Publications

Erik Zhivkoplias, Paul Dunshirn, Jean-Baptiste Jouffray, Robert Blasiak. 2025. From genes to innovation: exploring the use of marine genetic resources in biotechnology. One Ocean Science Congress. https://doi.org/10.5194/oos2025-498

Marine genetic resources (MGRs) are crucial for understanding marine biodiversity and tracking changes in ecosystems, while also providing a valuable foundation for biotechnological innovation. The recent adoption of the UN Treaty on Biodiversity Beyond National Jurisdiction (BBNJ Treaty) and the inclusion of digital sequence information in this legally binding agreement open new opportunities for protecting biodiversity in th...

Paul Dunshirn, Erik Zhivkoplias. 2024. Conducting marine genetic research for whom? Mapping knowledge flows from science to patents. npj Ocean Sustainability. https://doi.org/10.1038/s44183-024-00088-0

Marine genetic resources hold great value for biotechnological innovation and sustainability-oriented research. However, studies indicate that intellectual property rights pertaining to these resources are concentrated in a handful of companies and countries, triggering contentious international debates. This paper highlights an overlooked dimension: the flow of scientific knowledge in the provision and use of marine genetic r...

Frida Bengtsson, Jean-Baptiste Jouffray, Shinnosuke Nakayama, Erik Zhivkoplias, Colette C. C. Wabnitz, Robert Blasiak, Elizabeth R. Selig, Henrik Österblom. 2024. Who owns reefer vessels? Uncovering the ecosystem of transshipment in fisheries. Science Advances. https://doi.org/10.1126/sciadv.adn3874

A central barrier to effective governance and accountability in fisheries is the limited transparency of corporate ownership. Transshipment—the transfer of catches, fuel, parts, or crew between fishing and cargo vessels known as reefers—is often criticized for its opacity and poor governance. Better insight into the beneficial ownership of vessels involved in transshipment and their operational patterns could lead to more effe...

Tilde Krusberg, Lova Schildt, Jean-Baptiste Jouffray, Erik Zhivkoplias, Robert Blasiak. 2024. A review of marine genetic resource valuations. npj Ocean Sustainability. https://doi.org/10.1038/s44183-024-00081-7

Marine biotechnology is a rapidly growing sector of the ocean economy, but efforts to assess its value, and that of the genetic resources that enable it, remain contentious. Through a comprehensive literature review, we identified 67 distinct valuations of marine genetic resources. We analysed these using the IPBES Values Assessment typology and found a predominance of behaviour-based valuations using economic value indicators...

Erik Zhivkoplias, Jean-Baptiste Jouffray, Paul Dunshirn, Agnes Pranindita, Robert Blasiak. 2024. Growing prominence of deep-sea life in marine bioprospecting. Nature Sustainability. https://doi.org/10.1038/s41893-024-01392-w

Marine bioprospecting, which involves the exploration of genetic and biochemical material from marine organisms, can be used towards addressing a broad range of public and environmental health applications such as disease treatment, diagnostics and bioremediation. Marine genetic resources are important reservoirs for such bioprospecting efforts; however, the extent to which they are used commercially for natural product discov...

Erik Zhivkoplias, Agnes Pranindita, Paul Dunshirn, Jean-Baptiste Jouffray, Robert Blasiak. 2023. Novel database reveals growing prominence of deep-sea life for marine bioprospecting. Nature Sustainability/Research Square. https://doi.org/10.21203/rs.3.rs-3136354/v1

Perceptions that marine bioprospecting will deliver vast commercial benefits have placed ‘marine genetic resources’ at the center of key policy processes yet our knowledge about their importance remains limited. Here, we introduce a novel global database of marine gene sequences referenced in patent filings, the MArine Bioprospecting PATent (MABPAT) Database. It includes 25,682 sequences from 1,092 marine species associated wi...

Robert Blasiak, Jean-Baptiste Jouffray, Diva J. Amon, Joachim Claudet, Paul Dunshirn, Peter Søgaard Jørgensen, Agnes Pranindita, Colette C. C. Wabnitz, Erik Zhivkoplias, Henrik Österblom. 2023. Making marine biotechnology work for people and nature. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-022-01976-9

Francesco Marzolla, Przemysław Nowak, Rohit Sahasrabuddhe, Chakresh Singh, Matteo Straccamore, Erik Zhivkoplias, Elsa Arcaute. 2023. Spaces of innovation and venture formation: the case of biotech in the United Kingdom. arXiv. https://doi.org/10.48550/ARXIV.2306.17547

Patents serve as valuable indicators of innovation and provide insights into the spaces of innovation and venture formation within geographic regions. In this study, we utilise patent data to examine the dynamics of innovation and venture formation in the biotech sector across the United Kingdom (UK). By analysing patents, we identify key regions that drive biotech innovation in the UK. Our findings highlight the crucial role ...

Daria Antonova, Viktoriia V. Belousova, Erik Zhivkoplias, Mariia Sobinina, Tatyana Artamonova, Innokentii Vishnyakov, Inna Kurdyumova, Anatoly Arseniev, Natalia Morozova, Konstantin Severinov, Mikhail Khodorkovskii, Maria V. Yakunina. 2023. The Dynamics of Synthesis and Localization of Jumbo Phage RNA Polymerases inside Infected Cells. Viruses. https://doi.org/10.3390/v15102096

A nucleus-like structure composed of phage-encoded proteins and containing replicating viral DNA is formed in Pseudomonas aeruginosa cells infected by jumbo bacteriophage phiKZ. The PhiKZ genes are transcribed independently from host RNA polymerase (RNAP) by two RNAPs encoded by the phage. The virion RNAP (vRNAP) transcribes early viral genes and must be injected into the cell with phage DNA. The non-virion RNAP (nvRNAP) is co...

Erik K. Zhivkoplias, Oleg Vavulov, Thomas Hillerton, Erik L. L. Sonnhammer. 2022. Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops. Frontiers in Genetics. https://doi.org/10.3389/fgene.2022.815692

The regulatory relationships between genes and proteins in a cell form a gene regulatory network (GRN) that controls the cellular response to changes in the environment. A number of inference methods to reverse engineer the original GRN from large-scale expression data have recently been developed. However, the absence of ground-truth GRNs when evaluating the performance makes realistic simulations of GRNs necessary. One aspec...