CMBI - Centre for Molecular and Biomolecular Informatics

1. CMBI - Centre for Molecular and Biomolecular Informatics • Dutch national centre for computational molecular sciences research • Research groups • Comparative Genomics & Systems Biology (Huynen) • Bacterial Genomics (Siezen) • Computational Drug Design (De Vlieg) • Bioinformatics of Macromolecular Structures (Vriend) • Training & Education • BSc, MSc, PhD and PostDocprogrammes • International workshops • Hotel Bioinformatica • High school courses • Computational facilities, databases, and software packages via (inter-)national service platforms (NBIC, EBI, etc) • NBIC: National BioInformatics Centre. Bioinformatics @CMBI

2. Computational Drug Discovery (CDD) Group • Head: Prof. Jacob de Vlieg • Key Research Fields • Structural bioinformatics for drug design • Bioinformatics for genomics (microarray analysis, text mining, etc) • Translational medicine informatics CDD Applications Exciting real life problems ‘wet’ validation Academic Research New scientific approaches Training & education Bridging academic research and applied genomics Bioinformatics @CMBI

3. lactococcus listeria Bacterial Genomics Group • Head: Prof Roland Siezen • Research interest: Biological questions in the interest of Dutch Food Industry • How can we improve: • fermentation • safety • health • Micro-organisms studied: Gram-positive food bacteria: • lactic acid bacteria (Lactococcus, Lactobacillus) • spoilage bacteria (Listeria, Clostridium, Bacillus cereus) Bioinformatics @CMBI

4. Comparative Genomics Group • Head: Prof. MartijnHuynen • Research Focus: • How do the proteins encoded in genomes interact with each other to produce cells and phenotypes ? • To predict such functional interactions between proteins as there exist e.g. in metabolic pathways, signalling pathways or protein complexes Which genes do twogenomes share (and which genes do theynot share) and can we relate thistotheirphenotype? Comparativegenomics Prediction of protein function, pathways Bioinformatics @CMBI

5. Bioinformatics of macromolecular structures • Head: Prof. GertVriend • Research Focus: Understanding proteins (and their environment) • Proteins are the core of life, they do all the work, and they give you feelings, contact with the outside world, etc. • Topics: • Homology modeling technology and applications • Protein engineering • Application of bioinformatics in medical research (HankaVenselaar) • Structure validation and structure determination improvement • Molecular class specific information systems (e.g. GPCRDB & NucleaRDB) • Data mining • WHAT IF molecular modelling and visualization software Bioinformatics @CMBI

6. Homology Modeling The three mutated residues are all important for the correct positioning of Tyrosine 111 Tyrosine 111 is important for substrate binding Ahmed et al., Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans. Nat Genet. 2008 Nov;40(11):1335-40. Interested? Contact HankaVenselaar (h.venselaar@cmbi.ru.nl)Project HOPE: Have yOur Protein Explained Bioinformatics @CMBI

7. Human genome, great expectations Data ≠Knowledge, insight !!! Bioinformatics