JoinLab2.jpg

Student projects


 

We warmly welcome students wishing to pursue a Bachelor or Master thesis project, as well as student projects and student assistantships. We offer a wide variety of topics and methods with a focus on the interface between theoretical and experimental biology. Find out more about current projects and join us! Open student projects are listed below, when available. If there are no offers listed, please feel free to send a research proposal.

 

  • Currently open projects:

  • Database for Cell Lines and Experiments in Cancer Research

    Possible as

    Studienprojekt - 3 months, Bachelor - 3 months, Projektmodul - 6 months, Master - 6 months

    Contact

    Maria Dost

     

    Introduction

    Cancer research utilizes cell lines with a known mutation profile like HeLa. These cell lines are often cultivated for many generations and subjected to laboratory specific conditions and experiments and thus might show different phenotypes in quasi identical experiments.

    Throughout the generations these cell lines might also develop new mutations that influence the cells' behavior.

    We are currently designing a database to assess the quality of published data and state of the art experiment documentation. The aim of this assessment is to improve comparability and accessibility of data.

    The basic database structure and interface has been established, but still needs adjustments and testing. We are looking for students to insert publication data into the database and help us improve the database structure. The data entered into the database should then be analyzed and evaluated regarding the quality of the experimental data and the consistency of the results and conclusions.

     

    Topics and Keywords

    Database, Meta-Analysis, Cell Lines

     

    Tasks and Milestones

    1. Evaluating published data by reading publications

    2. Filtering important information

    3. Entering information in the database

    4. Finding errors and “construction sites” within our database structure

    5. Analysing data

    6. Thesis/report writing



    Literature

    https://www.quackit.com/database/tutorial/what_is_a_database.cfm

    As examples of publications we want to put in the database:

    Zhang, Qi, et al. "Bromodomain containing protein represses the Ras/Raf/MEK/ERK pathway to attenuate human hepatoma cell proliferation during HCV infection." Cancer letters 371.1 (2016): 107-116.

    Shields, Janiel M., et al. "Understanding Ras:‘it ain’t over’til it’s over’." Trends in cell biology 10.4 (2000): 147-154.

    Dhawan, Neil S., Alex P. Scopton, and Arvin C. Dar. "Small molecule stabilization of the KSR inactive state antagonizes oncogenic Ras signalling." Nature 537.7618 (2016): 112.

     

     

  • Extending and parameterizing an existing single cell volume model to allow for multiple cell cycles.

    Possible as

    Studienprojekt - 3 months, Bachelor - 3 months, Projektmodul - 6 months, Master - 6 months

    Contact

    Björn Goldenbogen

     

    Introduction

    Single cell growth is subject to current research. Of particular interest is  the volume development of the asymmetric dividing fungus Saccharomyces cerevisae. After birth the spherical single cells expand in size and form smaller buds which separate from the mother cell after cytokinesis. Based on first principles, we already formulated a model to describe the combined growth of the mother cell and its bud. We are now searching for a student to extend the current  model to reflect the separation of both compartments and to cover multiple cell cycles, including several budding events. The model is implemented in the human readable and systems biology markup language (SBML) related modeling language Antimony (L. P. Smith et al., 2009) and simulated with the tellurium package for Python. For parameterization of the extended model a comprehensive data set of single cell volume trajectories is available.

     

    Topics and Keywords

    S.cerevisiae, single cell growth, mathematical modelling, Python

     

    Tasks and Milestones

    1.  Understand the current model

    2. Integrate the termination of the first cell cycle

    3. Allow for consecutive cell cycles

    4. Parameterize the model  with experimental data

    5. Thesis/report writing



    Literature

    Smith LP, Bergmann FT, Chandran D, Sauro HM. Antimony: a modular model definition language. Bioinformatics. 2009;25(18):2452-4.

    Garmendia-Torres C, Tassy O, Matifas A, Molina N, Charvin G. Multiple inputs ensure yeast cell size homeostasis during cell cycle progression. Elife. 2018;7:e34025. Published 2018 Jul 4. doi:10.7554/eLife.34025

    Burgert I., Fratzl P. (2006) Mechanics of the Expanding Cell Wall. In: Verbelen JP., Vissenberg K. (eds) The Expanding Cell. Plant Cell Monographs, vol 6. Springer, Berlin, Heidelberg

    Tellurium Package: http://tellurium.analogmachine.org/

     

  • 1