Research Departments Center for Molecular and Biomolecular Informatics

Center for Molecular and Biomolecular Informatics

The Center for Molecular and Biomolecular Informatics (CMBI) does research and education, and provides services in bioinformatics and cheminformatics.


Staff & scientists at the CMBI


Contact Head of the CMBI

head of department

+31 (0)24 361 93 90
contact


Mission & vision

Our mission is:

to add value to personal health data by their translation into integrative knowledge and actionable information.

Our vision 

  • CMBI develops bioinformatics approaches that contribute to the understanding of disease mechanisms, personalized therapies and interventions, and a learning health care system
  • CMBI is committed to the reusability of their data, tools, and services
  • CMBI provides  bioinformatics researchers in Radboudumc with a platform for exchange of knowledge and expertise
  • CMBI contributes to the education of BMW, MLW, and MMD students so that they can apply and understand the principles behind (existing) bioinformatics tools

Radboudumc Technology Center Bioinformatics

The Bioinformatics technology center aims to raise and solve biological questions using the most recent computer technologies and big data solutions.

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Education

Our mission is to provide a basic understanding in Bioinformatic principles. Follow-up courses are available for those who want to gain greater insight in our field.

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Education

Researchers at the CMBI contribute to several courses at both the Faculty of Science and the Medical Faculty. We provide courses in Structural Bioinformatics, Comparative Genomics, Data Analysis, and programming courses such as Java. We specifically focus on the Molecular Life Science students, Biomedical Sciences students and participants in the master Molecular Mechanisms of Disease, although some of our courses can be chosen by Biology, Chemistry or Medical students as well. 

Our mission is to provide a basic understanding in Bioinformatic principles for bachelor students as this was shown to be beneficial for those who want to pursue a career in Life Sciences. Follow-up courses are available for those who want to gain greater insight in our field. 

For MLS/Biology students it is even possible to follow the B-track by choosing a combination of (master) Bioinformatics courses and internships at Bioinformatics departments. 

Our researchers also teach in special interest courses and summer schools here at the Radboudumc, the Radboud University and elsewhere.

 

For more information, you can contact dr. Hanka Venselaar, education coordinator at the CMBI.

 

 


Internships

The CMBI offers a wide range of possibilities for internships.

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Internships

Both bachelor and master students from studies such as Molecular Life Sciences, Biomedical Sciences, Chemistry and MMD are welcome. In general, we are flexible in terms of internship length, type of internship and type of research. 

Below you can find a few examples of internships possiblities:


  • Description:

    Alternative splicing plays a major role in proteomic diversity (Liu et al., 2017). Long-read transcriptomics technology has allowed for the detection of many novel transcript structures, among which intron retention and exon skipping. These events have been found extensively in various forms of cancer, for example (Dvinge & Bradley, 2015). However, intron retention events are widespread and occur in normal biological settings to regulate gene expression (Braunschweig et al., n.d.; Wong, Au, Ritchie, & Rasko, 2016). We would like to know whether we can detect these events on the protein level and what possible (effect of) IR/ES occurs in healthy cells, using the well-studied cell line NA12878.

    Outline steps:

    1. Literature review.
    2. Use data available for NA12878 and/or other long read datasets with paired proteomics data.
    3. Identify intron retention and exon skipping events on the transcriptome level.
    4. Create customized search dictionary to be able to identify these events.
    5. Quantify events/identify patterns or associations with other genes, and interpret biological/medical significance.
    6. Write up.

    Requirements:

    • Master in computational biology, bioinformatics or similar.
    • Basic programming skills (python preferred), knowledge of Linux command line.
    • Solid statistical knowledge.
    • Prior experience handling large datasets preferred.
    • 6 months or longer available for internship.

    Reference:

    • Braunschweig, U., Barbosa-Morais, N. L., Pan, Q., Nachman, E. N., Alipanahi, B., Gonatopoulos-Pournatzis, T., … Blencowe, B. J. (n.d.). Widespread intron retention in mammals functionally tunes transcriptomes. https://doi.org/10.1101/gr.177790.114
    • Dvinge, H., & Bradley, R. K. (2015). Widespread intron retention diversifies most cancer transcriptomes. Genome Medicine7(1), 1–13. https://doi.org/10.1186/s13073-015-0168-9
    • Liu, Y., Gonz├ález-Porta, M., Santos, S., Brazma, A., Marioni, J. C., Aebersold, R., … Wickramasinghe, V. O. (2017). Impact of Alternative Splicing on the Human Proteome. Cell Reports20(5), 1229–1241. https://doi.org/10.1016/j.celrep.2017.07.025
    • Wong, J. J.-L., Au, A. Y. M., Ritchie, W., & Rasko, J. E. J. (2016). Intron retention in mRNA: No longer nonsense. BioEssays38(1), 41–49. https://doi.org/10.1002/bies.201500117


    Internship supervisor:                  Prof. dr. Peter-Bram ‘t Hoen
    Daily supervisor:                           Renee Salz, PhD student (Renee.Salz@radboudumc.nl )
    Starting date:                                 September/October 2020


Bioinformatics Services

We maintain computational facilities, databases, and software packages in bioinformatics.

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Organisation


Our researchers CMBI

A list of researchers connected to this department.

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Research groups CMBI

Discover some of our research that is related to molecular and biomolecular informatics.

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Contact Business manager

Business manager

+31 (0)24 3686538
contact

Contact Operational manager

Operational manager

+31 (0)24 361 93 90
contact

Getting there

Entrance: Radboud Institute for Molecular Life Sciences
Route: 260

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Getting there

Visiting address

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

Research themes

Affiliated institutes

Radboud Institute for Health Sciences

This department is affiliated with RIHS. The research at this institute aims to improve clinical practice and public health. institute pages

Radboud Institute for Molecular Life Sciences

This department is affiliated with RIMLS. Their main aim is to achieve a greater understanding of the molecular mechanisms of disease. institute pages