Meet the Team Behind Phagenomics Software
Meet the expert team behind Phagenomics BatchQC and Phagenomics Core!
We are pleased to introduce the team whose expertise has formed the foundation for Phagenomics’ next-generation phage bioinformatics software, designed to accelerate phage-based research and applications.
The Phagenomics platforms bring together the specialized expertise of our multidisciplinary team in phage science, bioinformatics, software development, quality, and compliance. Learn more about our team’s background and explore our scientific publications in this article!
Phagenomics Software for Unmet Needs
– Our team at PrecisionPhage specializes in phage bioinformatics and software development. We develop advanced bioinformatics solutions that provide a solid foundation for phage R&D and GMP-compliant manufacturing of phage products, says Ville Hoikkala, lead developer of Phagenomics platforms and Chief Information Technology Officer (CITO) and co-founder of PrecisionPhage.
– With the Phagenomics software, we are building the infrastructure required for the revival of phage therapy at the onset of the post-antibiotic era. Our phage-specific workflows simplify and accelerate analysis while adhering to the requirements imposed by GMP-level regulations, Hoikkala says.
The Phagenomics platforms enable scientists, phage producers, and quality assurance and regulatory experts to leverage advanced phage bioinformatics without the need for coding expertise and instead focus their own domain expertise on making decisions based on those results. With purpose-built bioinformatics solutions, they overcome the challenges of complex bioinformatics analyses, paving the way for a new era of phage discovery and understanding.
Dedicated Phage Bioinformatics Team
Our bioinformatics and software development team brings together PhD-trained specialists in phage science, bioinformatics, and software engineering. Our expertise is rooted in the bioinformatic study of phage-bacterium interactions, which has resulted in numerous scientific publications in high-impact journals such as Nature and Nucleic Acids Research, revealing entirely new molecular components in the interplay of phages and their hosts. Explore our team’s bioinformatics articles.
We view the genomic interactions between phages and their hosts as a constantly shifting, fluid battlefield, and pulling useful signal from the data requires tools built specifically for that context. Our experience with the genomic peculiarities of phages and their hosts, combined with modern software engineering practices, puts us at the forefront of phage-centric application development. We are pleased to bring this expertise to our customers through advanced software and expert support, helping them scale their work, streamlining complex analyses, and achieving reliable results faster.
In our solutions, we apply our knowledge using the latest sequencing technologies (Illumina, Nanopore, PacBio) with bioinformatics approaches that utilise existing, well-characterised and peer-reviewed scientific tools as well as in-house-built solutions for more specific problems. Phagenomics software combines modern software development practices with rigorous regulatory frameworks such as GAMP 5, ISO 27001 and ISO 9001, resulting in reliable and scientifically accurate products. Building on this foundation, we are passionate about providing our customers with integrated, user-friendly web platforms that bridge the gap between complex scientific pipelines and the people who need to use them. We build the entire chain from bioinformatics pipelines to intuitive platform interfaces, under one roof, combining multidisciplinary expertise.
Decades at the Forefront of Phage Research
PrecisionPhage is built on deep scientific expertise in phage research, drawing on the team’s 40 years of combined experience in phage biology, spanning areas such as phage therapy, host–phage interactions, plasmid-dependent phages, virus taxonomy, and phage resistance.
Two of the company’s founders, Matti Jalasvuori and Saija Kiljunen, lead phage research groups at Finnish universities and also serve as scientific experts for the company’s phage solutions, ensuring that our development is grounded in deep scientific expertise and robust scientific evidence. See the latest article by Matti and Saija on phage therapy in Nature Reviews Methods Primers, and explore more of our team’s phage research in our articles.
Pioneering Phage Therapy Research in Finland
Saija has been among the pioneers of clinical phage therapy research and treatment in Finland for more than a decade, working as a group leader at the University of Helsinki. Her extensive research in phage therapy spans topics such as phage-host interactions, developing methods for phage purification, QC analysis and formulation, and studying the efficacy of phage therapy in animal trials.
In the recent trial treatment of Saija’s research, phage-antibiotic combination therapy was used to treat recurrent Pseudomonas septicemia in a patient with an arterial stent. The treatment resulted in a successful clinical outcome, with the phage treatment demonstrating synergy with antibiotic therapy. Read more about the study.
