KJE-3604 Bioinformatics: Microbial genomics and metagenomics - 10 stp

Bioinformatics is a combination of biological science and information technology used in analyzing and deriving conclusions from large data sets. This course introduces the students to bacterial genomics and metagenomics. Genome-scale sequencing projects have led to an explosion of genetic information (gene sequences) available for analysis. The student will learn how these sequences can lead to a much fuller understanding of many biological processes.

The aim is to provide a theoretical introduction of the topics, tools and current trends in bacterial genomics and metagenomics, followed by practical exercises using the methodology on Next generation sequence data. Major topics will include:

• Genome sequencing: Quality control of sequence data, sequence assembly, assembly evaluation and functional annotation
• Comparative genomics: Contrasting multiple genome sequences and visualization of results
• Transcriptomics (RNA-sequencing): Identification of differential expressed genes
• Whole genome phylogenetic analysis: Reconstruction of phylogeny based on complete genome sequences
• Metagenome sequencing: Preprocessing of raw sequence data and preparation for downstream sequence analysis
• Taxonomic classification of metagenomes: Taxonomic profiling of bacterial communities and comparison of profiles from different communities

Applicants from Nordic countries: 1st of December for the spring semester.

Applicants from outside the Nordic countries: 1st of October for the spring semester

Required: A bachelor’s degree in chemistry or biotechnology or equivalent, with a grade C or better in the Norwegian grading system.

Recommended: KJE-2004 or equivalent.

The student will have acquired a solid and broad theoretical basis to understand bioinformatics. This means that the student

Knowledge

• has advanced knowledge in genomics and the analysis of this type of data including:
• quality control and assembly of sequence data
• evaluation of sequence assemblies
• functional annotation of DNA sequences
• RNA sequence analysis
• whole genome phylogeny
• taxonomic and functional profiling and binning of metagenomes
• has thorough knowledge of the scholarly or artistic theories and methods in the field
• can apply knowledge to new areas within the academic field
• can analyze academic problems on the basis of the history, traditions, distinctive character and place in society of the academic field

Skills

• can analyze and deal critically with various sources of information and use them to structure and formulate scholarly arguments
• can analyze existing theories, methods and interpretations in the of microbial genomics and metagenomics, and work independently on practical and theoretical problems
• can use relevant bioinformatical analysis methods for research and scholarly development work in an independent manner
• can carry out an independent, limited research or development project under supervision and in accordance with applicable norms for research ethics

Competence

• can analyze relevant academic, professional and research ethical problems
• can apply his/her knowledge and skills in new areas in order to carry out advanced assignments and projects
• can communicate extensive independent work and masters language and terminology used in the field of microbial genomics and metagenomics
• can communicate about academic issues, analyses and conclusions in the field of microbial genomics and metagenomics, both with specialists and the general public
• can contribute to new thinking and innovation processes

Evaluation of orally presented report. Pass/fail.

Work requirement: Minimum eight out of ten reports submitted in Canvas.

Students who fail the exam may register for re-sit the following semester.

The date for the exam can be changed. The final date will be announced at your faculty early in May and early in November.