The Netherlands X-omics Initiative will have a strong focus on training and outreach and in this respect, will organize different types of events & activities in the coming 5 years. You can register for these events and activities at this website.

News

In our news section you will find interesting news and information related to x-omics technologies, research and its activities.

Summary X-omics online workshop series “Strategies to Overcome Your Challenges in Multi-omics Data Integration”

In June, X-omics organized its first online workshop series. Different aspects of challenges and solutions related to multi-omics data integration were addressed in four workshops:

#1 Data standards and multi-omics data integration
#2 Linked data in practice: An RDF based-approach with SPARQLing-genomics
#3 Showcases of multi-omics data integration
#4 Pitch your own multi-omics project

The workshop series was a  success and we want to thank all those who participated, the speakers, the invited experts and the workshop organizing committee.

An overview of all workshop highlights, key take-home messages, presentations and a link to the workshop recordings has been compiled and can be found in the training schools section

We hope to see you again during future X-omics events.

Workshop series

High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells

Researchers from our partner institution Utrecht University have worked together with researchers from the Hubrecht Institute and in collaboration with other research teams and generated an in-depth description of the hormone-producing cells in the human gut. 

These are very rare and unique cells to different species of animals which makes them difficult to study. An extensive toolbox has been developed by the researchers to study human hormone-producing cells in tiny versions of the gut grown in the lab (organoids). These tools allowed them to uncover secrets of the human gut.

More information about this research

The study findings and results are presented in the scientific journal Cell.

PMID: 32407674

 

Training schools

We will keep an archive available of the webinars that we have given. In this archive you will find highlights of every webinar, including the key take-home messages, presentations and recordings.

Events

In our event section we will keep you updated on all events organized by x-omics and other organizations that relate to one of X-omics pillars (Genomics, Proteomics, Metabolomics, Data Analysis, Integration & Stewardship) or a combination of these fields.

X-omics Festival 2020 

festival poster

Where Where icon Nijmegen, the Netherlands
When  Calendar icon   September 28

HUPO 2020

HUPO2020

Where Where icon Stockholm, Sweden
When  Calendar icon   October 18

Visit hupo2020.org

Highlights

In our highlight section we will keep you posted about the purchase of new equipment, publications created with the help of the X-omics infrastructure and we will provide a platform to young investigators to introduce themselves.

Anna Niehues

Anna NiehuesAnna Niehues is a postdoc at Radboudumc, Nijmegen, where she works at the Center for Molecular and Biomolecular Informatics (CMBI), led by Peter-Bram ’t Hoen, and the Translational Metabolic Laboratory, led by Alain van Gool. She is currently involved in the X-omics project and the European EATRIS-Plus project. Anna previously studied Biosciences at the University of Münster (WWU) in Germany, where she also obtained her PhD. She has been working as a bioinformatician on mass spectrometry data analysis in the context of quantitative proteomics, and structural analysis of carbohydrate oligo- and polymers. 

Within the X-omics project, she works as data scientist in the data analysis, integration and stewardship pillar, together with Peter-Bram ’t Hoen (work package leader) and Gurnoor Singh (data steward) from Radboudumc and other X-omics collaborators across the Netherlands. She is interested in the integration of mass spectrometry-derived data such as metabolomics data with other types of omics data in order to e.g. increase the power of biomarker studies or gain additional insights into the relationships between different molecular levels and their association with disease phenotypes. She is also interested in FAIR data analysis workflows which, alongside FAIR data, provide the means for reproducibility of multi-omics data analyses.

Gurnoor Singh

Anna Niehues Gurnoor Singh works as a data-steward at the CMBI. After completing his Masters in Life Science informatics from the University of Bonn, Gurnoor pursued a Ph.D. in developing linked data graphs from genomics data from Wageningen University & Research. For the X-omics project, Gurnoor is working towards standardizing meta-data and data schema for harmonizing and fairify X-omics data workflows. He is also involved in the FAIR Genomes project, which aims to develop a national guideline to promote optimal (re)use of NGS data in research and healthcare. Gurnoor Singh strongly believes in the usability of the FAIR data principles in the creation of semantic data infrastructure for diverse X-omics data. 

Gurnoor and Anna are coordinating the data FAIRification and multi-omics integration tasks, respectively, of the first X-omics data integration and FAIRification demonstrator, which is a collaboration between X-omics and NTR. They are both also involved in conducting various workshops for adequate data management and planning for research data.

Publications

In our publications section you will find an archive of publications on which our X-omics consortium members have worked, relevant technological publications and interesting x-omics publications. In the highlight section we will highlight the latest publications.

The publications of the X-omics consortium will be listed here!

  • 2020

    Dekker, LJM. et al. (2020). Metabolic changes related to the IDH1 mutation in gliomas preserve TCA-cycle activity: An investigation at the protein level. FASEB J. 34, 3646 – 3657.

    PMID: 31960518
    Lamers, MM. et al. (2020). SARS-CoV-2 productively infects human gut enterocytes. Science.

