About

Eileen Marie Hanna

Assistant Professor of Computer Science

I am an assistant professor of computer science in the Department of Computer Science and Mathematics. I joined LAU as a visiting assistant professor of computer science and bioinformatics from spring 2020 until summer 2022. Prior to that I spent three years as a postdoctoral fellow at the Computational Biology Unit at the University of Bergen in Norway where I was part of “dCod 1.0: Decoding the systems toxicology of Atlantic cod.” This project combined multidisciplinary competencies that went beyond the traditional departmental boundaries to study cod’s adaptations and reactions to environmental stressors. More details on this experience here. 

Research Interests and Projects

I have been leading a subsequent project to generate the first genome-scale metabolic reconstruction of Atlantic cod. Gene expression data from exposure experiments can be mapped to resulting genome-scale models to explicate metabolic response mechanisms to environmental toxicants. In addition, my current research focuses on developing network-based approaches for the integration and analysis of large-scale biological and medical data. 

With a Computer Science background, I am specialized in bioinformatics since pursuing my MS studies and working on my thesis at the Microsoft Research - University of Trento Centre for Computational and Systems Biology. I then pursued my PhD at the United Arab Emirates University where I developed a computational method for the detection of protein complexes in protein-protein interaction networks and gene-disease association.

I have participated in several workshops on various topics including omics data integration, fish toxicology in silico, data management for large research projects, and responsible research and innovation. I was also a member of the organizing committee of a workshop, in Norway, on Network Biology/Integromics Bioinformatics – Applications Towards Medicine that hosted keynote talks by distinguished international speakers in the field. 

Selected publications

  1. Hanna, E. M., Blaser, N., Yadetie, F., Eide, M., Brun, M., Goksøyr, A. and Jonassen, I., 2020. “Topological Edge Set Enrichment Analysis for Enhanced Detection of Dysregulated Pathways”. In preparation.
  2. Hanna, E.M., Zhang, X., Eide, M., Fallahi, S., Furmanek, T., Yadetie, F., Zielinski, D.C., Goksøyr, A. and Jonassen, I., 2020. “ReCodLiver0.9: Overcoming challenges in genome-scale metabolic reconstruction of a non-model species”. Submitted.
  3. Khan, E.A., Zhang, X., Hanna, E.M., Bartosova, Z., Yadetie, F., Jonassen, I., Goksøyr, A. and Arukwe, A., 2020. “Quantitative transcriptomics, and lipidomics in evaluating ovarian developmental effects in Atlantic cod (Gadus morhua) caged at a capped marine waste disposal site”. Environmental Research, 109906.
  4. Yadetie, F., Zhang, X., Hanna, E.M., Aranguren-Abadía, L., Eide, M., Blaser, N., Brun, M., Jonassen, I., Goksøyr, A. and Karlsen, O.A., 2018. RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo [a] pyrene and 17α-ethynylestradiol. Aquatic toxicology, 201, pp.174-186.
  5. Hanna, E.M., Zaki, N. and Amin, A., 2015. Detecting protein complexes in protein interaction networks modeled as gene expression biclusters. PloS one, 10(12), p.e0144163.
  6. Hanna, E.M. and Zaki, N., 2014. Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure. BMC bioinformatics, 15(1), p.204.
  7. Bouktif, S., Hanna, E.M., Zaki, N. and Khousa, E.A., 2014. Ant colony optimization algorithm for interpretable bayesian classifiers combination: application to medical predictions. PloS one, 9(2), p.e86456.

International conferences

  1. Hanna, E. M., Blaser, N., Yadetie, F., Eide, M., Brun, M., Goksøyr, A. and Jonassen, I., “Discovering pathway perturbations with topological edge set enrichment analysis (TESEA)”. International Study Group for Systems Biology, Tromsø, Norway, Sep. 2018.
  2. Eide, M., Zhang, X., Karlsen, O.A, Hanna, E. M., Blaser, N., Puntervoll, P. and Goksøyr, A., “Modelling the chemical defensome networks - a comparative dynamic visualisation of the involved genes and interactions in two fish species and humans”.  31st Congress of European Society for Comparative Physiology and Biochemistry, Porto, Portugal, Sep. 2018.
  3. Hanna, E.M. and Zaki, N.M., “Detecting Protein Complexes using Gene Expression Biclusters”. In Proceedings of the 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB’15), Niagara Falls, Canada, Aug. 2015.
  4. Hanna, E.M., Mohamed, N. and Al-Jaroodi, J., “The cloud: requirements for a better service”. In 2012 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (ccgrid 2012) (pp. 787-792). IEEE.

Academic degrees

  • PhD in Computer Science, United Arab Emirates University
  • MS in Computer Science, with specialization in Bioinformatics, University of Trento
  • BS in Computer Science, American University of Technology