Anastasis Oulas

CSMM Academic Staff

Current Position

Research fellow at the Bioinformatics Group, The Cyprus Institute of Neurology and Genetics (CING).
Group leader: Dr Giorgos Spyrou.

Education

2003 - 2009         University of Crete. Postgraduate program of Molecular Biology and Biomedicine.
PhD Title: Computational Prediction of Gene Classifiers and miRNAs in Cancer. 

2001 - 2002          Imperial College of Science, Technology and Medicine. Department: School of Biological Sciences.
MSc in Computational Genetics and Bioinformatics. (MSc was completed with a distinction).          

1998 - 2001        University of Sussex. Department: School of Biological Sciences.
BSc in Molecular Genetics in Biotechnology.Degree class:  2.1 honours.
                        
ACADEMIC APPOINTMENTS

01/07/16- present    Research fellow at the Bioinformatics Group, The Cyprus Institute of Neurology and Genetics (CING). Group leader: Dr Giorgos Spyrou.

01/01/12- 01/07/16    Senior research fellow at the Institute of Marine Biology, Biotechnology and Aquacultures - Hellenic Centre for Marine Research. Head of laboratory: Dr Georgios Kotoulas and Dr Christos Arvanitidis.

01/01/11-31/12/11    Postdoctoral fellow at the RNA Laboratory, Institute of Molecular Biology, Foundation of Research and Technology. Head of laboratory: Dr.Kriton Kalantidis (Assis. Professor).

01/10/09 - 14/09/10         Postdoctoral fellow at the Bioinformatics Laboratory, Division of Medicine,
University of Crete. Head of laboratory: Dr. Ioannis Iliopoulos.

01/02/03 - 30/09/03          Research assistant at the Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, under the supervision of Dr. Yiota Poirazi. 
 

Research Interests

Early research interests focused on the improvement of classification algorithms for the successful analysis of microarray expression data obtained from cases with varying pathological conditions or different grades of cancer. He implemented machine-learning algorithms and applications, which aim to aid in the diagnosis of complex genetic diseases such as cancer, by providing supplementary information to compliment classical clinical, histopathological and existing genetic information available today.
Dr Oulas also pursued research in the field of microRNAs (miRNA). His work in this field entailed the computational prediction of novel human miRNA genes and their targets residing within cancer associated genomic regions (CAGRs). 
In addition, Dr Oulas has been involved in research related to the development as well as the application of bioinformatics tools and software for the specific analysis of bacterial diversity using genomic and metagenomic data. 
With the advent of Next Generation Sequencing (NGS) and the increasing need for analysis of transcriptomic and genomic data derived from these technologies, Dr Oulas shifted his focus to analysis tools used specifically to address RNA-Seq, whole exome and genome sequencing data. He is involved in numerous ongoing projects involving germline variation detection and annotation and is mainly focused in the classification of variants of unknown or uncertain significance in association with specific diseases. 
Other interest involve making use of already implemented pipelines as well as modifying and setting up new procedures and methodologies for the analysis of NGS data specifically to address variation detection and annotation.
 

Biography

Dr Anastasis Oulas is a postdoctoral researcher in Bioinformatics Group at The Cyprus Institute of Neurology and Genetics. He was drawn by the rapidly evolving field of computational analysis of biological data from the very start of his academic career. Having completed a BSc in Molecular Genetics at Sussex University (UK), his interests turned to computing and the implementation of mathematical algorithms for deciphering the enormous amount of information retrieved from large-scale biological experiments. He enriched his knowledge within this field by completing a MSc in Computational Genetics and Bioinformatics at Imperial College (UK). He then moved to the Foundation of Research and Technology, Hellas (FORTH) in Crete, Greece, where he conducted research that led to the attainment of his PhD in Computational Prediction of Gene Classifiers and miRNAs in Cancer. Prior to his current position, Dr Oulas has held three postdoctoral positions at the Bioinformatics laboratory of the Division of Medicine, the RNA laboratory, both affiliated with the University of Crete, as well as the Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR). 
Dr Oulas has participated in numerous European projects and has hands-on experience in project management and work package coordination. Dr Oulas is the currently the Cyprus representative in the EU-COST programme, EPITRAN (European Epitranscriptomics Network). He serves as a reviewer and has editorial duties for several scientific journals. He has organized several scientific conferences, mostly at the national level, and has contributed towards lectures for numerous conferences and workshops both locally and abroad. He has also received an A.G. Leventis Foundation Grant/Fellowship for postgraduate studies, based on academic excellence (2004-2006).


SELECTED PUBLISHED RESEARCH MANUSCRIPTS

  1. Anastasis Oulas, George Minadakis, Margarita Zachariou, Kleitos Sokratous, Marilena M Bourdakou, George M Spyrou – “Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches” – Brief Bioinform. 2017 Nov 27. doi: 10.1093/bib/bbx15 
  2. Christina Pavloudi, Jon B Kristoffersen, Anastasis Oulas, Marleen De Troch, Christos Arvanitidis – “Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s "species minimum" concept” – PeerJ. 2017 Oct 13;5:e3687. doi: 10.7717/peerj.3687.
  3. Christina Pavloudi, Anastasis Oulas, Katerina Vasileiadou, Elena Sarropoulou, Georgios Kotoulas, Ioannis Karakassis, Christos Arvanitidis. “Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea)” (Marine Genomics, Jan 2016, DOI: 10.1016/j.margen.2016.01.005).
  4. Anastasis Oulas, Paraskevi N. Polymenakou, Manolis Mandalakis, Paraskevi Nomikou, Steven Carey, Stephanos Kilias, Christos Christakis, Georgios Kotoulas, Antonios Magoulas,  H.James Tripp, A. David Paez Espino, Natalia N. Ivanova, Nikos C. Kyrpides. “Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology”. Environ Microbiol. 2016 April. doi: 10.1111/1462-2920.13095.
  5. Anastasis Oulas, Christina Pavloudi, Paraskevi Polymenakou, Georgios A. Pavlopoulos, Nikolas Papanikolaou, Georgios Kotoulas, Christos Arvanitidis and Ioannis Iliopoulos, “Metagenomics: tools and insights for analyzing next generation sequencing data derived from biodiversity studies”, Bioinformatics and Biology Insights. 2015 May 5;9:75-88, Libertas Academia.
  6. Paraskevi N. Polymenakou, Christos A. Christakis, Manolis Mandalakis, Anastasis Oulas, “Pyrosequencing analysis of microbial communities illuminates the dominance of cosmopolitan species in deep sea sediments of the Eastern Mediterranean Sea”, Res Microbiol. 2015 Apr 20. pii: S0923-2508(15)00057-1.
  7. G. A. Pavlopoulos, A. Oulas, E. Iacucci, A. Sifrim, Y. Moreau, R. Schneider, J. Aerts and I. Iliopoulos. “Unraveling genomic variation from next generation sequencing data”, BioData Mining, 6:13, 2013
  8. A. Oulas, N. Karathanasis, A. Louloupi, I. Iliopoulos, K. Kalantidis and P. Poirazi. “A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2” RNA Biol. 2012 Sep 1;9(9).
  9. A. Oulas, A. Boutla, K. Gkirtzou, M. Reczko, K. Kalantidis, and P. Poirazi, “Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach" Nucleic Acids Res, vol. 37, pp. 3276-87, 2009.
  10. L. P. Petalidis, A. Oulas, M. Backlund, M. T. Wayland, L. Liu, K. Plant, L. Happerfield, T. C. Freeman, P. Poirazi, and V. P. Collins, “Improved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data” Mol Cancer Ther, vol. 7, pp. 1013-24, 2008.
     
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