to process and analyze their own  sequencing data, as well as getting updates on the latest technologies and current genomic tools.

Examples of previous tutorials:

  • Data visualization with Python
  • Basic BAM file manipulations with Pysam
  • Productivity tools
  • Github and Jupyter notebooks

When: at irregular intervals - interested PhD (and master) students should send an email to get information about upcoming tutorials

Instructor: Gregor Rot

BIO 395 Concepts in Evolutionary Biology

Concepts in evolutionary biology are often used ambiguously, partly because the same terms may have different usage in other fields in biology. The course is designed for graduate students with interdisciplinary projects encompassing evolutionary biology and other disciplines, and provides lectures and simple calculation exercises in population and quantitative genetics.

BIO 395 in Course Catalogue UZH

When: Oct 25-26, 2021

Instructors: Kentaro Shimizu, Michael Krützen, Catalina Pimiento Hernandez, Anne Roulin, Wolf Blanckenhorn, Anna Lindholm, Simon Aeschbacher, Andrei Papkou

BIO 555 Scientific Writing for Evolutionary Biologists

All scientists have to write. Some love it, some hate it… This course provides tools and food for thought to enhance your writing and to overcome difficulties in the writing process. We will address the following topics:

• Publishing in Evolutionary Biology: how to write and communicate in the reviewing process

• Writing concise and attractive abstracts: how to structure and summarize complex topics

• Targeting your audience: how to adapt to your readers’ background and interests

• Getting ready to write: approaches to deal with procrastination and how to make use of your chronotype characteristics

The course will provide a cheerful setting to work on these topics, by means of exercises, guided group work, input talks, discussions and individual feedback.

BIO 555 in Course Catalogue UZH

When: Nov 19, 22

BIO 609 Introduction to UNIX/Linux and Bash Scripting

Practical computing skills are becoming essential in modern biology for data processing and analysis. The goal is to introduce the students to the Linux operating system and command-line tools taking a hands-on approach. Students will learn to write simple bash scripts.

This is a preparatory 1-day course for the courses BIO 610 and BIO 634.

BIO 609 in Course Catalogue UZH

When: April 20, 2021

Instructors: Carla Bello, Gregor Rot

 

BIO 610 Next-Generation Sequencing for Model and Non-Model Species

Handling of the huge data produced by next generation sequencers (NGS) requires us experimental knowledge and computational skills. The aim of this course is to familiarize the participants with experimental methods and data analysis about NGS. Topics will include: fundamental analysis of the sequence data, UNIX tools, and RNA-seq analysis.

BIO 610 in Course Catalogue UZH

When: April 21-22, 2021

Instructors: Kentaro Shimizu, Masaomi Hatakeyama, Sun Jianqiang, Jun Sese, Rie Shimizu Inatsugi, Shoji Tatsuma, Carla Bello, Gregor Rot

BIO 624 Human Genetic, Demographic and Cultural Diversity

Genetics studies have been extensively used in the past decades to elucidate human history and understand present patterns of diversity. The aim of this course is to review the major insights into human genetic history, in the context of our extensive cultural and ecological diversity. Topics will include: history of genetic studies, principles of population genetics, methods to detect selectionss, major findings concerning human genetic history, and relationships between genetic and cultural diversity.

BIO 624 in Course Catalogue UZH

When: probably again in HS2022

Instructors: Mark Stoneking (MPI for Evolutionary Anthropology, Leipzig), Chiara Barbieri, Kentaro Shimizu

BIO 634 Next-Generation Sequencing for Model and Non-Model Species 2: Transcriptomes, Variant Calling and Biological Interpretation

The aim of this course is to introduce students to the design and analysis principles of widely used NGS applications based on the course BIO 610. The focus of this follow-up course lies in SNP calling, transcriptome analysis and biological interpretation of gene lists. This course also provides hands-on computer training on the Linux/Unix command line and shell scripting.

BIO 634 in Course Catalogue UZH

When: June 3-4, 2021

Instructors: Carla Bello, Gregor Rot

BIO 692 Introduction to Genome-Wide Association Studies (GWAS)

In this course, we will discuss one of the main tools for identifying genes that underlie natural phenotypic variation: genome-wide association studies (GWAS). At the beginning of the course, we will provide an introduction to GWAS and a brief introduction to python. Then, we will discuss the history of gene mapping and the genetic and statistical background on which GWAS are based. The course has a strong practical component, and students will gain experience analyzing real data on the computer. At the end of the course, students will be able to interpret GWAS results and carry out their own analyses with their own data. We will also discuss basic concepts (and challenges) in population genetics, genomics, and quantitative genetics.

More information (PDF, 85 KB)

BIO 692 in Course Catalogue UZH

When: probably in FS2021

Instructors: Matthew Horton, Ümit Seren (Gregor Mendel Institute of Molecular Plant Sciences, Vienna)