X-omics

Welcome to the website of the Netherlands X-omics Initiative! 

On this website, you will find information and regular updates on the latest developments, results and activities of the project.​

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X-OMICS FESTIVAL

X-omics festival: "The future is now! ", @Nijmegen, April 6th 2020.

The X-omics consortium will organise a X-omics festival in Nijmegen, on April 6th 2020. The festival will contain several elements:

  • Keynote lecture (learn about the X-omics approach!)
  • Lectures from investigators (X-omics fields of expertise and specific application area's)
  • Technology pitches
  • Meet & greet with the speakers
  • Live Q&A with the experts
  • Scientific posters
  • Networking opportunities

Register for the 2020 festival

Program details will follow shortly.

We hope to meet you in Nijmegen!

Kind regards,
X-omics project management team.

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JOIN THE X-OMICS COMMUNITY

The Netherlands X-omics Initiative is a National Roadmap Large-Scale Research Infrastructure, partially funded by NWO with a total budget of 40 million euro.

X-omics aims to realise the next generation 'omics' infastructure across the Netherlands, by combining technologies in the field of genomics, proteomics, metabolomics and data analysis, integration & stewardship.

This infrastucture will be accessible to all researchers. To allow communication between the users of the infrastucture a X-omics community will be established. 

This community will interact via:
● Meetings
● News letters
Social media

If you would like to join the X-omics community, please send an e-mail to: This email address is being protected from spambots. You need JavaScript enabled to view it. 

SSIEM CONFERENCE 2019

During the SSIEM annual symposium 2019 taking place in Rotterdam (September 3-6), several partners involved with the Netherlands X-omics Initiative were present:

  • Ines Thiele (National University of Ireland), part of the scientific advisory board of X-omics, gave a presentation in the P5 theme “Metabolomics/System biology” with the title: “ Modeling human metabolism in health and disease.”
  • X-omics core team member, Thomas Hankemeier (Leiden University) gave a presentation within the same p5 theme with the title: “Innovative analytical tools for metabolomics-driven systems biology to investigate monogenetic and complex disorders.”
  • Consortium member Karlien Coene (Radboudumc) gave a presentation in Parallel Session 2B: “Advances in diagnostics (including omics)” with the title “Discovery of novel antiquitin deficiency biomarkers through the combination of untargeted metabolomics and infrared ion spectroscopy.” For more details see under O-012 in the abstract book.
  • Posters from several partners were presented. For example, P-032 and P-037. See abstract book for more details: https://ssiem2019.org/book-of-abstracts/
X-OMICS SUMMERSCHOOL

The departments Center for Molecular and Biomolecular Informatics (CMBI), Translational Metabolic Laboratory (TML) and Human Genetics organized a successful Radboud summerschool on “Integrative X-omics Analyses Empowering Personalized Healthcare”. The course coordinators Prof. Alain van Gool and Prof. Peter-Bram ‘t Hoen are looking back at an exciting week, in which 20 participants from all over Europe convened for a week full of lectures, practicals, and labtours.

The week started with an introduction into biomarkers for personalized healthcare by Alain van Gool (TML). Marcel Nelen (Human Genetics) introduced them into novel genomics technologies, and Hans Wessels and Jolein Gloerich (TML) did the same for novel proteomics technologies. Peter-Bram ‘t Hoen presented a range of X-omics data integration strategies. Other topics like metabolomics, methylation and network-based data integration were covered by external speakers from the Netherlands X-omics Initiative.

Throughout the week, the participants worked on an assignment for which they needed to design a X-omics study, and define a data analysis and management plan. The participants worked in multidisciplinary teams of four. Their different scientific backgrounds helped to address this assignment form different angles. On Friday, the participants presented their exciting studies covering a range of different topics:

  • from the study of the influence of microbiome on constipation in Parkinson's disease, to the identification of early marker signals for infection in rheumatoid arthritis patients after treatment with tocublizimab
  • risk assessment in prostate cancer based on combined imaging and -omics profiling
  • the molecular mechanisms of non-alcoholic fatty liver disease
  • the early detection of cerebral course of disease in X-linked adrenoleukodystrophy

The organizers are looking forward to a next edition.

More information about the program click here.

x omics summerschool 2019

x omics summerschool 2019 2

HANDBOOK OF BIOMARKERS AND PRECISION MEDICINE NOW AVAILABLE

The Handbook of Biomarkers and Precision Medicine was published May 1, 2019.

Several members of the X-omics consortium have been involved in the creation of this handbook:

  • Alain van Gool (coordinator of X-omics) and Mark Fidock (SAB member of X-omics) are editors of this handbook.
  • X-omics consortium members Edwin Cuppen, Theo Luider and Rainer Bischoff have contributed to this handbook.

The handbook provides comprehensive insights into biomarker discovery and development which has driven the new era of Precision Medicine. A wide variety of renowned experts from government, academia, teaching hospitals, biotechnology and pharmaceutical companies share best practices, examples and exciting new developments. The handbook aims to provide in-depth knowledge to research scientists, students and decision makers engaged in Biomarker and Precision Medicine-centric drug development.

