Research Interests

​I work mostly on knowledge discovery technologies with applications in Bioinformatics and Computational Biology. ​My research interests include Machine Learning, Artificial Intelligence and Data Analysis of NGS-derived data. I have worked extensively on the prediction of distal DNA regulatory elements focusing of the category of enhancers. I am also involved in many other projects related to  pathway-based inference of host pathogen interactions as well as prediction of miRNA genes and targets.

Selected Publications

  • Progress and Challenges in bioinformatics approaches for enhancer identification
    Kleftogiannis D, Kalnis P, Bajic VB
    Briefings in Bioinformatics Accepted Manuscript, (2015)
  • Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures
    Kleftogiannis D, Kalnis P, Bajic VB
    PLoS ONE 8(9): e75505. doi:10.1371/journal.pone.0075505, (2013)
  • DEEP: A general computational framework for predicting enhancers
    Kleftogiannis D, Kalnis P, Bajic VB
    Nucleic Acids Research, Accepted Manuscript, (2014)
  • Hi-Jack: A novel computational framework for pathway-based inference of host-pathogen interactions
    Kleftogiannis D, Wong L, Archer JC and Kalnis P
    Bioinformatics, Accepted Manuscript, (2015)

Education Profile

  • ​2011-Present: PhD in Computer Science at KAUST, Thuwal, SA. Advisor: Panos Kalnis.
  • 2009-2011:    Masters Degree in Informatics for Life Sciences, Medical School, University of Patras-Greece
  • 2003-2009:    Diploma in Computer Engineering,Computer Engineering and Informatics Department, University of Patras-Greece

Professional Profile

  • 2015 Oct / 2015 Dec Research trainee at RIKEN Yokohama labs. This project is related to enhancer/promoter exploration using CAGE, ChIP-seq and ChIA-PET  data. The scope is to develop a new methodology for analyzing clinical data produced by RIKEN labs.
  • 2013 Nov / 2014 Oct  Research assistant at Computational Biolofy Lab at National University of Singapore (NUS). During my internship in NUS I studied host-pathogen interactions at the metabolic pathway level. Outcome was the development of an algorithm called Hi-Jack, which identifies interconnections between human, and Mycobacterium Tuberculosis based on the idea of metabolite hijacking. I was under the supervision of Limsoon Wong.
  • 2011 Fall/Spring semesters computer science lecturer at vocational training institute of Pyrgos-Greece
  • 2010 Fall semester Instructor of computer science seminars at Greek Trade Development Center
  • 2006 summer Internship at the National Electrical Company (Greece)​
  • 2005 summer Internship at the National Electrical Company (Greece)

Scientific and Professional Memberships

  • ​Reviewer to Bioinformatics, Scientific Reports , Artificial Intelligence Review​ , Journal of Biomedical Informatics, Plos ONE , Applied Soft Computing, Journal of Bioinformatics and Computational Biology​


  • ​2003-2007: Undregraduate Scholarship by John S. Latsis Fountation
  • 2010-2011: Postgraduate Scholarship by John S. Latsis Foundation

KAUST Affiliations

  • ​Extreme Computing Research Center(ECRC)