Kurskatalog forskarutbildning - VT19

  • Ansökan kan ske mellan 2018-10-15 och 2018-11-15
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Titel Omics data analysis: From quantitative data to biological information
Kursnummer 2523
Program 1-Ingår i flera program
Språk Engelska
Antal högskolepoäng 3.0
Datum 2018-11-05 -- 2018-11-16
Kursansvarig institution Institutionen för onkologi-patologi
Särskild behörighet
Kursens syfte During recent years omics data has become an integral part of many biomedical and clinical research projects. This broad introductory course aims at bridging the gap between classical biomedical research, omics technologies and bioinformatics. The course will give students an introduction to omics technologies and basic knowledge of omics data analysis workflows.
Kursens lärandemål After completed course, the student will be able to:
* Understand the principles and perform the basics of high-throughtput technologies and the omics data analysis workflow (genomics, transcriptomics, proteomics,)
* Understand the principles aspects of study design, experimental planning and sample selection
* Know how to do basic quality control of data by use of boxplots, PCA etc
* Know what normalization, data transformation etc means and what it does to your data
* Know the principles of some basic statistics such as t-test and false discovery rate
* Know the principles of dimensionality reduction methods such as PCA and tSNE
* Use tools for hierarchical clustering, functional enrichment and pathway analysis
* Use tools for gene ontology (GO) annotation/enrichment
Kursens innehåll * The omics data analysis workflow: from quantitative data to biological information (emphasis on analysis of genomics, transcriptomics, and proteomics data) * Introduction to omics technologies and data structures * Omics experimental design and sample selection * Introduction to data transformation and normalisation * Introduction to basic statistics in omics data analysis: significance test/p-values/multiple testing correction/false discovery rate * Introduction to dimensionality reduction PCA/MDS/tSNE * Introduction to Gene Ontology and enrichment analysis * Introduction to correlation analysis and hierarchical clustering * Introduction to network and pathway analysis * Introduction to online bioinformatics resources and analysis tools * Introduction to the R statistical programming language * Literature study with a critical view on how omics data is analyzed in clinical research. * Current state of the art in omics data analysis is highlighted through case studies, literature studies and demonstrations
Arbetsformer The teaching activities for the course will be based on lectures, workshops and data analysis cases. The students will participate in a literature study with discussions in seminar groups as well as an independent data analysis exam project. The students will also be able to download and use some of the software in workshops during the course.
Obligatoriska moment * Attendance on lectures and data analysis demonstrations. * Attendance to literature study discussion seminar. * Attendance to examination seminar and hand in the written examination assignments. * Extra written literature study can be used to compensate absence.
Examination The course assessment is based on two type of assignments: a literature study with a critical view on an omics data analysis subject performed in groups and an individual written omics data analysis project illustrating the different topics covered during the course.
Kurslitteratur och övriga läromedel Literature will consist of recent original and review articles and will be provided to students as PDF files.
Antal studenter 15 - 25
Urval av studenter 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.
Övrig information Lectures will be given at Widerströmska huset, Tomtebodavägen 18a, Solna and at SciLifeLab, Tomtebodavägen 23a, Solna. Schedule and additional information will be uploaded at the course web site closer to course start. Course website: https://pingpong.ki.se/public/courseId/12933/lang-sv/publicPage.do?item=11900112.
The course is jointly organised by the doctoral programmes Allergy, immunology and inflammation (Aii), Biology of Infections and Global Health (BIGH), Development and Regeneration (DevReg) and Tumor biology and oncology (FoTO). See: https://ki.se/en/staff/doctoral-programmes.
Ytterligare kursledare This course has two course responsibles, Lukas Orre and Mattias Vesterlund.
Tidigare omdöme av kursen omdöme
Kursansvarig Lukas Orre
Institutionen för onkologi-patologi

Kontaktpersoner Lukas Orre
Institutionen för onkologi-patologi


Mattias Vesterlund
Institutionen för onkologi-patologi