Graduate School of health and Medical Sciences

Bioinformatics analysis of gene expression data
Provider: Faculty of Health and Medical Sciences

Activity no.: 3675-22-00-00
	Enrollment deadline: 03/01/2022

Date and time	24.01.2022, at: 09:00 - 10.02.2022, at: 14:00
Regular seats	15
Course fee	10,800.00 kr.
Lecturers	Stefan Seemann
ECTS credits	5.20

Contact person	Stefan Seemann E-mail address: sse@sund.ku.dk

Enrolment Handling/Course Organiser	PhD administration E-mail address: phdkursus@sund.ku.dk

Aim and content This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at graduate schools in the other Nordic countries. All other participants must pay the course fee. Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from Nordic countries. After the enrollment deadline, available seats will be allocated to applicants on the waiting list. Learning objectives A student who has met the objectives of the course will be able to: 1. Analyze RNA sequencing data by applying relevant bioinformatic tools 2. Assess the quality of sequence data 3. Assess the results of bioinformatic tools 4. Interpret the implications of a data analysis in broader context than the specific analyzed data 5. Apply the statistical software R for data manipulation and analysis Content Driven by the technological progress, biology continuously undergoes a revolution that started in the late 1990s with the sequencing of the human genome. This revolution is on a scale that constantly redefines our basic understanding of biology and reaches deep into human and animal science, for example with respect to diseases and nutrition. Understanding the opportunities that come with the technological development is crucial for strategy planning and experiment design. The course will introduce tools to analyze the high-throughput sequencing data generated from a selected range of technologies with high relevance for human and animal science. To this end, basic concepts of sequence alignment and genome analysis will be introduced with special focus on transcriptomics (e.g. gene expression and gene transcript variation). Furthermore, the functional context of genes will be addressed through the studies of biochemical pathways and networks, in which information from sequencing data will be employed to interpret the functional aspects of genes. Major software tools introduced and applied during the course are the web-based platform Galaxy for running data intensive bioinformatic analysis pipelines, the statistical software R for statistical computing, and Cytoscape for visualization and interpretation of biological networks. Participants Students should have a background in genetics or bioinformatics. The target group are students that are exposed to high-throughput sequencing data during their PhD study and want to learn how to analyse the data. A basic knowledge of statistics and previous experience with the software R are recommended. Relevance to graduate programmes The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH: Biostatistics and Bioinformatics Veterinary Clinical Sciences Molecular Mechanisms of Disease Language English Form The course combines theoretical lectures, tutorials, and student projects. Each participant will define a data analysis project based on their own PhD project and data or relevant publicly available sequencing data. Students with related data and/or scientific questions are encouraged to work together in small groups. Each participant will give an oral presentation of the project work at the last course day and deliver a short report after the course. Students are expected to work on their project during the course hours and six additional hours per week. Course director Ernst Stefan Seemann, Associate Professor, IVH, sse@sund.ku.dk Teachers Ernst Stefan Seemann, Associate Professor, IVH Jan Gorodkin, Professor, IVH Dates 24 January - 10 February 2022 (Mondays 9:00-12:00, Tuesdays 9:00-16:00, and Thursdays 9:00-14:00) Course location Department of Veterinary and Animal Sciences (IVH), Univ. of Copenhagen Registration Please register before 3 January 2021 Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrolment. Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

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