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 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

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.

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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 our internship projects:


  • Research questions:

    • How preserved is the splicing between Weri-Rb cells and PPCs compared to the retina?
    • Optional: validation of splicing events with RT-PCR

    Description

    Inherited retinal diseases (IRDs) are the most common cause of blindness in adults. IRDs are often caused by variants that alter splicing. To identify splice altering variants in IRD patients, splice assays are used. At the moment, splice assays are performed in human embryonic kidney (HEK293T) cells. The problem is that splicing is a tissue specific process. To correctly identify effects of possibly splice altering variants on the retina we need a better model to test the splice assays. Possible options to replace the HEK293T cells with more retina like cells are Weri-Rb cells and photoreceptor precursor cells (PPCs). Weri-Rb cells are human retinoblastoma cells. Photoreceptor precursor cells are post-mitotic precursor cells which can differentiate into cones or rods.

    New long read sequencing techniques have brought new insights into transcriptomics. By comparing pacbio long read RNA sequencing data for retina, Weri-Rb cells and PPCs we want to identify splicing events that are preserved. If the splicing of the cells is similar to the splicing in the retina, the cells can be used to replace HEK293T cells in the study of splice assays. After identifying splicing event in silico, it is possible to validate the findings in the lab with RT-PCR.

    Literature

    1. Sangermano R, Khan M, Cornelis SS, Richelle V, Albert S, Garanto A, Elmelik D, Qamar R, Lugtenberg D, van den Born LI, Collin RWJ, Cremers FPM. ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease. Genome Res. 2018 Jan;28(1):100-110. doi: 10.1101/gr.226621.117. Epub 2017 Nov 21. PMID: 29162642; PMCID: PMC5749174.
    2. Albert S, Garanto A, Sangermano R, Khan M, Bax NM, Hoyng CB, Zernant J, Lee W, Allikmets R, Collin RWJ, Cremers FPM. Identification and Rescue of Splice Defects Caused by Two Neighboring Deep-Intronic ABCA4 Mutations Underlying Stargardt Disease. Am J Hum Genet. 2018 Apr 5;102(4):517-527. doi: 10.1016/j.ajhg.2018.02.008. Epub 2018 Mar 8. PMID: 29526278; PMCID: PMC5985352.

     

    Supervisors: Tabea Riepe / Peter-Bram ‘t Hoen / Frans Cremers

    Proposed duration: 5 month or more

    Preferred background: MSc: MLS/BMS/BIO/MMD

    Requirements: basic programming skills (python preferred), command line

    Contact: tabea.riepe@radboudumc.nl


Bioinformatics Services

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

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Organization


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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Getting there

Entrance: Radboud Institute for Molecular Life Sciences
Route: 260

get directions

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