Bioinformatics

Who we are

At the Radboudumc Technology Center Bioinformatics we believe that computational biology and big data solutions are key in shaping the data-driven healthcare of the future. We provide complete data analysis solutions, give access to state-of-the-art bioinformatics methods and to the expertise and capabilities of Radboudumc’s bioinformatics community. The RTC is a one-stop-shop for biodata analysis with rapid deployment, with no sacrifices on data safety and privacy, to contribute to Radboudumc’s mission to have a significant impact on healthcare.

Our goals

  • Provide bioinformatics advice, tools, infrastructure  and services with clear price structures
  • Arrange user groups, courses, network events and expert meetings to bolster interaction
  • Enhance research and diagnostics through synergy, specialization and collaborations
  • Leverage expertise to create opportunities and funding for clients and consortia’s
  • Implement data and software standards for better safety, reproducibility and scaling

Bioinformatics

At the Radboudumc Technology Center Bioinformatics we believe that computational biology and big data solutions are key in shaping the data-driven healthcare of the future.

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How can we help enhance your research?

Sander Bervoets MSc
Technology center representative

+31 (0)24 361 96 74
contact

Services & expertise


What is bioinformatics?

Bioinformatics combines expertise from many scientific disciplines, and concerns the processing and analyzing of large amounts of bio-data using computational methodologies.

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What is bioinformatics?

The field of bioinformatics concerns the processing and analyzing of large amounts of biological data using computational methodologies. Bioinformatics combines expertise from many scientific disciplines, like biology, mathematics, statistics, computer science and biochemistry. Bioinformatics analysis can be applied to all sorts of biodata, but the biggest source of data comes from within the cell; genetics and DNA organization, gene expression and protein structures.

How do we apply bioinformatics?

Since the completion of the human genome and introduction of high throughput sequencing, the application of bioinformatics has shifted towards more clinical use-cases.

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How do we apply bioinformatics?

Since the completion of the human genome and introduction of high throughput sequencing, the application of bioinformatics has shifted from a purely academic venture towards more clinical use-cases. With the revolution in sequencing, more and more reliable information can be gathered from our cells. Think of investigating disease causing mutations, finding gene expression profiles that lead to cancer metastasis, or analyzing protein structures to identify drug targets.

The RNA-DxP pipeline

We aim to create a RNA-Seq data analysis workflow which is robust, reproducible and scalable, while still being innovative and feature complete.

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The RNA-DxP pipeline

At the RTC Bioinformatics, we get the most support requests for RNA Sequencing analysis. In order to both serve our clients and to contribute to a data-driven heathcare, we created the RNA-DxP pipeline. With this pipeline we aim to create a RNA-Seq data analysis workflow which is robust, reproducible and scalable, while still being innovative and feature complete. RNA-DxP is suitable for both biological as biomedical research, human and model organisms. We are working together with the Radboudumc department of Genetics to make RNA-DxP available for patient diagnostics purposes. The current features are:
  • Advanced QC and Metrics
  • Differential Gene Expression
  • Alternative and Differential Splicing
  • Fusion Gene detection
  • Splice Junction analysis
  • Pathway & GO Enrichment
  • EnrichR and String Annotation
  • RNA Variant Calling and Annotation
  • Automated reporting and visualizations
  • Scaled for projects of any size

Our analysis services and solutions

  • RNA Sequencing
  • DNA Sequencing
  • Protein Structure analysis
  • Metagenomics
  • Data Science
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Our analysis services and solutions

RNA Sequencing

  • Thorough and interactive visualized QC analysis
  • Differential Gene Expression Analysis
  • Pathway analysis and Annotation
  • Single Cell data analysis
  • Transcriptome analysis
  • Isoform detection and Rare disease diagnostics
  • Publication-grade graphics and plots

DNA Sequencing

  • Single Nucleotide and Structural Variant calling and annotation
  • Sequence analysis and pattern recognition
  • Genome assembly, annotation and visualization
  • Comparative Genomics and Phylogenetics
  • Bacterial classification and Pathogen marker analysis
  • Somatic/Tumor variant calling

Protein Structure analysis

  • Protein homology modeling and function prediction
  • 3D-analysis of mutational effects
  • Analysis of structures and complexes based on 3D projections

Metagenomics

  • 16S and Marker Gene classification
  • Microbiome Functional annotation
  • Metagenome assembly
  • Comparative Microbiomics analysis

Data Science

  • Ontology and Text mining
  • Integration with biostatistics
  • Investigating use of Machine/Deep learning
  • Big data visualizations
  • Data management
  • Data analysis automation and upscaling

Future Developments

To facilitate the data-intensive future of medicine, bioinformatics technologies can be a driver for new hypotheses and solutions.

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Future Developments

To facilitate the data-intensive future of medicine, bioinformatics technologies can be a driver for new hypotheses and solutions.
  • By leveraging combined infrastructure and expertise, standardized data analysis workflows will be setup that can deal with both singular research questions and large-scale projects.
  • Pooled recourses and scaling up computational infrastructures will result in shorter turnover times and faster answers.
  • Hybrid revenue models and external or commercial projects will help with creating a workforce that can deal with big biodata for all stakeholders.
  • Integrating bioinformatics pipelines with available R&D infrastructure will create a one-stop-shop for biodata analysis with rapid deployment, yet with no sacrifices on data safety and privacy.
  • Software development and data management practices will be upgraded to industry standards, which will provide better reproducibility and efficiency.
With these developments in mind, we aim to make bioinformatics an enabling technology for better science and medical services. Together with you, we will have a significant impact on healthcare.
 

HOPE User-friendly web service

HOPE analyzes the structural effects of a point mutation in a protein sequence. Input your protein sequence and the mutation and HOPE will collect and combine available information from a series of web services and databases and will produce a report, complete with results, figures and animations. go to HOPE

News & agenda

Collaborations


Bringing together expertise

Bioinformatics is a cross border discipline that brings together expertise from a variety of groups, technology centers and research fields.

Getting there

Entrance: Radboud Institute for Molecular Life Sciences
Route: 260 - ground floor

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Getting there

Visiting address

Centre for Molecular and Biomolecular Informatics
Radboud Institute for Molecular Life Sciences
Geert Grooteplein 28
6525 GA Nijmegen

Directions

Enter building at: Radboud Institute for Molecular Life Sciences
Follow route 260 - ground floor (Centre for Molecular and Biomolecular Informatics)