Bioinformatics

The Bioinformatics group focuses on fundamental and applied bioinformatics research in the green life sciences. We develop and apply novel computational methods for the analysis and integration of –omics data. We teach bioinformatics and data analysis to students at the bachelor, master and PhD levels.

Our courses

The Bioinformatics Group offers several courses and thesis projects.

More courses Thesis projects

Genetic variation in tomato

The analysis of genetic variation in 84 tomato accessions was published in the plant journal. It is available here.

Scaffold rearrangement in the tomato genome

Scaffolds in v2.40 of the tomato genome could be rearranged based on FISH data and optical mapping. The work is now published in G3. The changes resulted in a new release of the tomato genome, v2.50.

Algorithms in Bioinformatics

In period 6 we taught the first edition of the course "Algorithms in Bioinformatics". Seven MSc students took up the challenge.

Mobile promoters

Harm Nijveen has worked with Mark van Passel and Lindi Wahl on the discovery of mobile promoter regions in prokaryotic genomes, a potential new class of mobile elements. A paper describing their finding was recently published in the Genetics journal.

Protein classification

A paper by Bastiaan van den Berg describing a user-friendly, generic sequence-based protein classification web tool (SPiCE) was published in BMC Bioinformatics. It is available at http://helix.ewi.tudelft.nl/spice.

Comparing Brassica genomes

Ke Lin has published a paper in BMC Genomics on collaborative work with Guusje Bonnema (Plant Breeding) comparing three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. The question he tries to answer is what genetic variations drive the extreme diversity in the forms these plants take.

Dr. Judith Risse

Judith Risse sucessfully defended her PhD thesis "Text mining for metabolic reaction extraction from scientific literature" on Monday April 7. Congratulations, dr. Risse!

MSc thesis Heleen de Weerd

Heleen de Weerd successfully defended her MSc thesis, entitled "Families of paralogous non-coding elements in plant species" on March 25, 2014.

MSc thesis Martijn Derks

On March 18, 2014, Martijn successfully defended his MSc thesis, entitled "The winter moth (Operophtera brumata) genome provides insight in Lepidopteran evolution".

Dr. Harm Nijveen

On December 5th 2013 Harm Nijveen successfully defended his PhD thesis, entitled "Applications in Computer-Assisted Biology".