Course catalogue doctoral education - VT22

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Title Bioinformatics analysis of gene regulation in omics data and its applications to medical problems
Course number 3027
Programme Cellbiologi och genetik
Language English
Credits 3.0
Notes The course meets the requirements for a general science course.

Date 2022-03-10 -- 2022-03-24
Responsible KI department Institutionen för biovetenskaper och näringslära
Specific entry requirements
Purpose of the course To increase the understanding of the basic principles of bioinformatics and to gain practical skills in bioinformatics analysis of genomic sequencing data.
Intended learning outcomes After the completed course, the participants will be able to understand the principles and perform basic bioinformatics analysis of genomics sequencing data. The participants will be able to plan experimental designs and to critically evaluate the appropriateness of the different sequencing based omics methods and technologies for genome-wide gene regulation studies.
Contents of the course Principles of gene regulation in non-disease cases and dysregulation in diseases at individual locus level as well as on genome-wide level. Principles of sequencing based genomics technologies and corresponding bioinformatics data analysis. Concrete bioinformatics data analysis by the students of selected published projects.
Teaching and learning activities The course consists of preparatory work, lectures, discussion, seminars and hands-on bioinformatics analysis.
Compulsory elements The preparation is done in the first course week without the need to be present on-site. Week 2 consists of tasks, lectures, discussions, seminars and hands-on practicals. Both parts are compulsory. Absence has to be compensated for according to the instructions from the course leader.
Examination The students will be examined for all learning outcomes by their performance in (a) submitted replies to tasks given for course week 1, (b) discussions and quizzes during the course week 2, and (c) individual presentations at the last course day of their bioinformatics analysis results conducted during course week 2.
Literature and other teaching material Recent articles and websites.
Number of students 20 - 30
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) start date of doctoral studies (priority given to earlier start date).
More information The first week of the course (2022-03-10 to 2022-03-16) is in the form of individual homework assignments (distance course), as preparation for the second week of the course. Week 2 of the course (2022-03-17 to 2020-03-24) consists of tasks, lectures, discussions, and seminars in the mornings. In the afternoons, course participants will conduct data analysis in small groups under guidance of a tutor to redo key figures of selected published papers. The statistical language R will be used for the hands-on practical. It is recommended that participants have previous experiences with R.

The course is given in collaboration with the RIKEN Center for Integrated Medical Sciences (RIKEN IMS, http://www.ims.riken.jp/english/). The course faculty consists of invited speakers from the RIKEN IMS and from Karolinska Institutet. The course Week 2 takes places at RIKEN Yokohama in Japan. Course participants would travel to Japan and arrive in Japan latest 2022-03-16. Departure from Japan would be earliest 2022-03-25.

The traveling and accommodation costs for Swedish students will not be covered by the course. Financial support for some participants (KI doctoral students/KI post docs) might be available but depends on the outcome of ongoing funding applications. Please state clearly in your course application if you are also applying for travel and accommodation support. Give detailed motivation why you would need the financial support to be able to attend the course. The relevance of your motivation will be the basis to selected the funded course applicants. The recipients of this support will be selected by the course directors based on their motivation presented in their course participation application. Also, the financial support will not be shared equally over all applicants but an amount of approx. 10,000 SEK will be given to the selected participants.
Additional course leader The course director is Dr. Carsten Daub from Karolinska Institutet and the co-director is Dr. Piero Carninci from RIKEN IMS.
Latest course evaluation Course evaluation report
Course responsible Carsten Daub
Institutionen för biovetenskaper och näringslära

Carsten.Daub@ki.se
Contact person Matti Nikkola
Institutionen för cell- och molekylärbiologi

Matti.Nikkola@ki.se