To keep you up to date with the latest developments in virus bioinformatics, especially new tools that might help you in your research, the European Virus Bioinformatics Center is organising a regular lecture series entitled viruses in silico.
The lectures will usually take place on the last Thursday of the month at 4 pm CET/CEST | 10 am EST/EDT | 7 am PST/PDT.
The lectures take place online via Zoom – Use the registration form below to receive the login details (registration is possible until 1 hour before the start of the event). Registration is only necessary once, you will then receive updates about all upcoming speakers (you can unsubscribe at any time). Please note that the lectures are not recorded. Exceptions can be requested in advance – please contact us beforehand.
Upcoming lectures
27 November 2025 | 4 pm CET
Emma Hodcroft (Swiss Tropical and Public Health Institute and SIB Swiss Institute of Bioinformatics, Switzerland)
Pathoplexus: A Community-Driven Solution for Transparent and Equitable Viral Genomic Data Sharing
Sharing viral genomic data is critical for scientific research and informing public health responses. Although, platforms like the International Nucleotide Sequence Database Collaboration (INSDC: NCBI, ENA, DDBOJ) and GISAID facilitate data sharing, they do not fully address specific needs of the pathogen genomics community. Persistent concerns about data misuse, “scooping,” and limitations on data reuse from protected repositories highlight the need for more flexible and equitable data-sharing. Pathoplexus is a specialized, community-driven viral genomics database designed to balance data utility with autonomy. It combines open-source technologies with transparent governance, allowing data submitters to control how their data is used for up to one year if desired, while promoting rapid data access to researchers and public health officials. All Pathoplexus submissions are automatically uploaded to INSDC: either immediately if fully open or after one year if initially shared as “restricted-use.” Features like SeqSets, which provide citable DOIs to contributors, ensure submitters receive appropriate credit while supporting open, flexible data-sharing terms. Pathoplexus leverages on Loculus, an open-source tool for managing viral sequence databases which can be replicated by laboratories or organizations in setting up their own databases. The platform’s web interface and API ensure accessibility for both interactive and programmable analyses. Pathoplexus is a non-profit association governed by an international Executive Board and includes members from 10 countries across 5 continents, reflecting a commitment to equity and diverse public health needs. Though Pathoplexus launched only recently, it has already made an impact in the pathogen sharing community, and as of mid-Nov 2025, contains over 8,900 directly-submitted sequences. Pathoplexus hosts the first available Ebola sequence collected during the February 2025 outbreak in Uganda and the September 2025 outbreak in DRC, and contains over 900 Restricted-Use sequences i.e. sequences that may not have been shared prior to publication without this protection. We aim to actively expand the number of supported pathogens through community feedback and engagement. In parallel, Pathoplexus is working to broaden support to include raw read data, enhancing viral evolution insights, and implement a federated network of nodes to foster decentralized sequence sharing. This will empower regions to maintain data ownership while contributing to a resilient, global system. In this talk, we introduce Pathoplexus and highlight its potential to enhance data sharing through collaboration and transparency for long-term public health impact.
26 February 2026 | 4 pm CET
Sebastian Böcker (Friedrich Schiller University Jena, Germany)
SIRIUS and beyond: Turning tandem mass spectra into metabolite structure information
Liquid Chromatography Mass Spectrometry is a highly sensitive experimental platform for the analysis of metabolites and other small molecules. Unfortunately, structural elucidation of metabolites from tandem MS data remains highly challenging; in untargeted metabolomics experiments, only a small percentage of spectra can be annotated via spectral libraries. For more than a decade, my group has been developing computational solutions for this task. In my talk, I will explain CSI:FingerID searches a query MS/MS spectrum in a molecular structure database; how CANOPUS assigns thousands of compound classes to a query spectrum, even when the compound is missing from all structural and spectral databases; and, how COSMIC assigns confidence to database search results. I will then describe new features of SIRIUS 6, such as the integration of MSNovelist for de novo structure elucidation, and Epimetheus for combinatorial fragmentation and validation of results. In the last part of my talk, I will show how our tools can be applied in virus research in the future, targeting oxylipins and cyclic oligonucleotides.