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.

Contact Head of the CMBI

Peter-Bram 't Hoen
head of department

+31 (0)24 361 93 90
contact


Mission & vision

Our mission

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. read more

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. read more

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. read more

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 our internship projects:


  • The analysis of gene expression at the single cell level by RNA sequencing is a technically and bioinformatically rapidly developing field that is at the forefront of biomedical science, allowing the characterization of the variation of heterogeneous systems like the immune response. We are actively involved in a collaboration with Dimitri Diavatopoulos of the LabGNK and Rogier Thurlings of the Reumatology department in studying how T cells, a central player in the immune response, function in vaccination, infection and autoimmune disease. Antigen-specific naïve T cells respond to vaccination through expansion to form a memory pool with increased capacity to recognize and respond to infection. The function of these memory T cells is driven by transcriptional and epigenetic programming and is strongly influenced by the vaccine types. The goal of the specific project that the student will be involved in, is to determine how T cells respond to primary vaccination with different vaccine types during infancy. To study this, we have previously performed a vaccination study in newborns. Using blood samples collected from newborns, we have performed single cell multi-omics to obtain paired information on both gene expression and T-cell receptor sequences.  The student that will perform this project will be involved in the analysis of the data. He/she will get hands-on training in the analysis of single cell genomic data, and the interpretation of the results. The student will be embedded in the CMBI, in an active collaboration of bioinformaticians, experimental immunologists and clinicians.

    Required:

    An ambition to work with large datasets and basic programming skills (R, python). Research interests in immunology.

    Preferred background: MMD, MLW, BMW or Medical Biology

    Information:

    Supervision: Prashant Singh, Martijn Huynen, Dimitri Diavatopoulos

    Duration: minimally 6 months

    Reference for single cell analysis: Szabo et al, Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease Nat Commun 2019 Oct 17;10(1):4706. doi: 10.1038/s41467-019-12464-3. PMID: 31624246

    Reference for the specific disease we will be working on:

    Functional Programming of Innate Immune Cells in Response to Bordetella pertussis Infection and Vaccination. Gillard J, van Schuppen E, Diavatopoulos DA. Adv Exp Med Biol. 2019;1183:53-80. doi: 10.1007/5584_2019_404. PMID: 31432398

    Contact:

    Martijn.Huijnen@radboudumc.nl

     

     


Bioinformatics Services

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

Diagnostics-in-3D progress update 2021

Update on the EFRO funded project Diagnostics-in-3D. read more

Diagnostics-in-3D progress update 2021

About 7,000 rare hereditary diseases affect ±8% of the EU population, which translates to ±36 million people. Identification of causative mutations of such diseases thus, forms an essential step towards diagnosis as well as towards development of treatment. At CMBI, along with a multidisciplinary team of experts from BioProdict and Vartion, we are making efforts to predict (and eventually explain) functional effects of variants of unknown clinical significance.

Our EFRO funded project Diagnostics-in-3D uses an advanced deep learning framework known as DeepRank where we leverage information on protein structural features surrounding missense variants, coupled with the evolutionary significance of variant positions, and allow neural networks to learn from such variant environments. This exercise produces a probability estimate classifying whether a variant is disease-causing or not.

We have tailored DeepRank's 3D-CNN framework to help address our problem statement. One of the key aspects of this project is the diversity in variant environments captured from protein structures that differ depending on various protein families they belong to. Taking this aspect into account, we are now in the process of performance evaluation of our tool.

Organization


Our researchers CMBI

A list of researchers connected to this department. read more

Getting there

Entrance: Radboud Institute for Molecular Life Sciences
Route: 260

get directions

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

Contact Business manager

Nicolai Giling
Business manager

+31 (0)24 3686538
contact

Contact Operational manager

Barbara van Kampen
Operational manager

+31 (0)24 361 93 90
contact

Contact Management assistent

Sandra de Leeuw
Management assistent

contact

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