Expertise and insights gained from the compassionate use of phage therapy, particularly regarding phage product quality, genome stability, and factors that may affect treatment, contribute in many ways to the development of Phagenomics software.
Quality & Compliance Expertise for GMP Environments
Quality and compliance are fundamental to our company, enabling us to develop sustainable, high-quality practices across our operations while meeting recognized industry standards and certification requirements. Quality is also at the core of our flagship bioinformatics software, Phagenomics BatchQC, which is designed for GMP environments and developed with quality principles guiding every stage of the process.
– We are committed to supporting our customers staying at the forefront of regulatory compliance and ensuring safe phage production. Our upcoming Phagenomics BatchQC software provides next-generation phage genome quality control for GMP manufacturing and production with the highest quality standards, says Matti Jalasvuori, CEO of PrecisionPhage.
Within our team, quality and compliance efforts are led by experienced quality professional Johanna Ekholm, ensuring a systematic approach to maintaining high standards, continuous improvement, and regulatory compliance across our operations. Johanna is a senior medical device regulatory and quality expert with extensive experience across regulatory authority, industry, and clinical practice. She has held leadership roles in EU MDR compliance, global registrations, post-market surveillance, and ISO 13485 quality systems, and serves in PRRC-level responsibilities. With a background from the Finnish Medicines Agency and international device companies, she combines regulatory insight with practical implementation to deliver compliant, efficient, and business-aligned solutions.
Pharmaceutical & Healthcare Industry Expertise
Understanding the highly specific needs of our customers is at the center of all our operations at PrecisionPhage. We are committed to delivering high-quality, tailored solutions that create value across a broad range of applications involving the development and use of phage-based technologies.
To support this, our team’s deep industry expertise spans the phage and pharmaceutical sectors. Olli Pitkänen, the company’s Chief Development Officer, brings extensive insight into the phage industry, its unique dynamics and evolving landscape, as well as the strategic needs and opportunities driving the growth of companies across the sector.
Pauliina Lajunen, PrecisionPhage’s Chief Business Officer, brings years of experience in the pharmaceutical and life science industries, along with extensive insight into highly regulated environments and their requirements. Pauliina is an experienced business and commercial executive with a solid background in pharma, healthcare, and medical devices. She has a strong track record in international commercialization and change management in regulated markets.
Explore Our Team’s Scientific Research & Publications
We hope this article has provided a closer look at our team and their expertise. Below, you can explore our team members’ research profiles and publications, as well as a selection of articles published in recent years.
- Saija Kiljunen’s research projects on The University of Helsinki research group website
- Matti Jalasvuori’s research projects on The University of Jyväskylä research portal
- Ville Hoikkala’s research on Google Scholar
- Matthieu Bruneaux’s research projects on his personal website
- Liisa Chisty’s research projects on Researchgate
- Nitin Agrawal’s research projects on Orcid
- Aditya Jeevannavar's research on Google Scholar
Phage therapy
Skurnik M., Alkalay-Oren S., Boon M., Clokie M., Sicheritz-Pontén T., Dąbrowska K., Hatfull G.F., Hazan R., Jalasvuori M., Kiljunen S., Lavigne R., Malik D.J., Nir-Paz R. & Pirnay J.-P. 2025. Phage therapy. Nature Reviews Methods Primers 5: 1–21. Read more
Otava U.E., Tervo L., Havela R., Vuotari L., Ylänne M., Asplund A., Patpatia S. & Kiljunen S. 2024. Phage-Antibiotic Combination Therapy against Recurrent Pseudomonas Septicaemia in a Patient with an Arterial Stent. Antibiotics (Basel, Switzerland) 13: 916. Read more
