Systems Bioinformatics Unit: Advancing Bioinformatics research in Cyprus, Europe, and beyond
Located at the University of Cyprus, the Systems Bioinformatics Unit within the Zanos laboratory, led by Dr. Anna Onisiforou, has a primary goal to bridge the gap between complex biological data and clinical applications, thereby accelerating the translation of findings from basic research into personalized therapeutic solutions. By establishing and employing novel advanced computational methodologies and algorithms, the unit aims to unravel the complexities of molecular interactions, signaling pathways, and genetic predispositions underlying brain diseases. This not only aids in identifying potential drug targets but also enhances our understanding of individual variability in drug responses, paving the way for personalized treatments and the development of more effective therapeutic interventions for brain diseases including, but not limited to neuropsychiatric, neurodevelopmental and neurodegenerative diseases.
Our Bioinformatics Unit is a highly inter-disciplinary research unit supporting:
- drug repurposing
- in silico drug modeling
- molecular docking
- network analysis
- multi-omics analysis
- single-cell analysis
- machine learning
- deep learning
- clinical bioinformatics
- chemoinformatics
- immunoinformatics
- pathogen-host interactions analysis
In our pursuit, we are utilizing state-of-the-art High-Performance Computing (HPC), facilitating efficient handling and comprehensive analysis of extensive, complex biological datasets.
We are happy to offer our Systems Bioinformatics expertise to collaborating investigators!
Team Members (more details in the Team Members section)
Dr. Anna Onisiforou, BA, BSc, MSc, MSc, Ph.D.
Head of the Systems Bioinformatics Unit
Dr. Onisiforou holds a B.Sc. (Hons) in Natural Sciences with direction in Biology and Chemistry, a M.Sc. in Medicinal Chemistry, and a Ph.D. in Neuroscience. She also holds a B.A. (Hons) in Accounting and Finance and a M.Sc. in Finance and Financial Law.
Dr. Onisiforou completed her Ph.D. in Neuroscience, at The Cyprus Institute of Neurology & Genetics, hosted in the Bioinformatics Department, from 2018 to 2022. Her multifaceted expertise spans bioinformatics, neuroscience, medicinal chemistry, as well as business, accounting, finance, and financial law. During this period, her research focused on pioneering Systems Bioinformatics methodologies to explore the intricate interplay between viruses and host processes, particularly their implications in neurodegenerative diseases.
Her doctoral work was instrumental in identifying key viral-pathogenic mechanisms through innovative approaches like virus-host protein-protein interactions, molecular mimicry, and microbiota-virus interactions. These methodologies not only shed light on the role of viruses in neurodegenerative diseases but also hold promise in studying other diseases influenced by pathogenic organisms, ranging from autoimmune diseases to neuropsychiatric disorders.
Dr. Onisiforou’s contributions expanded further amid the COVID-19 pandemic, where her research delved into the mechanisms linking COVID-19 to neurological diseases and neuropsychiatric disorders. Her work provided critical mechanistic insights, paving the way for future studies on prophylactic treatments and therapeutic targets for neurodegenerative diseases, considering viral infections in their pathogenesis.
Dr. Onisiforou’s excellence extends beyond her Ph.D. studies. Her current role as a Research Associate and head of the Systems Bioinformatics Unit in the Translational Neuropharmacology Laboratory at the University of Cyprus highlights her continued success in both computational and experimental neuroscience.
Current projects led by Dr. Onisiforou include the identification of viral-mediated pathogenic mechanisms by which viruses can lead to the development of comorbid Alzheimer’s Disease and major depression using Systems Bioinformatics. This project is funded by a grant obtained by Drs. Onisiforou and Zanos from the IDSA Foundation. For more information on this work, please see our recent publication:
https://academic.oup.com/jid/article/230/Supplement_2/S128/7754707
Additionally, Dr. Onisiforou’s current work involves investigating comorbid diseases, with a particular focus on comorbid neuropsychiatric disorders and neurodegenerative diseases, among others. In a recent publication in collaboration with the Neuroepidemiology Department of The Cyprus Institute of Neurology & Genetics, we employed systems bioinformatics methods to analyze single-nucleus RNA and bulk mRNA transcriptomic data of Parkinson’s Disease (PD) and Major Depressive Disorder (MDD). Mood disorders, such as depression, are prevalent in neurodegenerative disorders. Importantly, neuropsychiatric symptoms may manifest before neurological symptoms, leading to misdiagnoses of neuropsychiatric disorders in one-third of individuals. In the case of PD, non-motor symptoms, including depression, can appear up to a decade prior to motor features. Therefore, the identification of diagnostic biomarkers is crucial for accurately diagnosing PD during its prodromal or early stages. This analysis allowed us to identify common and unique molecular characteristics that define PD and MDD in both peripheral and brain tissues. For more information on this work, please see recent publication:
https://www.frontiersin.org/articles/10.3389/fnagi.2023.1273855/full.
Other ongoing projects involve employing both in silico, pre-clinical, and clinical drug repurposing approaches to discover novel pharmacotherapies for the treatment of depression and opioid use disorders. For more information on this work, please see our publication:
https://www.biorxiv.org/content/10.1101/2023.12.07.570550v1.
