MU OmicsLab
(Computational Toxicology & Bioinformatics Lab) is a growing research direction led by Assoc. Prof. Yordan Yordanov (Toxicology Section, Department of Pharmacology, Pharmacotherapy and Toxicology, Faculty of Pharmacy, Medical University – Sofia).
The lab bridges experimental toxicology with bioinformatics, AI-assisted analysis, and reproducible workflows—from cell-based models to omics interpretation and computational toxicology.
- MU OmicsLab is currently a small unit (PI-led) and is actively building capacity through diploma and PhD mentorship, collaborations, and shared infrastructure.
- Want to collaborate or join? → contact us · свържете се с нас
What we do
- Computational toxicology: mechanism-focused interpretation of toxicological effects using multi-omics and structured data.
- Bioinformatics: RNA-seq and transcriptomics; pathway and signature analysis; integrative interpretation.
- RNA therapeutics & delivery (computational support): design logic for RNA constructs and evaluation strategies aligned to cellular pathways.
- Image analysis: quantitative microscopy workflows and ML-assisted segmentation/phenotyping.
- AI for biomedical decision support: safe, transparent prototypes for summarization and contextual interpretation (research use only).
Explore
Keywords: computational toxicology · bioinformatics · transcriptomics · image analysis · reproducible research · AI/ML
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Related Topics
- About
About MU OmicsLab
MU OmicsLab (Computational Toxicology & Bioinformatics Lab) is a research direction at the Faculty of Pharmacy, Medical University – Sofia, focused on connecting experimental toxicology with bioinformatics and computational analysis.
The lab is led by Assoc. Prof. Yordan Yordanov, an expert with a long-standing interest in data-driven mechanistic interpretation and practical experience in in vitro toxicology (cell culture models) and in vivo work (rats, mice, Drosophila).
How we are positioned
MU OmicsLab is tightly connected with the Toxicology Section in the Department of Pharmacology, Pharmacotherapy and Toxicology. Many experimental efforts are supported through team expertise in in vitro and in vivo toxicology, while MU OmicsLab contributes bioinformatics, automation, and computational interpretation.
- Research
MU OmicsLab focuses on computational toxicology and bioinformatics, with an emphasis on methods that can be applied across projects and shared with collaborators.
1) Bioinformatics for toxicology
- RNA-seq / transcriptomics workflows (QC → DE → enrichment → signatures)
- Context-aware interpretation: pathways, mechanisms, drug–gene relationships
- Integrative thinking across experimental systems and public resources
2) Computational toxicology & mechanism modeling
- Hypothesis-driven interpretation of toxicity phenotypes
- Translating omics signals into pharmacodynamic targets and mechanism narratives
- Risk-aware interpretation and reporting (limitations, uncertainty, reproducibility)
3) Image analysis & ML-assisted microscopy
- Quantitative microscopy pipelines (segmentation, feature extraction, scoring)
- ML for robust, scalable analysis of phase-contrast and fluorescence images
- Reproducible reporting for experimental toxicology studies
4) RNA therapeutics & delivery (bioinformatics/logic support)
- Design logic for RNA constructs aligned to cellular markers and pathways
- Computational evaluation strategies for target selection and safety reasoning
- Collaboration with experimental teams working on nanoparticles and delivery systems
5) AI-assisted research tools (research prototypes)
- LLM-supported summarization and contextualization for complex biomedical knowledge
- Transparent, safety-aware workflows for research—not clinical decision-making
Want to discuss a project idea? → contact us · свържете се с нас
- Publications
Strong bioinformatics focus
- Yordanov Y, Tzankova V, Stefanova D, Georgieva M, Tzankova D. Exploratory Data Analysis of the In Vitro Effects of Novel Hydrazide-Hydrazone Antioxidants in the Context of In Silico Predictors. Antioxidants. 2025 May 8;14(5):566.
- RNA-seq study (poster at EuroTox): Yordanov Y, Bozhilova R, Tzankova V, Mohr T. P06-16 Application of transcriptomic analysis to an MPP+-induced in vitro 2D model system for studying Parkinson’s disease in search of potential drug modulators. Toxicology Letters. 2024 Sep;399:S158-.
Image analysis
- Monograph: Yordanov Y. Image Analysis in Experimental Toxicology (Bulgarian).
- Yordanov Y. Hep G2 cell culture confluence measurement in phase-contrast micrographs–a user-friendly, open-source software-based approach. Toxicology mechanisms and methods. 2020 Feb 12;30(2):146-52.
- Kalinova R, Yordanov Y, Tzankov B, Tzankova V, Yoncheva K, Dimitrov I. Cinnamyl modified polymer micelles as efficient carriers of caffeic acid phenethyl ester. Reactive and Functional Polymers. 2020 Dec 1;157:104763.
- Georgiev GP, Tubbs RS, Olewnik Ł, Zielinska N, Telang M, Ananiev J, Dimitrova IN, Slavchev SA, Yordanov Y, LaPrade RF, Ruzik K. 2022. A comparative study of the epiligament of the medial collateral and anterior cruciate ligaments in the human knee: Immunohistochemical analysis of CD 34, α-smooth muscle actin and vascular endothelial growth factor in relation to epiligament theory. The Knee, 39, pp.78-90.