Kiljunen S. & Resch G. 2024. Editorial: Standards in personalized phage therapy: from phage collection to phage production. Frontiers in Cellular and Infection Microbiology 14. Read more
Tuomala H., Verkola M., Meller A., Van der Auwera J., Patpatia S., Järvinen A., Skurnik M., Heikinheimo A. & Kiljunen S. 2021. Phage Treatment Trial to Eradicate LA-MRSA from Healthy Carrier Pigs. Viruses 13: 1888. Read more
Sozhamannan, S., McKinstry, M., Lentz, S. M., Jalasvuori, M., McAfee, F., Smith, A., ... & Read, T. D. (2008). Molecular characterization of a variant of Bacillus anthracis-specific phage AP50 with improved bacteriolytic activity. Applied and environmental microbiology, 74(21), 6792-6796. Read more
Phages, plasmids and antibiotic resistance
Jonsdottir I., Given C., Penttinen R. & Jalasvuori M. 2023. Preceding Host History of Conjugative Resistance Plasmids Affects Intra- and Interspecific Transfer Potential from Biofilm. mSphere 8: e00107-23. Read more
Penttinen R., Given C. & Jalasvuori M. 2021. Indirect Selection against Antibiotic Resistance via Specialized Plasmid-Dependent Bacteriophages. Microorganisms 9: 280. Read more
Ruotsalainen P., Penttinen R., Mattila S. & Jalasvuori M. 2019. Midbiotics: conjugative plasmids for genetic engineering of natural gut flora. Gut Microbes 10: 643–653. Read more
Jalasvuori, M., Friman, V. P., Nieminen, A., Bamford, J. K., & Buckling, A. (2011). Bacteriophage selection against a plasmid-encoded sex apparatus leads to the loss of antibiotic-resistance plasmids. Biology letters, 7(6), 902-905. Read more
Ojala, V., Laitalainen, J., & Jalasvuori, M. (2013). Fight evolution with evolution: plasmid‐dependent phages with a wide host range prevent the spread of antibiotic resistance. Evolutionary applications, 6(6), 925-932. Read more
Phage-bacterium co-evolution
Ashrafi R., Bruneaux M., Sundberg L.-R., Hoikkala V. & Karvonen A. 2023. Multispecies coinfections and presence of antibiotics shape resistance and fitness costs in a pathogenic bacterium. Molecular Ecology 32: 4447–4460. Read more
Laanto E., Hoikkala V., Ravantti J. & Sundberg L.-R. 2017. Long-term genomic coevolution of host-parasite interaction in the natural environment. Nature Communications 8: 111. Read more
Bruneaux M., Ashrafi R., Kronholm I., Laanto E., Örmälä-Tiznado A.-M., Galarza J.A., Zihan C., Kubendran Sumathi M. & Ketola T. 2022. The effect of a temperature-sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen. Molecular Ecology 31: 5402–5418. Read more
Cairns, J., Koskinen, K., Penttinen, R., Patinen, T., Hartikainen, A., Jokela, R., ... & Jalasvuori, M. (2018). Black queen evolution and trophic interactions determine plasmid survival after the disruption of the conjugation network. Msystems, 3(5), 10-1128. Read more
Hiltunen, T., Cairns, J., Frickel, J., Jalasvuori, M., Laakso, J., Kaitala, V., ... & Becks, L. (2018). Dual-stressor selection alters eco-evolutionary dynamics in experimental communities. Nature Ecology & Evolution, 2(12), 1974-1981. Read more
Marta Orzechowski, Ville Hoikkala, Haotian Chi, Stephen McMahon, Tracey Gloster, Malcolm F White; A viral SAVED protein with ring nuclease activity degrades the CRISPR second messenger cA4. Biochem J 19 November 2025; 482 (22): 1707–1719. Read more
Chi H., Hoikkala V., Grüschow S., Graham S., Shirran S. & White M.F. 2023. Antiviral type III CRISPR signalling via conjugation of ATP and SAM. Nature 622: 826–833. Read more
Hoikkala V., Ravantti J., Díez-Villaseñor C., Tiirola M., Conrad R.A., McBride M.J., Moineau S. & Sundberg L.-R. 2021. Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System. mBio 12: 10.1128/mbio.03338-20. Read more
Hoikkala V, Almeida GMF, Laanto E, Sundberg LR. Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage. Philos Trans R Soc Lond B Biol Sci. 2019;374(1772):20180100. Read more
Hoikkala V., Graham S. & White M.F. 2024. Bioinformatic analysis of type III CRISPR systems reveals key properties and new effector families. Nucleic Acids Research 52: 7129–7141. Read more
See more
- Phagenomics BatchQC – GMP-compatible platform for phage genome quality control in phage production
- Phagenomics Core – Phage genome assembly, annotation, and genomic comparison software
