NBIK14006U Principles in Genomic Studies

Volume 2015/2016
Education
MSc Programme in Biology
MSc Programme in Bioinformatics
Content

 

The goal of this course is to give students a thorough introduction to the types and applications of the different genomic tools available, including understanding their usability and limitations. We will introduce students to the concepts of genomic, metagenomic, and transcriptomic data acquisition and analyses, with an emphasis on organisms where little genomic data is available beforehand.

 

During the course the students will write an essay in the form of a grant proposal in which they formulate their own research question and describe an experimental study design using genomics to answer this question. The essay is part of the course assessment and will function as a starting point for discussion at the oral exam.

The course is directed at biology students who want to become familiar with the use of genomic data for hypothesis development and testing, and for bioinformatics and biochemistry students with an interest in applying their skills outside classic genomic model systems. Please note that this course will focus on the principles and concepts of genomic study design, not the exact analysis methods. For practical experience with the analysis of genomic data we recommend other courses, e.g. Biological Sequence Analysis or Bioinformatics of High Throughput Analysis.

Specific topics covered:

  • Sequencing technologies
  • Genome assembly
  • Genome annotation
  • Pathway reconstruction
  • Comparative genomics
  • RNA-seq
  • CHIP-seq
  • Methylomics
  • Metagenomics
  • Host-symbiont interactions
  • Evolutionary genomics
  • Ancient genomics
Learning Outcome

Knowledge:

By completing the course the student obtain knowledge of:

  • Different sequencing technologies (e.g. 454, Illumina) and their applications in different "omics"-type experiments (e.g. genomics, transcriptomics, methylomics and metagenomics).
  • The concepts of different analysis methods of data (e.g. assembly, annotation and expression analyses).
  • The broad range of research questions that can be addressed with these techniques, e.g. within ecology, evolution, symbiosis, development and behavior.

 

Skills:

By completing the course the student can:

  • explain the strengths and limitations of different sequencing technologies
  • explain the principles behind, and limitations of, different analysis methods
  • discuss and evaluate scientific literature that uses genomics-type methods
  • choose suitable genomics methods to address specific biological questions.

 

Competences:

By completing the course the student can:

  • formulate scientific hypotheses that can be investigated using genomic methods
  • independently design, plan, and present experimental setups using genomic methods
  • independently retrieve information to help formulate hypotheses and choose appropriate methods.

See Absalon.

We expect students to have a life science background roughly equivalent to the first two years of Biology or Biochemistry in the Bachelor program of Copenhagen University. Introductory courses in bioinformatics will be an asset, but are not required for successfully completing this course.
The course will entail ca. nine confrontation hours per week for seven weeks, and will primarily consist of lectures and seminars, but supplemented with computer exercises. In addition, the course will include guest lectures by specialists who use genomic tools to answer questions in ecology, organismal and evolutionary biology. In the theoretical seminars, the students will discuss and critically evaluate studies from the literature that utilize genomic data to address questions in a broad range of biological disciplines.
  • Category
  • Hours
  • Colloquia
  • 28
  • Exam Preparation
  • 30
  • Lectures
  • 17
  • Practical exercises
  • 6
  • Preparation
  • 75
  • Project work
  • 50
  • Total
  • 206
Credit
7,5 ECTS
Type of assessment
Written assignment
Oral examination, 25 min.
A short essay written as a grant proposal, in which students choose a biological system of their own interest (e.g. an organism, a symbiosis, a disease), present a hypothesis, and explain how genomic tools and data can be used to test the hypothesis. The essay will function as a starting point for discussion in a final 25-minute oral exam. 50:50 weight of the essay and oral exam.
The essay and the oral exam must be passed separately, and the essay and the exam must be passed in the same exam period.
Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners
Re-exam
One-week take-home assignment.
Criteria for exam assesment

In order to achieve the grade 12 the students gives an excellent performance displaying a high level of command of all aspects of the relevant material, with no or only a few minor weaknesses.