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.

X-omics @ online events

In October, X-omics will be present at three online conferences, HUPO2020, BioSB2020 and Metabolomics2020.

During these online conferences, X-omics will be presenting its virtual booth in the exhibit halls. Our staff is present to answer any specific questions you have via chats and to videotalk to you!

Not attending any of these events and want to check out our virtual booth? No problem, you can find it here.

BioSB2020
On October 28th, Peter-Bram ‘t Hoen (leader of the X-omics data pillar), will present in the parallel topic session “ELIXIR-NL: FAIR resources and training”. He will talk about “Applying the FAIR Data principles to a Rare Disease registry: a case study of the VASCA registry.” Go check out this presentation at 10:15 AM CET.

Also, make sure to check out the poster sessions, a lot of excellent work done by other consortium members will be shown here.

Metabolomics2020
Consortium members Karlien Coene and Purva Kulkarni will be present to show their latest work during the poster sessions:

• 175, “Identification of novel diagnostic biomarkers for classical homocystinuria through untargeted metabolomics/next generation metabolic screening” by Karlien Coene, Radboudumc.
• 228, “Towards precision diagnostics: Untargeted metabolomics for the diagnosis of inborn errors of metabolism in individual patients” by Purva Kulkarni, Radboudumc.

We hope to see you online during these conferences!

HUPO webinar

HUPO Connect 2020 will organize a series of 60 minute webinars as a prelude to the main Congress sessions.

On Thursday 24 September 2020, 16:00 CEST, our leader of the innovation core Proteomics, Albert Heck will participate in the webinar “New Innovations in Proteomics” and talk about “Fishing Within the Proteome with Phosphate and Phosphonate Handles”.

Attendees will be able to submit questions via a text chat or live Q&A directly after the presentations.

Go register yourself for this amazing webinar and receive a discount for the main congress registration.

More information and registration

 

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.

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.

Yanick Hagemeijer

Anna NiehuesI’m a PhD student at the University of Groningen (UG), where I work at the European Research Institute for the Biology of Ageing (ERIBA) and at Groningen Research Institute of Pharmacy (GRIP), my 2 promoters are Peter Horvatovich, from the department of Analytical Biochemistry at the UG and Victor Guryev from the Group of Genome Structure and Ageing (University Medical Center Groningen, UMCG) are both part of X-omics Netherlands Infrastructure Consortium as well. Currently, I am involved in the X-omics project with the goal of making a ‘portable’ pipeline to perform proteogenomics analysis from start to end.

I previously studied Bioinformatics at the Hogeschool van Arnhem & Nijmegen. During my Bsc I did an internship at the bacterial genomics group at the Center for Molecular and Biomolecular Informatics (CMBI). Following this research experience, I did another at the Hubrecht institute in Utrecht where Victor Guryev was my supervisor. After I graduated I went to Wageningen University & Research centre (WUR). Here, I did my master theses at the departments of Animal Breeding and Genetics (ABG) and Systems & Synthetic Biology (SSB). After finishing I applied for a job at the department of Experimental Cardiology at the UMCG. During my research there, I was working as a data-analyst/bioinformatician focused on performing GWAS analysis in the context of medical/cardiac phenotypes.

I regretted focusing solely on genomics and transcriptomics and not learning more about proteomics and other omics layers. This PhD within the X-omics Consortium allows me to work at the crossroads of sequencing and mass spectrometry data as part of the data integration and stewardship pillar. I’m interested in bringing the complexities of genomics and transcriptomics to the proteomics field. The integration of the patient specific protein variants to create personalized protein sequence databases, which can be used for database searching large LC-MS/MS datasets and to identify patient specific variants that have implications in complex diseases such as cancer and COPD. Currently, proteomics analysis pipelines rely on canonical sequences from (curated) public databases such as Ensembl and Uniprot. Simply including all possible ‘translate-able’ sequences leads to a large search space and low statistical power to identify protein variants. The goal of my PhD project is to provide a proteogenomics pipeline, which uses genomics and/or transcriptomics data to make a protein database containing all protein variants present in a clinical/biological proteomics sample that is both small and accurate without including large amounts of hypothetical proteins for which there is no support in the genomics or transcriptomics data. In case you have similar interests - let’s collaborate!

Pleguezuelos-Manzano, C. et al. (2020)

Mutational signature in colorectal cancer caused by genotoxic pks + E. coli. Nature

PMID: 32106218

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