Publications

Selected publications by Biovista R&D team.

• The FAIR AOP roadmap for 2025: Advancing findability, accessibility, interoperability, and re-usability of adverse outcome pathway Holly M. Mortensen, Maciej Gromelski, Ginnie Hench, Marvin Martens, Clemens Wittwehr, Saurav Kumar, Vikas Kumar, Karine Audouze, Vassilis Virvilis, Penny Nymark, Michelle Angrish, Iseult Lynch, Stephen Edwards, Barbara Magagna, Marcin W. Wojewodzic. Computational Toxicology, Volume 35, 2025. DOI: 10.1016/j.comtox.2025.100368.
• Benchmarking Artificial Intelligence Algorithms for Drug Repurposing on Open Targets Platform Peter-Bram ‘t Hoen, Christo Sasi, Jelle Piepenbrock, Vassilis Virvilis, Eftychia Lekka et al 2025. DOI: 10.14293/iDR.25.005PB
• Nymark P. et al. (2024). Building an Adverse Outcome Pathway network for COVID-19. Systems and Synthetic Immunology. Volume 4 DOI: 10.3389/fsysb.2024.1384481
• Why adverse outcome pathways need to be FAIR Wittwehr, C., Clerbaux, L.-A., Edwards, S., Angrish, M., Mortensen, H., Carusi, A., Gromelski, M., Lekka, E., Virvilis, V., Martens, M., Bonino da Silva Santos, L. O. and Nymark, P. (2023), ALTEX – Alternatives to animal experimentation. DOI: 10.14573/altex.2307131.
• Wittwehr, C. et al. (2023). Methods2AOP: An International Collaboration to Integrate Assay Annotations into the AOP Key Event Descriptions. Society of Toxicology 62nd Annual Meeting and ToxExpo 2023, Nashville, TN, March 19 – 23, 2023. DOI: 10.23645/epacomptox.23564160
• GABA_A receptor-mediated seizure liabilities: a mixed-methods screening approach
  Konstantina Bampali, Filip Koniuszewski, Florian D. Vogel, Jure Fabjan, Christos Andronis, Eftychia Lekka, Vassilis Virvillis, Thomas Seidel, Annie Delaunois, Leandro Royer, Michael G. Rolf, Chiara Giuliano, Martin Traebert, Gautier Roussignol, Magali Fric-Bordat, Ludmilla Mazelin-Winum, Sharon D. Bryant, Thierry Langer & Margot Ernst Cell Biol Toxicol (2023). DOI: 10.1007/s10565-023-0
• IND02-05 The NeuroDeRisk toolbox: DeRisking chemical structures for neurotoxic adverse outcomes
  D. Bryant, G. Ibis, T. Seidel, S. Kohlbacher, J. Heider, M. Ernst, K. Bampali, F. Koniuszewski, V. Virvilis, E. Lekka, A. Persidis, M.-A. Mayache, D. Weissmann, T. Langer September 2022 Toxicology Letters 368:S82 DOI: 10.1016/j.toxlet.2022.07.239
• Molecular basis of mood and cognitive adverse events elucidated via a combination of pharmacovigilance data mining and functional enrichment analysis Christos Andronis, João Pedro Silva, Eftychia Lekka, Vassilis Virvilis, Helena Carmo, Konstantina Bampali, Margot Ernst, Yang Hu, Irena Loryan, Jacques Richard, Félix Carvalho & Miroslav M. Savić Archives of Toxicology 94, 2829–2845 (2020) DOI: 10.1007/s00204-020-02788-1
• Topiramate protects apoE-deficient mice from kidney damage without affecting plasma lipids Stefano Manzini, Marco Busnelli, Cinzia Parolini, Lucia Minoli, Alice Ossoli, Elena Brambilla, Sara Simonelli, Eftychia Lekka, Andreas Persidis, Eugenio Scanziani, Giulia Chiesa Pharmacol Res. 2019 Mar;141:189-200. DOI: 10.1016/j.phrs.2018.12.022. Epub 2018 Dec 26.
• Systematic Drug Repositioning chapter in Drug Repositioning 2017 Spyros N. Deftereos, Aris Persidis, Andreas Persidis, Eftychia Lekka, Christos Andronis, Vassilis Virvillis DOI: 10.4324/9781315373669
• Drug repurposing of Pirlindole for Multiple Sclerosis Spyros N. Deftereos, Eftychia Lekka, Christos Andronis, Andreas Persidis figshare Feb 2017 DOI: 10.6084/m9.figshare.4658932.v5
• Association of microbiome organisms to Regulatory T Cell function in cancer and inflammation. Eftychia Lekka, Christos Andronis figshare Nov 2016 DOI: 10.6084/m9.figshare.4056489.v1
• Binary Relation Extraction from Biomedical Literature using Dependency Trees and SVMs Anuj Sharma, Vassilis Virvilis, Tina Lekka, Christos Andronis bioRxiv October 2016 DOI: 10.1101/082479
