Scientific Visualization and Computer Graphics > CS > JBI > FWN > RUG

Gene regulatory network identification and visualization (2001-2005).

Funding:

This is part of a larger research program on Computational genomics of prokaryotes, funded by the Netherlands Organization for Scientific Research (NWO), Program on Biomolecular Informatics (BMI).

People:

  • PhD student Dinne Bosman (2001-2004)
  • PhD student Evert-Jan Blom (2002-2006)
  • Postdoc Dr. Patrick Ogao (2001-2005)

Collaboration

Project goal

development of bioinformatics tools for automatic and interactive visualization of "virtual cell" components/networks, providing a framework for direct visualization of transcriptome, proteome and metabolome data. For details, see the project summary.

Genomics pathway and network visualization (2001-2005).

Funding:

This project is part of the Biorange project funded by the Netherlands Bioinformatics Center (NBIC); see http://www.cs.rug.nl/~michel/biorange.

People:

Collaboration

Project goal

To visualize data and data models in different contexts, such as metabolic pathways and gene regulatory networks. The aim is to develop bioinformatics tools for automatic and interactive visualization of "virtual cell" components: the complete picture of metabolic pathways, signalling and information pathways, transport routes, replication machinery, protein (secretion) dynamics, etc.

Visualization of genome expression and regulatory network dynamics in a genomic and metabolic context. In: Visualization in Medicine Life Sciences, Linsen L., Hagen H., Hamann B., (Eds.), Visualization and Mathematics. Springer Verlag, Berlin, Germany, 2007, pp. 293--312.

The GENeVis program developed by Westenberg was elected second-best bioinformatics application during the Application Showcase contest of the national BioRange Meetings in 2007 and 2008.

Selected publications

  • Evert-Jan Blom, R. Breitling, K. J. Hofstede and J. B. T. M. Roerdink, and S. A. F. T. van Hijum and O. P. Kuipers (2008) Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics, 9:495, 2008.
  • Evert-Jan Blom, Sacha A. F. T. van Hijum, Klaas J. Hofstede, Remko Silvis, and Jos B. T. M. Roerdink and Oscar P. Kuipers (2008) DISCLOSE: DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites. BMC Bioinformatics, 9:535, 2008.
  • Michel A. Westenberg, Sacha A. F. T. van Hijum and Oscar P. Kuipers, and Jos B. T. M. Roerdink (2008) Visualizing Genome Expression and Regulatory Network Dynamics in Genomic and Metabolic Context. Computer Graphics Forum, 27(3):887894, 2008.
  • Michel A. Westenberg, Sacha A. F. T. van Hijum and Andrzej T. Lulko, Oscar P. Kuipers, and Jos B. T. M. Roerdink (2007) Interactive Visualization of Gene Regulatory Networks with Associated Gene Expression Time Series Data. In Visualization in Medicine Life Sciences, pages 293312. . Springer Verlag, 2007.
  • P.J. Ogao, M.P. Visser, and J.B.T.M. Roerdink (2007) Performance Metrics of a 3D Multiple Selection User Interface Tool in Virtual Environment. In Proc. 1st International Conference in Computer Science and ICT (COSCIT), 5-7th February, Nairobi, Kenya. Pages 8590, 2007.
  • Evert-Jan Blom, Dinne W. J. Bosman, Sacha A. F. T. van Hijum, Rainer Breitling, Lars Tijsma , Remko Silvis, Jos B. T. M. Roerdink, and Oscar P. Kuipers (2007) FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes. Bioinformatics, 23(9):11611163, 2007.
  • Diederik W. J. Bosman, Evert-Jan Blom, Ogao, Patrick J., Oscar P. Kuipers, and Jos B. T. M. Roerdink (2006) MOVE: A Multi-level Ontology-based Visualization and Exploration framework for genomic networks. In Silico Biology, 2006 http://www.bioinfo.de/isb/2006/07/0004