Dr Jean Paul Ebejer

Dr Jean Paul Ebejer

Dr Jean Paul Ebejer


Senior Lecturer

Centre for Molecular Medicine and Biobanking
Room 320
Biomedical Sciences Building
University of Malta
  +356 2340 3263
Dr Jean-Paul Ebejer read an undergraduate bachelors degree in I.T. at the University of Malta, graduating with honours in 2000. Immediately after he moved to Germany, where he worked for IBM as an IT specialist on Foreign Exchange and Money Market systems for Credit Suisse and Deutsche Bank. In 2004 he started working for Ixaris Systems, on their flagship product Entropay, where he eventually became a technical architect. Following an MGSS scholarship and his strong interest in biological systems, data sciences, and "anything for which an explanation is in short supply" he successfully completed, with distinction, an M.Sc. in Bioinformatics and Theoretical Systems Biology at Imperial College, London (2008-2009). He was then awarded a Marie Curie Fellowship to undertake a doctoral degree in structural bioinformatics and computational drug discovery at the University of Oxford. He completed his D.Phil. in early 2014 under the supervision of Prof. Charlotte Deane and Prof. Garrett Morris.

During his years in industry he has always kept a strong link with academia and has lectured a variety of technical courses. He is a keen Java enthusiast and has been an invited speaker at the Java Users Group. He finds it hard to admit that he prefers Python nowadays.

Dr Ebejer (but everyone calls him JP) has been rather concerned lately about the increasing number of media reports that the world is not going to end because of climate change, nuclear war, zombie (or alien) attack, or a second ice age, but rather because our current stock of medicines are fast becoming ineffective against evolving pathogens. As a consequence, he has used data science, bioinformatics and cheminformatics techniques to find novel, active molecules to help fight antibiotic resistance. Formally, he has done this in a number of EU projects. He has published several papers in peer-reviewed scientific journals. He is currently employed as a Lecturer at the University of Malta and, in the past, has been part of the problem setting committee of the yearly ICTSA Programming Competition.
  • Bioinformatics
  • Cheminformatics
  • Computer-Aided Drug Design
  • Virtual Screening
  • Data Science (and Analytics)
  • Machine Learning
  • Big Data (& Cloud Computing)

BONANNO, E. and EBEJER, J., 2020. Applying Machine Learning to Ultrafast Shape Recognition in Ligand-Based Virtual Screening. Frontiers in Pharmacology, 10, pp. 1675.

MAMO, N., MARTIN, G.M., DESIRA, M., ELLUL, B. and EBEJER, J., 2020. Dwarna: a blockchain solution for dynamic consent in biobanking. European Journal of Human Genetics, 28(5), pp. 609-626.

BUGEJA, B., EBEJER, J. and SPINA, S., 2019. N-Layered Feudal Network in an RTS Game Environment, 20th International Conference on Intelligent Games and Simulation, GAME-ON 2019 2019, pp. 37-44.

EBEJER, J., FINN, P.W., WONG, W.K., DEANE, C.M. and MORRIS, G.M., 2019. Ligity: A Non-Superpositional, Knowledge-Based Approach to Virtual Screening. Journal of Chemical Information and Modeling, 59(6), pp. 1549-9596.

AZZOPARDI, S., COLOMBO, C., EBEJER, J., MALLIA, E. and PACE, G., 2017. Runtime Verification using Valour, An International Workshop on Competitions, Usability, Benchmarks, Evaluation, and Standardisation for Runtime Verification Tools: RV-CuBES, Seattle, USA, 2017, Seattle, USA, Oct 2017 2017, Lecture Notes in Computer Science (LNCS).

BUHAGIAR, A.J., PACE, G.J. and EBEJER, J., 2017. Engineering Adaptive User Interfaces Using Monitoring-Oriented Programming, Software Quality, Reliability and Security (QRS), 2017 IEEE International Conference on 2017, IEEE, pp. 200-207.

BONETTA, R., EBEJER, J., SEYCHELL, B., VELLA, M., HUNTER, T. and HUNTER, G.J., 2016. Role of protein structure in drug discovery. Xjenza, 4(2), pp. 126-130.

EBEJER, J., CHARLTON, M.H. and FINN, P.W., 2016. Are the physicochemical properties of antibacterial compounds really different from other drugs? Journal of Cheminformatics, 8(1), pp. 1-9.

KHER, S.S., PENZO, M., FULLE, S., EBEJER, J.P., FINN, P.W., BLACKMAN, M.J. and JIRGENSONS, A., 2015. Quinoxaline-Based Inhibitors of Malarial Protease PfSUB1. Chemistry of Heterocyclic Compounds, 50(10), pp. 1457-1463.

KELM, S., VANGONE, A., CHOI, Y., EBEJER, J., SHI, J. and DEANE, C.M., 2014. Fragment-based modeling of membrane protein loops: Successes, failures, and prospects for the future. Proteins: Structure, Function, and Bioinformatics, 82(2), pp. 175-186.

WILMAN, H.R., EBEJER, J., SHI, J., DEANE, C.M. and KNAPP, B., 2014. Crowdsourcing Yields a New Standard for Kinks in Protein Helices. Journal of Chemical Information and Modeling, 54(9), pp. 2585-2593.

EBEJER, J., FULLE, S., MORRIS, G.M. and FINN, P.W., 2013. The emerging role of cloud computing in molecular modelling. Journal of Molecular Graphics and Modelling, 44(0), pp. 177-187.

EBEJER, J., HILL, J.R., KELM, S., SHI, J. and DEANE, C.M., 2013. Memoir: template-based structure prediction for membrane proteins. Nucleic acids research, 41(W1), pp. W379-W383.

EBEJER, J., MORRIS, G.M. and DEANE, C.M., 2012. Freely Available Conformer Generation Methods: How Good Are They? J.Chem.Inf.Model., 52(5), pp. 1146-1158.

WITHERS-MARTINEZ, C., SUAREZ, C., FULLE, S., KHER, S., PENZO, M., EBEJER, J., KOUSSIS, K., HACKETT, F., JIRGENSONS, A., FINN, P. and BLACKMAN, M.J., 2012. Plasmodium subtilisin-like protease 1 (SUB1): Insights into the active-site structure, specificity and function of a pan-malaria drug target. International journal for parasitology, 42(6), pp. 597-612.

  • ARI5902 - Research Topics in Artificial Intelligence
  • CIS5002 - Computing for Scientists
  • CPS3235 - Data Science: From Data to Knowledge
  • DLT5140 - Smart Contract Coding Literacy
  • DOC6046 - Introduction to LaTeX: Typesetting your Thesis or Research Paper
  • ICS5110 - Applied Machine Learning
  • ICS5114 - Big Data Processing
  • ICS5115 - Statistics for Data Scientists
  • MMB3002 - Introduction to Bioinformatics
  • MMB5009 - Bioinformatics
  • PAT5953 - Research Methodology
  • PHB2504 - Molecular Recognition and Computational Drug Design
  • PHB3504 - Bioinformatics
  • PHB5030 - Molecular Biology and Genetics