Online multi-omics data integration workshop series

January 2021

In January, 2021, an online X-omics workshop series will start. Different aspects of challenges and solutions related to multi-omics data integration are being addressed in four workshops.

Workshop program

preliminary
  Workshop #1: Multi-omics helpdesk, data-centric analysis platform and NGS diagnostics case study – January 20, 2021, 15:00 – 17:00 CET
  • Daniella Kasteel (X-omics): "Access to the X-omics helpdesk".
    The X-omics helpdesk can give you advice on a X-omics approach, on specific omics related sample or data analysis challenges and help you optimize your study design. In her talk, Daniella will highlight the application process and the support the X-omics helpdesk is offering researchers.
  • Leon Mei (LUMC): “Data-centric multi-omics analysis platform used in the BBMRI-NL project”.
    For BBMRI-NL researchers, all data shared by participating biobanks including genome-wide SNP data, limited phenotypes, RNA-seq and DNA methylation on all individuals can be analyzed on centralized computational facilities, namely the BIOS VM hosted at the SurfSARA High Performance Computing cloud. To provide a more flexible and scalable analysis platform, we have started using the new Research Science Cloud at SURFsara. In this talk, Leon will highlight the architecture, on-boarding procedure and lessons learned using this new infrastructure for future centralized multiomics data analysis within the BBMRI-NL community.
  • Joeri van der Velde & Lennart Johansson (UMCG): "Cutting-edge NGS diagnostics: from interpretation to FAIRification & challenges of large-scale Rare Disease cohort analysis".
    In this joint talk, Joeri will discuss the latest developments of computational tools and pipelines for genome diagnostics, as well as FAIRification of NGS data. Lennart will highlight the challenges and potential of analyzing NGS data in a cohort of 19,000 Rare Disease patients.
  Workshop #2: Multi-omics integration tools and platforms – February 10, 2021, 15:00 – 17:00 CET

We will have a look at the different tools and platforms mixOmics, cBioPortal and R2.

  • Remond Fijneman (NKI) 
  • Jan Koster (Amsterdam UMC)  
  • Kim-Anh Le Cao (University of Melbourne): Multivariate Data Integration with mixOmics
    Brief overview of the main concepts and methods implemented in mixOmics, which are based on Projection to Latent Structures algorithm. Some examples of applications in various omics data integration problems will be shown and the next methodological developments for the package will be briefly covered. 
  Workshop #3: Predictive multi-omics biomarker signatures – February 24, 2021, 15:00 – 17:00 CET

The third workshop will highlight –omics clocks and –omics risk scores.

  Workshop #4: Pitch your own research project – March 10, 2021, 15:00 – 17:00 CET

Finally, we invite you to pitch your own project and get advice from panelists and participants on experimental design and data integration strategies for a multi-omics approach.

Biosketches of our speakers

  • Daniella Kasteel

    Workshop #1

    Dr.Ir. Daniella Kasteel is the project manager of X-omics. She is an experienced project/research manager with a scientific background. Apart from the general project management tasks she is responsible for the marketing and communication of X-omics, organization of events and workshops, the X-omics helpdesk and building a X-omics community.

  • Leon Mei

    Workshop #1

    Leon Mei is the head of Sequencing Analysis Support Core at LUMC. He was also involved in the BBMRI-GoNL project and chaired the data management group in the BBMRI-BIOS project.

  • Joeri van der Velde

    Workshop #1

    Kasper Joeri van der Velde graduated on pathway visualization of kinase activity at the Groningen Bioinformatics Centre in collaboration with the UMC Groningen dept. of Cell Biology, and subsequently worked as scientific programmer on web-based databases, methods and visualization tools for various multi-omics research projects involving plants, mice and nematodes. He then moved to the UMC Groningen dept. of Genetics to complete his PhD on translational software infrastructure for medical genetics in the group of Prof. Morris Swertz, where he is now a Postdoc. Using a unique combination of machine learning and data infrastructure research, he aims to discover new ways to revolutionarize the speed, yield and applications of medical genomics and bring those innovations into clinical practice where they can truly make a difference. In his work, he is a strong advocate of open source programming, open access science, and FAIR (findable, accessible, interoperable, reusable) data.

  • Lennart Johansson

    Workshop #1

    Lennart F. Johansson graduated as a BASc Life Sciences and Technology on the implementation of comparative genomic hybridization for the purpose of hematological malignancies at the University Medical Center Groningen (UMCG) department of genetics in 2002 and obtained a BA philosopy in 2015. In his thesis he formulated an answer to the question: ‘does new knowledge about existing results give a moral duty to recontact in clinical genetics?’. In 2019 he completed his PhD at the UMCG department of Genetics on the topic ‘Novel algorithms for genetic variation detection’ in which he describes the development of algorithms to be used on different NGS methods for copy number variation calling, translocation calling and NIPT. Next to a general discussion two extra reflection chapters on the epistemology and ethics of NGS finalized his thesis ‘Looking through the noise’. Currently he is a postdoc/project coordinator focusing on rare disease projects, such as EJP-RD, Solve-RD and CINECA, both on the side of infrastructure (HPC Computing, (meta-)databases) as data-analysis.

  • Kim-Anh Le Cao

    Workshop #2

    Dr Kim-Anh Lê Cao develops novel methods, software and tools to interpret big biological data and answer research questions efficiently. Kim-Anh is committed to statistical education to instill best analytical practice. She has taught numerous statistical workshops for biologists and leads collaborative projects in medicine, fundamental biology or microbiology disciplines. Kim-Anh has a mathematical engineering background and graduated with a PhD in Statistics from the Université de Toulouse, France. She then moved to Australia first as a biostatistician consultant at QFAB Bioinformatics, then as a research group leader at the biomedical University of Queensland Diamantina Institute. She currently is Associate Professor in Statistical Genomics at the University of Melbourne. Kim-Anh has secured two consecutive NHMRC fellowships, published more than 90 articles and secured more than 8.5 million in competitive funding. In 2019, she received the Australian Academy of Science’s Moran Medal for her contributions to Applied Statistics, the Georgina Sweet Award for female scientists in quantitative biomedical science that recognize her contribution in multidisciplinary collaborations. She was selected to the international Homeward Bound leadership program for women in STEMM which culminated in a trip to Antarctica. 

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