Curriculum Vitae

CURRICULUM VITAEANASTASIS OULAS

PERSONAL INFORMATION

Nationality: Greek and Cypriot

Work Address:

The Cyprus Institute of Neurology and Genetics 

P.O.Box 23462 

1683 Nicosia 

Cyprus

Tel: +357 22 358 600 (Work)

E-mail Address: anastasioso@cing.ac.cy

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 AND PROFESSIONAL EXPERIENCE

01/07/20- present

Associate Scientist at the Bioinformatics Department, The Cyprus Institute of Neurology and Genetics (CING). Department Head: Dr George Spyrou.

01/07/16- 01/07/2020 

Senior research fellow at the Bioinformatics Group, The Cyprus Institute of Neurology and Genetics (CING). ERA Chair program (BIORISE). Coordinator: Dr Kyproula Christodoulou, Group Leader: Dr George Spyrou.

01/01/12- 01/07/2016         

Senior research fellow at the Institute of Marine Biology, Biotechnology and Aquaculture - Hellenic Centre for Marine Research. Head of laboratory: Dr. Christos Arvanitidis and Dr Giorgos Kotoulas.

01/01/11-31/12/11

Postdoctoral fellow at the RNA Laboratory, Institute of Molecular Biology, Foundation of Resarch 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.

BIOINFORMATICS RESEARCH SKILLS

• Metagenomics, genomics, RNA-Seq data analysis, microarray data analysis, classification analysis and clustering. Development of command-line based and graphic user interface stand alone software packages. Web service development for running bioinformatics related software (i.e. SSCprofiler - http://mirna.imbb.forth.gr/SSCprofiler.html). Computational prediction of microRNA genes and targets (Targetprofiler - http://mirna.imbb.forth.gr/Targetprofiler.html ).

WET LAB TECHNIQUES

• Cloning, sub-cloning, mini DNA preparation, PCR, competent cell preparation, transformation, ligation, agarose gel electrophoresis, northern blot analysis, transfection, growth of cell culture, luciferase assays. Experience in working with small-RNAs.

PUBLISHED RESEARCH MANUSCRIPTS

click here

EDITORORIAL DUTIES

1. Editorial member, “High-Performance Computing Infrastructure for South East Europe's Research Communities Modeling and Optimization in Science and Technologies”. Expected: Volume 2, 2014, pp 67-74

FUNDED SHORT VISITS

1. Short visit part of the MicroB3 program (EU-FP7 RESEARCH PROJECT). 8th Feb.-16th Feb. 2014. Host: Prof. Christos Ouzonis, (Researcher A) at CERTH, Thessaloniki, Greece.

2. Short Visit part of the Marbigen program (EU-FP7 RESEARCH PROJECT). 1st Aug.-1st Sep. 2013. Host: Dr. Nikos Kyrpides at the Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.

3. Short research mission as part of the COST Action ES1103: Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools. Host: Prof. Alice McHardy, Heinrich-Heine University, Dusseldorf, Germany – 11/06/12-29/06/12.

4. EU program Human Research Potential & the Socio-Economic knowledge base: Access to Research Infrastructures (ARI). Short visit - Linnaeus Center for Bioinformatics, Uppsala, Sweden, Project – “MiRNA gene prediction from human genomic sequences”. 1st-30th, June, 2005.

ATTENDED PROJECT MEETINGS:

1. ELIXIR - CONVERGE WP1 & WP2 F2F meeting. 29-31 March, 2023 – Prague, Czech Republic.

2. ELIXIR - CONVERGE WP1 & WP9 F2F meeting. 21-23 September, 2022 – Padova, Italy.

3. Integrated Precision Medicine Technologies Research Center of Excellence (IPMT) 3rd Meeting - 22nd-23rd March 2018 – Barcelona

4. Micro B3 “Work package 6 meeting” Task 6.2 Bacteria and archaea, Marseilles, France, 26th-29th Jan. 2015.SeaBioTech (EU-FP7 RESEARCH PROJECT KBBE-311932), 2rd Annual Meeting 17-21 April, 2014, Reykjavik, Iceland

5. SeaBioTech (EU-FP7 RESEARCH PROJECT KBBE-311932), 2rd Annual Meeting 17-21 April, 2014, Reykjavik, Iceland

6. Micro B3 “General Plenary Meeting”, Bremen, Germany, 22nd-27th April. 2014

7. COST Action ES1103 - Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools, WG 4-5 meeting / workshop: Bioinformatics meets microbial ecology (BMME), 15th -18th December 2013, Prague, Czech Republic.

8. SeaBioTech (EU-FP7 RESEARCH PROJECT KBBE-311932), 2nd Annual Meeting 17-18 October, 2013, HCMR-Crete.

9. 3rd COPWELL (EU-FP7 RESEARCH PROJECT KBBE-2010-4 265957  2011-2015)  Meeting, 1-2 October 2013, Espace ENCAN, Quai Louis Prunier, La Rochelle, France.

10. Micro B3 “Work package 6 meeting” Task 6.2 Bacteria and archaea, Istanbul, 6th-7th Dec. 2012 

11. 2nd COPWELL (EU-FP7 RESEARCH PROJECT KBBE-2010-4 265957, 2011-2015). Meeting, 3-5 October 2012, Hotel Imperial Belvedere, Hersonissos, Crete, Greece.

12. COST Action ES1103 - Microbial ecology & the earth system: collaborating for insight and success with the new generation of sequencing tools, Kick off meeting, at Newcastle upon Tyne 28th and 29th February 2012

13. Micro B3 (Biodiversity, Bioinformatics, Biotechnology) Kick-off Meeting February 1st – February 3rd, 2012, Jacobs University Bremen

CONTRIBUTIONS TO CONFERENCES

1. Hellenic Bioinformatics Conference, Heraklion, Greece, 11-13 October 2019. Oral presentation: Anastasis Oulas, “Bacterial Wars – a network-based method for the prediction of bacterial compatibility based on antimicrobial peptide sequence similarities”.

