Inhaltspezifische Aktionen

Open thesis topics

Within our group we can offer various topics in the field of applied bioinformatics, high-throughput data analysis, genome and metagenome research as well as postgenomics and systems biology. Below you can find a list of suggested open topics for BSc and MSc theses and student projects. For further details on each topic or alternative projects please contact us.

  • Comparative genome analysis of Streptococcus agalactiae (GBS) from elephants (M.Sc.)

Background

Group B Streptococci are fairly common. In livestock, they are the causative agent of an udder inflamation, most often seen in dairy cows. 

In elephants, S. agalactiae is associated with Paronchya.
Under human care, elephants are known to reach a high age. This comes with an age-related decline in their immune system, which can lead usually harmless skin- or foot diseases to become chronic. Gaining a better knowledge about the bacterial infections is a vital foundation for optimized treatments and therapeutic approaches. 

In a newer study done by the "Hessische Landeslabor" (Hesse state labratory (LHL)), some S. agalactiae isolates were compared, using microbiological methods and had extensive biochemical profiles created. 
Noticable was the high number of isolates, for which the serotypes could not be determined. For this reason some isolates got sequenced, so a full comparative genome analysis could be done, using the latest methods in bioinformatics.

Thesis aims

  • Implementation of typical bioinformatic analyses (Assembly, mapping, annotation...)
  • Comparative analysis of GBS Isolates (ABR, pan- and coregenome, virulence factors...)
  • Closer inspection of Genes for serotyping

Prerequisites

  • Interested in solving biological/veterenary questions by usage of bioinformatics
  • Extensive knowledge of the Linux command line
  • Ability to work independently and methodical

Contact: Linda Fenske

 

 

  • Workflow Design (Nextflow) (M.Sc.)

Analysing (bacterial) sequence data for biological/medical questions means often repeating certain standard processes (QC, Assembly, Annotation etc.)

For better reproduceability and simplification of these processes, flexible pipelines with a wide palette of tools are used. Often Nextflow (of similar workflow tools) is used to enable support for a variety of enviroments or to simplify the installation.

With DSL2, Nextflow recently introduced a significant development of the Nextflow language, which promises a better scalability and modulariziation of pipelines, along with a better design of workflows.

Thesis aims

  • Revision and updating of an existing workflow for analysing bacerial data
  • Transmission of the workflow from nf-DSL1 to DSL2
  • Visualising the results (creating a GUI)

Prerequisites 

  • Extensive knowledge of the Linux command line
  • Knowledge of Nextflow or motivation to become acquainted with Nextflow
  • Programming knowledge in Python, Groovy (Nextflow) or similar
  • Knowledge and interest in visualisation and processing of data

Contact: Linda Fenske