    PMID: 32358202
    Zajec, M. et al. (2020). Integrating Serum Protein Electrophoresis with Mass Spectrometry, A New Workflow for M-Protein Detection and Quantification. J Proteome Res.

    PMID: 31895568
  • 2019

    Körner, A. et al. (2019). Inhibition of ∆24-dehydrocholesterol reductase activates pro-resolving lipid mediator biosynthesis and inflammation resolution. Proc Natl Acad Sci U S A. 116, 20623 – 20634. 

    PMID: 31548397
    Lageveen-Kammeijer, GSM. et al. (2019). Highly sensitive CE-ESI-MS analysis of N-glycans from complex biological samples. Nat Commun. 10, 2137.

    PMID: 31086181
    Palmblad, M. et al. (2019). Automated workflow composition in mass spectrometry-based proteomics. Bioinformatics. 35, 656 – 664.

    PMID: 30060113
    van der Kant, R. et al. (2019). Cholesterol Metabolism Is a Druggable Axis that Independently Regulates Tau and Amyloid-β in iPSC-Derived Alzheimer’s Disease Neurons. Cell Stem Cell. 24, 363-275.

    PMID: 30686764
    Weintraub, ST. et al. (2019). Special Issue on Software Tools and Resources: Acknowledging the Toolmakers of Science. J Proteome Res. 18, 575.

    PMID: 30704244
    Lacobucci, C. et al. (2019). First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem. 91, 6953-6961.

    PMID: 31045356
    Masson, GR. et al. (2019). Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods. 16, 595-602.

    PMID: 31249422
    Ressa, A. et al. (2019). PaDuA: A Python Library for High-Throughput (Phospho)proteomics Data Analysis. J Proteome Res. 18, 576-584.

    PMID: 30525654
    Greisch, JF. et al. (2019). Expanding the mass range for UVPD-based native top-down mass spectrometry. Chem Sci. 10, 7163-7171.

    PMID: 31588283
    van der Laarse, SAM. et al. (2019). Targeting proline in (phospho)proteomics. FEBS J.

    PMID: 31863553
    van der Laan, T. et al. (2019). Fast LC-ESI-MS/MS analysis and influence of sampling conditions for gut metabolites in plasma and serum. Sci Rep. 9, 12370.

    PMID: 31451722
  • older

    Van Damme, T. et al. (2017). Mutations in ATP6V1E1 or ATP6V1A …. Am. J. Hum. Genet. 100, 216–227.
    van Gool, A. J. et al. (2017). Bridging the translational innovation gap …. Nat. Rev. Drug Discov.  
    Snijder, J. et al. (2017). Structures of the cyanobacterial circadian oscillator …. Science 355, 1181–1184.

    Blokzijl, F. et al. (2016). Tissue-specific mutation accumulation in human …. Nature 538, 260–264.
    Jansen, E. J. R. et al. (2016). ATP6AP1 deficiency causes an immunodeficiency …. Nat. Commun. 7, 11600.
    Liepe, J. et al. (2016). A large fraction of HLA class I ligands are …. Science 354, 354–358.
    Tarailo-Graovac, M. et al. (2016). Exome Sequencing and the … .N. Engl. J. Med. 374, 2246–2255.
    van Karnebeek, C. D. M. et al. (2016). NANS-mediated synthesis of sialic acid …. Nat. Genet. 48, 777–784.

    Huch, M. et al. (2015). Long-term culture of genome-stable bipotent stem cells…. Cell 160, 299–312.
    Liu, F., Rijkers, et. al. (2015). Proteome-wide profiling of protein a…. Nat. Methods 12, 1179–84.

    Dane, A. D. et al. (2014). Integrating metabolomics profiling …. Anal. Chem. 86, 4110–4.
    Hussein, S. M. I. et al. (2014). Genome-wide characterization of…. Nature 516, 198–206.
    Tegtmeyer, L. C. et al. (2014). Multiple Phenotypes in … N. Engl. J. Med. 370, 533–542.
    van Heesch, S. et al. (2014). Genomic and functional overlap between somatic and …. Cell Rep. 9, 2001–10.

    Altelaar, A. F. M., et. al. (2013). Next-generation proteomics: …. Nat. Rev. Genet. 14, 35–48.
    Gonzalez-Covarrubias, V. et al. (2013). Lipidomics of familial longevity. Aging Cell 12, 426–34.
    Kettleborough, R. N. W. et al. (2013). A systematic genome-wide analysis of…. Nature 496, 494–7.
    Low, T. Y. et al. (2013). Quantitative and qualitative proteome characteristics. Cell Rep. 5, 1469–78.
    Peironcely, J. E. et al. (2013). Automated pipeline for de novo …. Anal. Chem. 85, 3576–83.
    Raterink, R.-J et. al. (2013). T. Three-phase electroextraction: …. Anal. Chem. 85, 7762–8.

    van der Kloet, F. M. et al. (2012). Discovery of early-stage biomarkers …Metabolomics 8, 109–119.

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