Other members of the Unit
Dr. Eleftheria Charalambous, BSc, MSc, Ph.D.
Publications (Selected)
- Onisiforou, A., Charalambous, E., Zanos, P. Shattering the Amyloid Illusion: The Microbial Enigma of Alzheimer’s Disease Pathogenesis—From Gut Microbiota and Viruses to Brain Biofilms. Microorganisms. 2025, 13(1), 90. https://doi.org/10.3390/microorganisms13010090
- Onisiforou, A., Zanos, P. One path, two solutions: Network-based analysis identifies targetable pathways for the treatment of comorbid type II diabetes and neuropsychiatric disorders, Computational & Structural Biotechnology Journal, 2024, 23, 3610-3624. https://doi.org/10.1016/j.csbj.2024.10.011
- Onisiforou, A., Zanos, P. Network-Based Analysis Identifies Targetable Pathways in Comorbid Type II Diabetes and Neuropsychiatric Disorders, bioRxiv, 2024, 06.25.600630. https://doi.org/10.1101/2024.06.25.600630.
- Onisiforou, A., Zanos, P.,Georgiou, P. Molecular signatures of premature aging in major depression and substance use disorders. Scientific Data, 2024, 11, 968. https://doi.org/10.1038/s41597-024-03538-z
- Onisiforou, A., Zanos, P. From viral infections to Alzheimer’s Disease: Unveiling the mechanistic links through Systems Bioinformatics. Journal of Infectious Diseases, 2024, 230, S128–S140. https://doi.org/10.1093/infdis/jiae242.
- Onisiforou A., Zanos P. From Viral Infections to Alzheimer’s Disease: Unveiling the Mechanistic Links Through Systems Bioinformatics. bioRxiv (2023), 12.05.570187. https://doi.org/10.1101/2023.12.05.570187.
- Christodoulou C*, Onisiforou A*, Zanos P, Zamba-Papanicolaou E. Unraveling the transcriptomic signatures of Parkinson’s Disease and Major Depression using single-cell and bulk data. Frontiers Aging Neuroscience (2023) 15. *Equal Contribution. https://doi.org/10.3389/fnagi.2023.1273855.
- Onisiforou A, Spyrou GM. Systems Bioinformatics Reveals Possible Relationship between COVID-19 and the Development of Neurological Diseases and Neuropsychiatric Disorders. Viruses (2022) 14:2270. https://doi.org/10.3390/v14102270.
- Onisiforou A, Spyrou GM. Immunomodulatory effects of microbiota-derived metabolites at the crossroad of neurodegenerative diseases and viral infection: network-based bioinformatics insights. Frontiers in Immunology (2022) 13. https://doi.org/10.3389/fimmu.2022.843128.
- Onisiforou A, Spyrou GM. Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. Briefings in Bioinformatics (2021) 22. https://doi.org/10.1093/bib/bbab141.
- Tomazou M., Bourdakou M.M., Minadakis G., Zachariou M., Oulas A., Karatzas E., Loizidou E.M., Kakouri A.C., Christodoulou C.C., Savva K., Zanti M., Onisiforou A., et al. Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19. Briefings in Bioinformatics (2021) 22: https://academic.oup.com/bib/article/22/6/bbab114/6224262?login=false
Current Collaborations in Cyprus, Europe and beyond
- Prof. Johaness Hertel, Professor (W1) in Systems Biology and Transnational Psychiatry, Department of Psychiatry ad Psychotherapy, University Medicine Greifswald – https://www2.medizin.uni-greifswald.de/psych/ueber-uns/leitungmitarbeiter/johannes-hertel/
- Dr. Polymnia Georgiou, Assistant Professor of Neuroscience and Endocrinology, University of Cyprus, Cyprus and University of Wisconsin-Milwaukee, USA – https://polymniageo.wixsite.com/georgioulab
- PD Dr. med. Fabian Frost, Clinician Scientist at Department of Medicine A, University Medicine Greifswald, Germany – https://scholar.google.de/citations?user=R90o5jwAAAAJ&hl=de
- Dr. Christiana Christodoulou, Senior Scientist, Neuroepidemiology Department, Cyprus Institute of Neurology and Genetics – https://scholar.google.com/citations?user=txcJxewAAAAJ&hl=en
- Prof. Eleni Zamba Pananicolaou, Head of Neuroepidemiology Department and EMG Laboratory, Senior Consultant Neurologist, Cyprus Institute of Neurology and Genetics – https://www.cing.ac.cy/easyconsole.cfm/id/258
Systems Bioinformatics Unit: Secured Grants
| Grant Acronym | Grant Title | Funding Agency | Principal Investigator | Funding Amount |
|---|---|---|---|---|
| ALZHEIMER | Identification of viral-mediated pathogenic mechanisms in comorbid Alzheimer’s Disease and Major Depression using Systems Bioinformatics | Infectious Diseases Society of America (IDSA, USA) | Dr. Anna Onisiforou; co-PI: Dr. Panos Zanos | €96,941 |
| ALZ-RISK | Sex-Specific Mechanisms of HSV-1 and EBV in Alzheimer’s Disease Risk | Infectious Diseases Society of America (IDSA, USA) | Dr. Anna Onisiforou; co-PI: Dr. Panos Zanos | €100,000 |
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