Integrative bioinformatics with data model enabled data analysis: test case industrial microorganisms

General info

Date from - to

01 Jan 2005 - 01 Nov 2009

Project leader(s)

Siezen, Roland J. Prof. dr.

Participant(s)

Smilde, Age Prof. dr.

Breit, Timo Dr.

Prof. dr. Jos B.T.M. Roerdink

Poolman, Bert Prof. dr.

Kuipers, Oscar P. Prof. dr.

Abstract

Microorganisms are widely used as cell factories. To improve these factories, generate new products or enhance their performance, these factories must be studied as an integrated system. In this project, we use '~omics' data for discovery and hypothesis generation in the area of life sciences research based on a microorganism test case. For this, a new strategy is needed to enable integration of heterogeneous models and data, as well as methods for the analysis and visualization of such heterogeneous data. The use of data and knowledge models for data annotation and integration forms the basis for a powerful, robust, and scalable integrative bioinformatics methodology.

Link to the end report of this project

Publications

• Interactive Visualization of Gene Regulatory Networks with Associated Gene Expression Time Series Data
• Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation
• Functional rather than topological properties explain gene co-regulation in metabolic networks
• Can we rely on operon predictions?
• A critical view of metabolic network adaptations
• MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
• A critical view of metbolic network adaptations
• A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data