Projects per year
Personal profile
Research expertise
My scientific career is driven by the fundamental challenge of uncovering the link between genes and their functions, aiming to fill gaps in biological knowledge using computational algorithms tailored to big data. I have developed computational tools for constructing and analyzing regulatory networks in specific biological pathways. My primary goal is to enhance the integration of computational biology and data science into clinical research, particularly in tackling Mycobacterium tuberculosis (MTB) drug resistance.
Since transitioning to clinical sciences in September 2019, I have gradually expanded my research interests in multi-omics, which integrates information from orthogonal technologies (e.g., RNA/DNA NGS, proteomics, and structural biology) and different molecular layers (e.g., metabolites, proteins, and genes). Additionally, I have developed expertise in artificial intelligence, including the advanced use of large language models (LLMs) to integrate and analyze complex biological datasets, facilitating novel hypothesis generation and accelerating research workflows.
During my career, I have developed several computational user-friendly tools aimed at utilizing omics data sets for biological discoveries.
An example of these tools includes:
•MORPH http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/ is an algorithm designed to find candidate genes for specific metabolic pathways.
•MORPH.DB (http://bioinformatics.psb.ugent.be/webtools/coexpr/) a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins) are integrated across multiple plant species.
•CoExpNetViz (http://bioinformatics.psb.ugent.be/webtools/coexpr/) is a tool for construction of co-expression networks (either in a single species or in a comparative transcriptomic manner).
•The hfAIM web-based tool (http://bioinformatics.psb.ugent.be/hfAIM/) can be used to effectively perform genome-wide in silico screens of proteins that are potentially regulated by selective autophagy.
•Cedalion, is a hypothesis generation platform that assists biologists with the interpretation of a newly sequenced genome (https://gitlab.psb.ugent.be/deep_genome/pipeline).
Teaching expertise
Oren Tzfadia is dedicated to educating young scientists who wish to utilize bioinformatic tools for solving biological puzzles.
I teach:
- Introduction to Systems Biology
- Introduction to UNIX command line and WGS pipelines
- Introduction to AlphaFold and Protein Structural Analysis
I am also:
- Coaching master's students at ITM.
- Supervising PhD candidates at ITM and UA.
Education/Academic qualification
Bioinformatics
External positions
10%, University of Antwerp
Keywords
- B110-bioinformatics
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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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TB/NTM Cluster: TB/NTM Onderzoekscluster
Sengstake, S., Rigouts, L., Tzfadia, O., Ardizzoni, E., Lynen, L., Decroo, T., Hasker, E., Van Rie, A., Lynen, L., Hasker, E. & de Jong, B.
1/01/22 → 31/12/26
Project: Research Project
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IntegrOmicsDR: Multi Omics Data Integration to predict the M. tuberculosis Bedaquiline Resistance Phenotype from the Genotype
Tzfadia, O., de Jong, B. & de Jong, B.
1/01/22 → 31/12/25
Project: Research Project
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SNA_Leprosy: Improving leprosy prevention strategies by integrating social network analysis with spatial and molecular epidemiology data of Mycobacterium leprae in the Comoros
Peeters, K., Hasker, E., de Jong, B., Ronse, M., Verdonck, T., Braet, S., Tzfadia, O., Ramanantsoa, A. & Peeters, K.
Flemish Government - Department of Work, Economy, Science, Innovation
1/01/21 → 31/12/26
Project: Research Project
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Omics Data Integration to Predict Drug Resistance in Mycobacterium tuberculosis
Snobre, J., de Jong, B., Buyl, R. & Tzfadia, O.
27/04/22 → 5/09/25
Project: PhD-project
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Data integration to close the gap on Prediction of MTB Drug Resistance Mutations
de Jong, B., Tzfadia, O. & Janssens, N.
Flemish Government - Department of Economy, Science & Innovation
20/10/20 → 20/10/21
Project: Research Project
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Quality control and considering systematic MIC shifts are key when evaluating the role of mmpR5 (Rv0678) frameshifts in bedaquiline resistance
Snobre, J., Meehan, CJ., Mulders, W., Rigouts, L., Buyl, R., de Jong, BC., Van Rie, A. & Tzfadia, O., 2025, (E-pub ahead of print) In: Antimicrobial Agents and Chemotherapy. 3 p., e00317-25.Research output: Contribution to journal › Letter › peer-review
Open Access -
Frameshift mutations in the mmpR5 gene can have a bedaquiline-susceptible phenotype by retaining a protein structure and function similar to wild-type Mycobacterium tuberculosis
Snobre, J., Meehan, CJ., Mulders, W., Rigouts, L., Buyl, R., de Jong, BC., Van Rie, A. & Tzfadia, O., 2024, In: Antimicrobial Agents and Chemotherapy. 68, 12, 15 p.Research output: Contribution to journal › A1: Web of Science-article › peer-review
Open Access -
Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets
Tzfadia, O., Gijsbers, A., Vujkovic, A., Snobre, J., Vargas, R., Dewaele, K., Meehan, CJ., Farhat, M., Hakke, S., Peters, PJ., de Jong, BC., Siroy, A. & Ravelli, RBG., 2024, In: Microbiology Spectrum. 12, 8, 19 p.Research output: Contribution to journal › A1: Web of Science-article › peer-review
Open Access -
Volatile organic compound detection of Buruli ulcer disease: Headspace analysis of Mycobacterium ulcerans and used gauzes of Buruli-compatible ulcers
Chudy, SFJ., Phanzu, D. M., Kolk, AHJ., Sopoh, GE., Barogui, Y. T., Tzfadia, O., Eddyani, M., Fissette, K., de Jong, BC. & Brinkman, P., 2024, In: PLoS Neglected Tropical Diseases. 18, 9, 16 p., e0012514.Research output: Contribution to journal › A1: Web of Science-article › peer-review
Open Access -
Bedaquiline- and clofazimine- selected Mycobacterium tuberculosis mutants: further insights on resistance driven largely by Rv0678
Snobre, J., Villellas, M. C., Coeck, N., Mulders, W., Tzfadia, O., de Jong, B. C., Andries, K. & Rigouts, L., 2023, In: Scientific Reports. 13, 1, 11 p., 10444.Research output: Contribution to journal › A1: Web of Science-article › peer-review
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