NBIK11004U Genomic Approaches for Non-model Organisms

Volume 2013/2014
Content
The specific 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 limitations. We will introduce students to the concepts of genomic, metagenomic, and transcriptomic data acquisition and analyses, primarily during lectures and seminars, but supplemented with some computer exercises. In addition, the course will bring in guest lectures, who are specialists in their field and who use genomic tools to answer questions that are primarily driven by ecology, organisma, or evolutionary biology. In the theoretical seminars the students will present, discuss, and critically evaluate studies from the literature that incorporate genomic data to address questions in ecology, behaviour and evolutionary biology.
Learning Outcome
The increasing availability of genome data for non-model organisms creates new opportunities for research in ecology, behaviour and evolutionary biology. Such studies were previously restricted to sequencing single genes for phylogenetic reconstructions and to the use of neutral genetic markers for estimating genetic structure of populations. However, the application of second-generation genome sequencing technology means that non-model organisms will increasingly have sequenced genomes, allowing research that addresses the genetics of adaptations at unprecedented levels of detail. This will not only apply to individual study organisms, but also the communities of microbes that have important ecological functions and coevolutionary relationships with multicellular host organisms.
This course will identify and discuss the main applications of genomic data in ecology, behaviour and evolutionary biology, including various ways to identify single genes, genome annotation, pathway reconstruction, population genomics as natural extension of population genetics, community metagenomics, and the use of genomic data for the study of disease and symbiosis. By the end of the course, students will be able to critically evaluate the use and choice of genomic methods for hypothesis testing in biology.
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 model systems for which genomes were already sequenced many years ago.
 

Knowledge:

By completing the course the student can:

  • explain how genomic (and related) data can increase our understanding of research questions in diverse areas of biology such as ecology, behavior and evolutionary biology.
  • explain how different types of genomic data are obtained and how they can be analyzed.
  • describe and explain different types of experimental methods used in genomics.

 

Skills:

By completing the course the student can:

  • critically present and discuss in detail original scientific papers and reviews in ecology, behaviour and evolution that use genomic tools.
  • independently retrieve and organize information and data from the scientific literature in order to formulate scientific hypotheses that can be tested experimentally using genomic methods.

 

Competencies:

By completing the course the student can:

  • critically evaluate the use and choice of genomic methods for ecological, behavioural and evolutionary hypothesis testing.
  • formulate scientific hypotheses that can be tested experimentally using genomic methods.
  • independently design and plan scientific studies using genomic methods to solve biological questions.
Literature
See Absalon.
The course is open to masters students, and 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.
The course will entail ca. nine confrontation hours per week for seven weeks, with a combination of lectures, seminars, computer exercises, group discussions, and student presentations of original research papers.
Introductory courses in bioinformatics will be an asset, but are not required for successfully completing this course. The course will primarily focus on the principles and concepts of genomic studies. For practical analysis of genomic data other courses are available, e.g. Biological Sequence Analysis and Bioinformatics of high throughput analyses. The course is part of the qualification profiles: Ecology and Evolution and Microbiology. For all courses of the qualification profiles, see Course Portal for Department of Biology.
  • Category
  • Hours
  • Colloquia
  • 28
  • Exam
  • 30
  • Lectures
  • 17
  • Practical exercises
  • 6
  • Preparation
  • 75
  • Project work
  • 50
  • Total
  • 206
Credit
7,5 ECTS
Type of assessment
Written assignment
Oral examination
Successful completion of the course will require active participation during the course, including presentation and discussion of research papers. The final exam will be a short essay written as a grant proposal, in which students choose a biological system of their own interest (an organism, a symbiosis, a disease), present an evolutionary, behavioral or ecological hypothesis, and address how genomic tools/data can inform research to test the hypothesis. Developed hypotheses will be discussed in small groups of students, but the final grant proposal essay will be written and handed in by each student individually. 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.
Marking scale
7-point grading scale
Censorship form
External censorship
Re-exam
One-week take-home assignment in addition to the essay.
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.