For a BSc or MSc thesis project in our group, you can choose from one of the available research projects or research themes. There is no substitute for learning research than by doing research. So join our lab, and contact one of the responsible SSB staff members for their ideas on exciting thesis projects (both BSc and MSc), be it computational (dry) or experimental (wet). Check out the publications and different projects for topics that are currently being studied. Be aware that to start a thesis project you should already have gained sufficient background knowledge and that your study advisor has to sign for approval.
Our research focus is on deriving a deeper understanding of microbial systems by uncovering biological meaning from genome scale data and through multiscale data integration. All of our projects are in close collaborations with experimental partners. To answer biological questions we use a broad range of bioinformatics computational and statistical methods.
Contact person: dr. Peter Schaap, firstname.lastname@example.org
Improving CO2 Fixation: Modelling Synthetic Pathways
- Caco-2 specific miRNA-mRNA interaction network construction
- Consensus-based protein function prediction
- Greengenes: bioinformatics and modeling approaches for researching algal-bacterialsymbiosis
- Modelling metabolic changes induced by iron limitation in Staphilococcus Aureus
A main goal of the Laboratory of Systems and Synthetic Biology is to gain a systems understanding of industrially relevant micro organisms and to translate this knowledge tohigh-added value applications. Fungi form a class of relatively simple eukaryotic organisms that execute compartmentalized biological processes based on the same principles as inhigher eukaryotes. This makes fungi scientifically interesting objects to study basic principles of eukaryotic biological processes. We aim to develop fungal cell factories using genomics, synthetic biology and metabolic modeling approaches. Whenever necessary, we use Saccharomyces cerevisiae as a model system or host for the analysis of fungal processes by for example expressing Aspergillus niger genes in this yeast. Pseudomonas putida is another industrially relevant organism that we are making ready for a life as cell factory. We are developing methods to make easy re-programming of the lifestyle of P. putida towards production of bulk and specialty chemicals possible.
Contact person: dr. Rita Volkers, email@example.com
- Characterisation of genes in the thioredoxin system of Aspergillus niger N402 and its mutants
- Model driven re-programming of the Pseudomonas putida metabolic network in response to solvent stress
- Screening of alkane production in Pseudomonas putida
- Assesement of recombineering systems in Pseudomonas putida
- Characterizing promoters in Pseudomonas putida KT2440
Our research focus is on synthetic design of signalling networks and on the quantitative understanding of the regulation of developmental processes. Whereas we work largely theoretically, many of our projects are in close collaborations with an experimental partner. We use a broad range of methods, including analytical mathematical methods, statistical methods and computer simulations. Although individual projects often require a detailed understanding and the expansion/modification of the methods used, we always focus on the biological question.
Contact person: dr. Christian Fleck, firstname.lastname@example.org
Subject choice, planning, and thesis contract
Finding a suitable thesis project requires some groundwork. Start by reading the research themes and research projects pages. Identify research ideas that interest you. Next contact the contact person of the research project(s) of your choice, agree with your supervisor(s) on the research topic, the duration (i.e. credit points) and starting date. Optimally do all of this at least 3 months in advance. Upon agreement fill in the BSc or MSc thesis contract, obtain a copy of the BSc or MSc thesis evaluation form and send a copy of the signed thesis contract to your study advisor for approval and send in the undersigned filled-in thesis contract to the SSB secretary.
On your first day, visit the SSB secretary to:
- pick dates for a 20-min Colloquium
- arrange access to the building
- sign-off for having read the (VSNU) Netherlands Code of Conduct for Scientific Practice 2012, rules for appropriate storage of data, bio- and other research materials and rules on safety and other lab-rules as laid down in the short guide for employees and guests of the Laboratory.
Normally there are two intermediate evaluations: A 10-min introductory presentation of the project is given for the workgroup within 3 weeks. After approximately 1.5 months, the thesis-project will be evaluated with your supervisor.
The thesis project ends with handing in the report and giving a 20-min oral presentation. Writing the thesis report is an important part of the research project and you should reserve enough time for this activity. Three weeks before the final date, at least an outline of thesis should be ready. A draft version (digital word version) should be handed in to the supervisor for suggestion and comments before giving the final presentation. Grading will be done after your final examination, which normally will take place directly after your final presentation.
Once you have completed all the required activities and have handed in the final version of the thesis by E-mail as pdf file to the secretary the grade will be submitted.