Course catalogue doctoral education - VT24

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Title Genomics for Biomedical scientist: Handle your gene expression data.
Course number 3062
Programme Cellbiologi och genetik
Language English
Credits 1.5
Date 2019-02-04 -- 2019-02-08
Responsible KI department Institutionen för mikrobiologi, tumör- och cellbiologi
Specific entry requirements
Purpose of the course The biomedical field has experienced a revolution thanks to the development of the massive parallel sequencing technologies. Now we can obtain the complete genetic information of a patient in a few days and with a limited cost. However, there is a gap between the application of classical molecular biology tools and the full use of the current genomic and computational approaches. The course will give students an introduction to genomics of gene regulation, with special emphasis on how genomic tools can be applied to the student's research. The students will be made aware of ethical aspects in relation to the technical progress.
Intended learning outcomes At the end of the course the student should be able to:
- Understand the crosstalk across the different levels of gene expression regulation, with special emphasis on chromatin organization, polymerase activity and RNA biology.
- Know the principles of high-throughput technologies applied to the study of gene expression, their advantages and limitations.
- Get a deeper understanding about chromatin states dynamics and gene regulation, and how deregulation of such states contributes to human diseases.
- Design genome-wide experiments for studying the transcriptome and chromatin state, and to critically evaluate results obtained with those approaches.
- Use common bioinformatics tools to analyze ChIP-Seq and RNA-Seq experiments.
- Make use of public available genome-wide databases and publications to complement their own research.
Contents of the course The course covers the use of genome-wide approaches for the study of gene expression regulation and how these approaches have become key for biomedical research.
Particular attention will be paid to the understanding of advantages and limitations of those approaches, and applications to the study of human disease. The course will include both lectures and hands-on data analysis session, and provide the students tools to successfully navigate through the jungle of public available genome-wide datasets.
Teaching and learning activities The learning activities used in the course include lectures, research seminars, group discussions, problem-based learning activities and research article presentations by the students. The students will be able to use gene expression data analysis software during the course. Students will present in learning groups a recent publication in form of a journal club as well as design and develop a research project in which they apply what they have learned into their own ongoing research. Students will also be encouraged to actively participate in the course. There will be substantial time for discussions after the lectures and research seminars.
Compulsory elements The seminars, lectures, group discussions and journal club presentations are compulsory. Absence cannot be compensated for.
Examination The students will be examined for all learning outcomes. The examination is based on:
- The student participation and discussions during the course.
- The performance during the bioinformatic hands-on sessions.
- The student individual presentations during the last day of the course.
Literature and other teaching material Literature will consist of recent research articles and bioinformatics vignettes.
Those documents will be provided to students as PDF files prior to the course start.
Students will be asked to complete an online tutorial in R and Unix that will be available in advance to the course.
Number of students 10 - 20
Selection of students Selection will be based on 1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) date for registration as a doctoral student (priority given to earlier registration date)
More information The course most likely takes place at the SciLifeLab in Solna (alternatively at the Biomedicum in Solna).
Additional course leader
Latest course evaluation Not available
Course responsible Vicente Pelechano Garcia
Institutionen för mikrobiologi, tumör- och cellbiologi
Contact person Vicente Pelechano Garcia
Institutionen för mikrobiologi, tumör- och cellbiologi

Claudia Kutter
Institutionen för mikrobiologi, tumör- och cellbiologi