Revenues (of the X-omics consortium members) will go to charities for new translational biomarker research.

For more information and to order this handbook visit the following link.

Handbook of Biomarkers and Precision Medicine

BENELUX PRECISION MEDICINE FORUM 2019

During the Benelux Precision Medicine Forum on May 13-14 2019 in Utrecht, several consortium members of the Netherlands X-omics Initiative were present as speakers, with presentations and posters. For example:

  • Alain van Gool organised a workshop with the title 'X-omics to gain new insights and advance Precision Medicine' and also gave a lecture about 'Translational X-omics diagnostics to drive Personalized Healthcare'.
  • Peter-Bram t’Hoen gave a lecture with the title; “Data Integration: Overcoming the Challenges of Integrating Large Volumes of Complex Data from Heterogeneous Sources”.
  • Albert Heck gave a lecture with the title: “Proteomics: Towards Personalized Proteome Profiling”.
  • Thomas Hankemeier gave a lecture with the title: “Metabolomics: Developing Strategies for Metabolomics-Driven Systems Biology to Enable Personalised Medicine”.
  • Cisca Wijmenga joined the panellist of expert speakers during the presentation “Exploring the Future Direction of Precision Medicine: What We Hope to Achieve and Required Next Steps”.

For more information about the Precision Medicine Forum events click here.

ESTABLISHMENT OF A JOINT CENTER OF EXCELLENCE FOR TRANSLATIONAL OMICS

At the opening event of the Netherlands X-omics Initiative, Bruker and the Translation Metabolic Laboratory (TML) at Radboud University Medical Center (UMC)  jointly announced the establishment of a Center of Excellence (CoE) for Translational Omics. Under the leadership of Professor Alain van Gool, the joint CoE will focus on clinical translation of innovative metabolic profiling using various Omics approaches. The collaboration will center around the development of 4D omics methods using the timsTOF Pro ultra-high sensitivity, trapped ion mobility quadrupole time-of-flight mass spectrometer that was recently acquired by the TML.

For more information about the establishment please see the following link.

HEALTH-RI CONFERENCE 2019

During the HEALTH-RI conference 2019 on January 17th, several partners of the Netherlands X-omics initiative were present as chairs of sessions, with presentations and posters. For example:

  • ·The coordinator of X-omics, Alain van Gool(Radboudumc) chaired a session in the P4 theme “Prevention” with the title “Individuals are given tailored tools to prevent disease development”.
  • ·X-omics partner Gerrit Meijer(NKI) chaired a parallel session within the same P4 theme; “Optimizing the wellness of individuals by predicting disease and delivering personalized treatments”
  • ·One of the X-omics core team members Edwin Cuppen(UMCU - Hartwig Medical Foundation) gave a presentation: “Tumor whole genome sequencing for personalized cancer treatment”.
  • ·Posters from several partners such as BBMRI-NL, Surf and UMCG/RUG were presented, for example P18, P43, P44 and P45 (see abstract book for more details: https://www.health-ri.org/abstractbook-2019)

For the X-omics project management team this was the first occasion to present the project to the public and explain what the project is about. A lot of interested people and fruitful discussions!

Health RI meeting


Photo: Edwin Cuppen during his presentation. Made by Thijs Rooimans.

NEWSLETTER

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VACANCIES

Data scientist / Postdoctoral researcher X-omics

Within the contexts of the national large-scale X-omics research infrastructure (coordinated by prof. A. van Gool, Radboudumc) and the European Joint Programme on Rare Diseases (EJPRD, coordinated by dr. Julkowska, Inserm, Paris), we are looking for an ambitious data scientist, who develops data analysis and integration approaches for large-scale -omics data and is dedicated to the introduction of these approaches in personalized health care. The candidate is committed to the counselling and training of biomedical researchers in these computational approaches. The candidate will contribute to the realization of a digital research environment (DRE) where these computational approaches can be applied and which contributes to the Findability, Accessibility, Interoperability and Reusability (FAIRness) of data, tools and services.

Profile

  • PhD in a relevant discipline (data science, biology, bioinformatics, computer science, artificial intelligence);
  • Proven ability to develop new algorithms and / or methodology;
  • Ability to drive scientific projects, as apparent from publication record;
  • Excellent programming skills in a relevant language (python, R, Java, C++, …);
  • Experience with data modelling and knowledge of formal data representations is preferred;
  • Enjoying work in multidisciplinary teams;
  • Excellent writing and verbal communication skills;

For more information about this vacancy please contact Prof. dr. Peter-Bram 't Hoen (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Our Helpdesk

The Netherlands X-omics Initiative will establish a central helpdesk to provide access to the X-omics research infrastructure and its respective facilities.

You can contact the helpdesk assistant for:
  • Expert assistance to help design your X-omics experiments.
  • Analyses of samples in 1 of the facilities (the assistant can refer you to the right facility).
  • For general information about the X-omics project.
  • For information on specific activities such as the training schools or events organized by the consortium.

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This research was (partially) funded by NWO, project 184.034.019