Kurskatalog forskarutbildning - VT22

  • Ansökan kan ske mellan 2021-10-15 och 2021-11-15
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Titel Omics Data Analysis: From Quantitative Data to Biological Information
Kursnummer 3102
Program 1-Ingår i flera program
Språk Engelska
Antal högskolepoäng 3.0
Datum 2021-11-22 -- 2021-12-03
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 (genomics, transcriptomics, proteomics) and the omics data analysis workflow
* Understand the principle aspects of study design, experimental planning and sample selection
* Know how to do basic quality control of data by use of boxplots, principal component analysis (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 t-distributed stochastic neighbor embedding (t-SNE) / uniform manifold approximation and projection (UMAP)
* 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 quantitative Omics-data (e.g. proteomics, transcriptomics))
* 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/t-SNE/UMAP
* Introduction to GO 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.
For the final data analysis workshop students may be able to work on their own datasets, or datasets will be provided for them. The R statistical programming language will be used extensively in the course. Prior knowledge is not a requirement, but may prove useful.
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 types 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 16 - 24
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) start date of doctoral studies (priority given to earlier start date)
Övrig information This course has previously been given with number 2523. The course is given jointly by the doctoral programmes Allergy, immunology and inflammation (Aii), Tumor Biology and Oncology (FoTO), Biology of Infections and Global Health (BIGH) and Development and Regeneration (DEVREG). See: https://staff.ki.se/doctoral-programmes
Ytterligare kursledare
Senaste kursvärdering Kursvärderingsrapport
Kursansvarig Mattias Vesterlund
Institutionen för onkologi-patologi

Kontaktpersoner Ann-Sofi Sandberg
Institutionen för onkologi-patologi


Mattias Vesterlund
Institutionen för onkologi-patologi


Ghazaleh Assadi
Institutionen för onkologi-patologi