• Hypothyroidism is a Risk Factor for New-Onset Diabetes: A Cohort Study. Gronich, N., Deftereos, SN., Lavi, I., Persidis AS., Abernethy DR. & Rennert G. (2015) Diabetes Care. 2015 Sep;38(9):1657-64. DOI: 10.2337/dc14-2515. Epub 2015 Jun 12.
• Current therapeutic strategies for myalgic encephalomyelitis/chronic fatigue syndrome: results of an online survey. Spyros N. Deftereos, Suzanne D. Vernon & Andreas Persidis (2014) Fatigue: Biomedicine, Health & Behavior, DOI: 10.1080/21641846.2015.1126025
• Molecular docking cannot accurately predict drug off-target effects: implications for the role of voriconazole in the exacerbation of myasthenia gravis. Muscle & Nerve. Accepted for Publication. Deftereos SN.
• From depression to neurodegeneration and heart failure: re-examining the potential of MAO inhibitors. Deftereos SN, Dodou E, Andronis C, Persidis A. Expert Rev Clin Pharmacol. 2012 Jul;5(4):413-25.
• Business Development Strategies in the Repositioning Industry. Persidis, A. and Stark, E. T. (2012), in Drug Repositioning: Bringing New Life to Shelved Assets and Existing Drugs (eds M. J. Barratt and D. E. Frail), John Wiley & Sons, Inc., Hoboken, NJ, USA. DOI: 10.1002/9781118274408.ch13
• Mining Scientific and Clinical Databases to Identify Novel Uses for Existing Drugs. Andronis, C., Sharma, A., Deftereos, S., Virvilis, V., Konstanti, O., Persidis, A. and Persidis, A. (2012), in Drug Repositioning: Bringing New Life to Shelved Assets and Existing Drugs (eds M. J. Barratt and D. E. Frail), John Wiley & Sons, Inc., Hoboken, NJ, USA. DOI: 10.1002/9781118274408.ch6
• Drug Repositioning on the Cloud. Vassilis Virvilis, Anuj Sharma, Miltiadis Koutsokeras, Cloud Computing Technology and Science, IEEE International Conference on, pp. 577-581, 2011 IEEE Third International Conference on Cloud Computing Technology and Science, 2011. DOI: 10.1109/CloudCom.2011.88
• Letter to Editor: Is a single type of data sufficient for accurate computational drug repositioning? Deftereos SN and Andronis C. September 2011 Science Translational Medicine: 13 Sep 2011.
• Literature analysis for systematic drug repurposing: a case study from Biovista. Lekka, E., S.N. Deftereos, A. Persidis, A. Persidis, and C. Andronis. 2011. Drug Discovery Today: Therapeutic Strategies. 8:103–108.
• Literature mining, ontologies and information visualization for drug repurposing. Andronis, C., A. Sharma, V. Virvilis, S. Deftereos, and A. Persidis. 2011. Brief. Bioinformatics. 12:357–368. DOI: 10.1093/bib/bbr005
• Drug repurposing and adverse event prediction using high-throughput literature analysis. Deftereos, S.N., C. Andronis, E.J. Friedla, A. Persidis, and A. Persidis. 2011. Wiley Interdiscip Rev Syst Biol Med. 3:323–334.
• Discordant effects of rasagiline doses in Parkinson disease. Deftereos, S.N., and C.A. Andronis. 2010. Nat Rev Neurol. 6:1p following 410.
• Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach. Rinaldi, F., G. Schneider, K. Kaljurand, M. Hess, C. Andronis, O. Konstandi, and A. Persidis. 2007. Artif Intell Med. 39:127–136.
• Novel biological networks modulated by complement. Mastellos, D., C. Andronis, A. Persidis, and J.D. Lambris. 2005. Novel biological networks modulated by complement. Clin. Immunol. 115:225–235.
• Relation mining over a corpus of scientific literature. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Christos Andronis, Andreas Persidis, and Ourania Konstanti. 2005. In Proceedings of the 10th conference on Artificial Intelligence in Medicine (AIME’05), Silvia Miksch, Jim Hunter, and Elpida T. Keravnou (Eds.). Springer-Verlag, Berlin, Heidelberg, 535-544. DOI: 10.1007/11527770_70 .
• Systems literature analysis. Persidis, A., S. Deftereos, and A. Persidis. 2004. Pharmacogenomics. 5:943–947.

Additional Biovista articles can be found here …