The Master Bioinformatics is a research thesis-oriented program. Below you will find some example thesis’s.
Title: Genome annotation of NLT region of Zebra fish chromosome 1 and part of Fugu genome encoding novel receptors belonging to the innate and adaptive immunity.
- Objectives: To find the region on chromosome 1 of Zebra fish and the Fugu genome encoding novel receptors belonging to the innate immunity and to determine whether recently identified novel class I major histocompatibility genes are located in syntenic regions on the zebra fish and puffer fish genomes.
- Methods used: Database mining, profile hidden Markov models (hmm), Race amplication, Synteny – comparative genomics.
- Remark: This thesis work included some wet-bench experiments.
Title: PlantEST A plant EST, contig and SNP database.
- Objectives: To construct and evaluate a relational database system for plant EST, contig and polymorphism data. To allow fast and flexible access to plant EST data, to refine the annotation of EST data and to prove the functionality of the developed data structure in EST processing.
- Methods used: Use of ontologies, database design and setup using PostgreSQL and Python. Building of parsers and (web)interfaces.
- Remark: Thesis was performed in close cooperation with KeyGene a Dutch research company with a strong focus on molecular genetics and biotechnology for the plant breeding industry.
Title: Application of text mining to Toxicogenomics.
- Objectives: To find relations between genes and pathology via literature mining and use this knowledge to see whether it is possible to uncover toxic effects in microarray experiments
- Methods used: Building of a gene-pathology database, tools for Medline extraction, tools for keyword search using ontologies and tools to find orthologs between human mouse and rat. Building of scoring schemes and query web interface applications.
- Remark: This thesis work was performed at Organon. Organon is a global leader in the creation of innovative prescription medicines for gynecology, fertility, neuroscience and anesthesia.