- Georgiev GP, Kotov G, Iliev A, Slavchev S, Ovtscharoff W, Landzhov B. A comparative study of the epiligament of the medial collateral and the anterior cruciate ligament in the human knee. Immunohistochemical analysis of collagen type I and V and procollagen type III. Annals of Anatomy-Anatomischer Anzeiger. 2019 Jul 1;224:88-96.
- Stefanova D, Yordanov Y, Bogdanova R, Voycheva C, Tzankov B, Popova T, Kondeva-Burdina M, Tzankova V, Toncheva-Moncheva N, Tzankova D, Slavkova M. In Vitro Evaluation of the Safety and Antineoplastic Effects in Gastrointestinal Tumors of Nanostructured Lipid Carriers Loaded with Berberine. Pharmaceutics. 2025 Mar 4;17(3):331.
Parkinson’s Disease
- Yordanov Y, Stefanova D, Kondeva-Burdina M, Tzankova V. Sources of Oxidative Stress in Parkinson’s Disease: Pathways and Therapeutic Implications. Antioxidants. 2026 Feb 2;15(2):187.
RNA constructs
- Slavkova M, Yordanov Y, Voycheva C, Popova T, Spassova I, Kovacheva D, Tzankova V, Tzankov B. Synthesis of Folic Acid-Functionalized Hybrid Mesoporous Silica Nanoparticles and In Vitro Evaluation on MCF-7 Breast Cancer Cells. International Journal of Molecular Sciences. 2026 Jan 22;27(2):1092.
Ultrafine particle toxicology
- Vasileva K, Yordanov Y, Manasiev Y, Stefanova D, Kondeva-Burdina M, Tzankova V, Panev T, Naydenova I, Georgieva T. Aerosols produced during biomass conversion and their organic extracts–cytotoxic and oxidative response of a lung cell model system. Pharmacia. 2025 Aug 13;72:1-7.
If you want to propose a joint analysis or co-authorship pipeline → contact us · свържете се с нас
- Team
MU OmicsLab is a Research Unit inside the Toxicology Section at the Faculty of Pharmacy, MU–Sofia, lead by Prof. Virginia Tzankova. This Unit combines computational analysis with strong experimental toxicology expertise (in vitro and in vivo), enabling integrated projects, co-mentorship, and realistic validation plans.
Principal investigator (MU OmicsLab)
Faculty of Pharmacy, Medical University – Sofia
Research Institute of Innovative Medical Science (InnoMedSci), Division “Artificial Intelligence in Healthcare” - Collaborations
MU OmicsLab grows through collaboration—pairing experimental toxicology with bioinformatics expertise.
Within MU–Sofia
- Close integration with the Toxicology Section and all Sections and Departments at the Faculty of Pharmacy, MU - Sofia (in vitro / in vivo expertise and training environment)
Bulgaria (external)
- Toxicology collaboration with Prof. Tzveta Georgieva and sen. expert Krasimira Vasileva at the National Center of Public Health and Analyses (Sofia)
(example output) - Computational toxicology links with Acad. Ilza Pajeva, Prof. Ivanka Tsakovska and expert Petko Alov at Bulgarian Academy of Sciences
(example output)
International
- Long-standing collaboration roots connected to research stays in University of Siena, Italy
- Prof. Massimo Valoti
- Prof. Simona Saponara
- Prof. Maria Frosini
- Collaboration with Medical University - Graz, Austria
- Collaborations with computational toxicologists in OpenTox and Edelweiss Connect
- Dr. Barry Hardy
- expert Asmaa Ali
- Collaboration with bioinformatics experts from ScienceConsult—DI Thomas Mohr, University if Vienna, Medical University of Vienna:
- Dr. Thomas Mohr
If you have a dataset or a hypothesis that needs bioinformatics support → contact us · свържете се с нас
- News
This section shares:
- new collaborations and visits
- student thesis announcements
- project milestones and publications
- training opportunities in bioinformatics and reproducible analysis
If you want to be featured as a collaborator or student author → contact us · свържете се с нас
- Contact
- Email: yyordanov@pharmfac.mu-sofia.bg
- Affiliation: Faculty of Pharmacy, Medical University – Sofia
- Area: Computational Toxicology & Bioinformatics (MU OmicsLab)
What to include in your message
- Who you are and your affiliation
- What you want to achieve (paper / thesis / project / analysis)
- What data you have (type, size, format)
- Your expected timeline (if relevant)
BG page: свържете се с нас
- Resources
Computational Infrastructure
Our laboratory maintains high-performance computing resources for bioinformatics research and data analysis.
Available Resources
- Dedicated computational servers
- Bioinformatics software and tools
- Data storage and management systems
- Training and documentation
Access
Resources are available to laboratory members and authorized collaborators. Please contact us for access information.