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:


  • In this internship, you will have the possibility to work with a wide range of omics data types including whole genome sequencing, DNA methylation sequencing, mRNA sequencing, microRNA sequencing, proteomics, and metabolomics. Our data set comprises multi-omics profiles for more than 100 healthy individuals that are part of a demonstrator cohort of EATRIS-Plus – a flagship project of the European Infrastructure for Translational Medicine (EATRIS).

    We want to apply deep learning techniques (variational autoencoders) to uncover and correct for unwanted variation in the multi-omics data that originates from technical biases. This will be the basis for integration of data across omics layers, discovery of substructures or joint patterns in the data and identification of links between omics and phenotypic information. A detailed analysis plan for this internship project will be developed together with the student.

    In collaboration with the Netherlands X-omics Initiative and EATRIS-Plus – Flagship in Personalised Medicine, we develop tools to create FAIR (Findable, Accessible, Interoperable, Reusable) multi-omics data as well as FAIR and reproducible data analysis workflows. You will apply best practices of scientific software development (version control, documentation, containerization) to create a reusable data analysis workflow integrated into our data analysis infrastructure.

    Literature

    Requirements

    • Programming skills
      • Basic knowledge of Python and/or R are required
      • Knowledge of a workflow language (Nextflow, Snakemake) is useful
      • Knowledge of containerization tools (Docker, Singularity) is useful
    • Analysis methods
      • Experience with deep learning methods (variational autoencoders) is useful
      • Experience with the analysis of at least one type of omics data is useful

    Information

    • Duration: at least 5-6 months
    • Supervisor: Dr. Anna Niehues, bioinformatician / data scientist at the Center for Molecular and Biomolecular Informatics (CMBI, group of Prof. Peter-Bram 't Hoen) and the Translational Metabolic Laboratory (TML, group of Prof. Alain van Gool)

    Contact: Anna.Niehues@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