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BiGCAT – Department of Bioinformatics – Maastricht University

Contact Details

Maastricht University

Universiteitssingel 50 6229 ER Maastricht

Prof. Dr. C. Evelo

0031 43 38 81231 or 0031 43 38 81999

Hotel Description

The Department of Bioinformatics – BiGCaT at Maastricht University provides bioinformatics and systems biology tools and workflows for the integrated analysis of multi-omics data sets and the biological interpretation of the results. BiGCaT provides services in three focus points:
(i) pathway and network analysis, (ii) multi-omics data analysis workflows, and
(iii) semantic web approaches.
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• Pathway and network analysis:
Together with the Gladstone Institutes in San Francisco, BiGCaT focuses on the storage, creation and curation of biological pathway content on WikiPathways (www.wikipathways.org). In our stand-alone application PathVisio (www.pathvisio.org), the pathways from WikiPathways can be used in pathway analysis and visualization approaches. Furthermore BiGCaT provides a number of Cytoscape apps for data integration in network analysis.
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• Multi-omics data analysis workflows: BiGCaT’s web portal arrayanalysis.org (www.arrayanalysis.org) provides a number of data analysis modules, such as quality control, normalisation, statistical analysis and pathway analysis for different types of omics data. The modules can be combined in a workflow or used separately.
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Together with TNO and other partners, BiGCaT is involved in the Nutritional Phenotype data-sharing Infrastructure (dbNP/dbXP) that allows capturing of study design and storage and querying of multi-omics data.
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• Semantic web approaches: As part of Open PHACTS (www.openphacts.org/), BiGCaT is involved in the development of a web-based user interface for querying and viewing integrated semantic data within the Open PHACTS Discovery Platform. Identifier resolution is an important aspect of that for which we provide BridgeDB (www.bridgedb.org/) as modular installable software framework.

Bioinformatics
Public
  • Biomedical & health
  • Agri & Food
  • Study capturing
  • Omics data processing
  • Pathway and network analysis
  • Open data and semantic web approaches
  • BIoinformatics
  • Genomics
  • Nutrigenomics
  • Systems biology
  • Metabolomics
  • Cheminformatics

Expertise and Track Record

435000032 Joined forces in toxicogenomics: specialised bioinformatics to extend and automate diXa workflows for (hepato)toxicity prediction with dr. D.G.A.J. Hebels (UMC Maastricht)

We have a unique expertise in the integrative analysis and biological interpretation of omics data sets. We are very experienced in building and executing data analysis workflows, with a focus on the biologically centered interpretation of the results, and the dedicated application of bioinformatics and systems biology methods tuned to the research questions at hand. We also have ample experience in automating linking of data from other information sources, to be combined with the results of the experiment. Also, our group has a very strong background in working with open data/research/source approaches and the tools available to support this.

dbNP: tool for systematic capturing and annotation of studies and their data; ; main developer together with TNO and The Hyve (www.dbnp.org)
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ArrayAnalysis.org: tool for automated processing of transcriptomics and other omics data; main developer (www.arrayanalysis.org)
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WikiPathways: open repository for pathway curation and annotation; main developer together with Gladstone Insitutes (www.wikipathways.org)
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PathVisio: open source tool for pathway analysis; main developer together with Gladstone Insitutes (www.pathvisio.org)
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Cytoscape: tool for network analysis; we have contributed dedicated apps (e.g. CyTargetLinker; Wikipathways app) (apps.cytoscape.org)

Yes, this is a major focus of our department. [to be completed]

  • [to be completed]

Yes, we collaborate in several networks of this kind:
———–
Open PHACTS / ODEX: we participate in these projects developing and applying semantic web approaches for data interoperability.
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EuroDISH: here our role is in the identification of existing and required hard and soft research infrastructures for mechanical nutritional studies, and reporting on this to other ESFRI projects and the EU.
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eNanoMapper: we lead the work package on community outreach and are involved in the development of the ontology and use cases in the area of NanoQSAR.
———–
The Chemistry Development Kit – We are joint project leaders and contribute to the development and maintenance.
———–
National Resource for Network Biology (NRNB) – We participate in this programme together with several international groups developing tools for network biology.

Hotel Characteristics

  • postdoc: 1
  • technician: 0
  • lab manager: 1
  • biostatistician: 3
  • IT-specialist: 2

50/50

  • Computing cluster and servers of several types

No (but work with open science/source approaches and the Jenkins method for software development)

Yes, depending on the project e.g. in ArrayExpress (EBI), GEO (NCBI), dbNP, …