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Course module: B-MBIEG06
B-MBIEG06
Bioinformatics and evolutionary genomics
Course infoSchedule
Course codeB-MBIEG06
ECTS Credits3
Category / LevelM (Master)
Course typeCourse
Language of instructionEnglish
Offered byFaculty of Science; Graduate School of Life Sciences; Graduate School of Life Sciences;
Contact personprof. dr. B. Snel
E-mailb.snel@uu.nl
Lecturers
Lecturer
prof. dr. B. Snel
Feedback and availability
Other courses by this lecturer
Contactperson for the course
prof. dr. B. Snel
Other courses by this lecturer
Teaching period
W19B  (13/05/2019 to 05/07/2019)
Teaching period in which the course begins
W19B
Time slot-: Not in use
Study mode
Full-time
RemarkDate course: March 11 - 22 2019. Send an e-mail to b.snel@uu.nl for enrollment.
Enrolment periodfrom 28/01/2019 up to and including 24/02/2019
Course application processstudentenbalie
Enrolling through OSIRISNo
Enrolment open to students taking subsidiary coursesNo
Pre-enrolmentNo
Waiting listNo
Course placement processStudiepunt/Student desk
Course goals
After completing the module the student:
 
  • Has knowledge on the evolution of protein interactions and pathways.
  • Is able to use online and local bioinformatic tools to collect homologs from relevant species and construct a phylogenetic gene tree
  • Is able to root and interpret phylogenetic tree of genes;timeduplications of genes relative to the species tree, define orthologs and paralogs within the gene treeits origin.
  • Is able to recognize horizontal gene transfer and endosymbiotic gene transfer in gene trees.
  • Is able for a given protein, find its homologs, annotate its protein domains,
  • Understands the compuational pipeline for large scale bioinformatics analysis in papers describing genome evolution
  • Has knowledge about the different large scale methods to create orthology databases such as COG, ENSEMBL COMPARA, PANTHER, ORTHOMCL, and is able to browse a selection of them.
  • Has knowledge on the computational piplelines that have been used to recognizing genome duplications and consequences of genome duplications. And knows where most important genome duplications have taken place in the history of life.
  • Is able to intepret analyis databases containing information on genome duplications and recognizing potential genomie duplication events in gene trees.
  • Has knowledge about the eukaryotic tree of life and eykaryogenesis.
  • Understands the importance of key genomes in infering molecular evolutionary events.
Content
Currently, molecular biology is generating information on the molecular properties of cells and organisms at an incredible pace. For example, we know the complete genome sequence of an enormous and rapidly increasing number of species. Not only do these high-throughput experiments generate a complete view of the genetic information of cells, other techniques measure the level of expression of all genes at the same time or measure all the interactions between all the proteins present in a cell. Bioinformatics is obviously needed for the storage and primary analysis of these huge volumes of biomolecular data. More interestingly, the data uniquely allows bioinformatics to make biological discoveries that were not possible until now. This course introduces the concepts and approaches required to make evolutionary biological discoveries in this genome-scale data and presents examples of interesting pieces of biology that have been discovered using bioinformatics. Topics to be discussed include genome evolution (as opposed to single genes), and the origins of the eukaryotic cell.
 
The following subjects are discussed in the course:
1. Sequence homology, Protein domains
2. Gene trees and orthology
3. Genome evolution: evolution of the presence of genes, evolution of gene order
4. Formalizations of gene function (e.g. Gene Ontology)
5. Introduction to high-throughput (HTP) techniques such as micro-array, ChIP-on-chip and yeast-2-hybrid
6. Use of these HTP data to study evolution of function
7. Origin of Eukaryotes, endo-symbiosis, explosion of gene duplicates
8. Genome Evolution: Genome duplications
Entry requirements
Prerequisite knowledge
Bachelor of science in the same field
Required materials
-
Recommended materials
Software
Putty (linux)
Instructional formats
Computer practical

Guest lecture

Lecture

Private-study

Tests
Final result
Test weight100
Minimum grade-

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