2. The 4th OpenMultiMed Cost Training School in Systems Bioinformatics towards Network Medicine. May 29 – May 31, 2018. Oral presentation: Anastasis Oulas “Visualization of Network based approaches”.

3. Hellenic Bioinformatics Conference, Thessaloniki, Greece, 15-18 November, 2018. Poster presentation: Stephanie Constantinidou, Anastasis Oulas, Margarita Zachariou, George Minadakis, Georgios M. Hadjigeorgiou, Theodoros Kyriakides, Efthimios Dardiotis, Marios Pantzaris, George M. Spyrou, “Network-based approaches to integrate multisource information for multiple sclerosis towards biomarker discovery”.

4. Cyprus Society of Human Genetics (CSHG) conference, Nicosia Cyprus, 24-25 November, 2017, Oral presentation: Anastasis Oulas, George Minadakis, George M. Spyrou, “Classifying Variants of Unknown Significance by Combining Polygenic Risk Score and Network Analysis”.

5. Mares Conference 2016, Oral presentation:, Christina Pavloudi, Anastasis Oulas, Jon B Kristoffersen, Michael W Friedrich, Christos Arvanitidis, “Investigation of the suitability of Remane’s “species minimum” concept in a Mediterranean transitional waters ecosystem”. PeerJ journal

6. DEVOTES EUROMARINE SUMMER SCHOOL 2015, San Sebastian, Spain; 06/20156th, Oral presentation: Panagiotis D. Dimitriou, Theodore Patkos, Anastasis Oulas, Nikos Pattakos, Kostas Varsos, Edward Vanden, Antonio Fernandez-Guerra, Christina Pavloudi, Ioannis Karakassis, Christos Arvanitidis, “New tools for marine ecological analysis: Using the R-vLab for Ecological Status assessment”

7. Mikrobiokosmos conference, National Hellenic Research Foundation, 3-5 April, 2015. Oral presentation: “Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology”

8. HSCBB-14: 9th conference of the Hellenic Society for Computational Biology, and Bioinformatics, Agricultural University of Athens, Greece, October 10 - 12, 2014.

9.    HSCBB-13: 8th conference of the Hellenic Society for Computational Biology, and Bioinformatics, University of Thessaly, Lamia, Greece, November 22 - 24, 2013, Oral presentation: “Metagenomics of microbial communities inhabiting the Kolumbo volcano shallow-sea hydrothermal vent field and Santorini (caldera)”.

10. The Micro B3 Final Conference, Royal Flemish Academy of Belgium for Science and the Arts, Brussels, 2nd to 5th November 2015. Oral presentation: “Micro B3 summer school Crete: From sampling to analyzing microbial diversity & function”

11. Hellenic Bioinformatics Conference, Heraklion, Crete, Greece, 5-9 September, 2017. Oral presentation: Anastasis Oulas, George Minadakis, George M. Spyrou, “Network based approaches for classifying variants of unknown significance”.

12. HP-SEE User Forum, Belgrade, Serbia on October 17th-19th, 2012. Oral presentation titled: “A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2”.

13. HSCBB-12: 7th conference of the Hellenic Society for Computational Biology, and Bioinformatics, FORTH, Heraklion, Crete, 4-6/10/2012 Poster presentation: “A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2”.

14. 7th MICROSYMPOSIUM on SMALL RNAs, May 21 - 23, 2012, Novartis Campus, Basel, Switzerland Poster presentation: “A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2”.

15. ISMB/ECCB 2011: Vienna, Austria. Poster Title: “Prediction of miRNA gene targets – a combined computational and experimental approach”. Anastasis Oulas, Nestoras Karathanasis, Panayiota Poirazi, Kriton Kalantidis.

16. 62nd Conference of the Hellenic Society of Biochemistry and Molecular Biology, 9-11, December, 2011. Oral presentation: “Prediction of miRNA gene targets in cancer associated genomic regions”.

17. HSCBB-10: 5th conference of the Hellenic society for computational biology, Thraki Palace Conference Centre, Alexandroupolis, 17-19/12/2010 Poster spotlight talk titled: Improved prediction of miRNA gene targets.

18. HSCBB-09: 4th conference of the Hellenic society for computational biology, NHRF, Athens, 18-20/12/2009 Poster spotlight talk titled: Development of a microRNA target prediction tool.

19. HSCBB-08: 3rd Conference of the Hellenic Society for Computational Biology and Bioinformatics, CERTH, Thessaloniki, 30-31 Oct 2008. Poster spotlight talk titled: SSCprofiler: a combined Sequence, Structure and Conservation profile HMM tool accurately predicts microRNA gene.

20. 1st Cretan Bioinformatics Forum, FORTH. Building Scientific Networks (Invited Talk): Analysis of Microarray Data and Prediction of MiRNA genes using Computational tools , June 19, 2006

21. 2nd International Advanced Research Workshop on In Silico Oncology, Kolympari, Chania, Greece, 25th and 26th September 2006. “Prediction of novel miRNAs and their gene targets with implications in tumourigenesis”.

22. ISMB/ECCB 2004: Glasgow, Scotland, UK. Poster Title: Biologically Inspired Neural Network and Genetic algorithms for microarray data classification and Identification of informative genes. Anastasis Oulas , Martin Reczko, Panayiota Poirazi

WORKSHOPS

1. Hellenic Bioinformatics - Proteomics Workshop – Hands-on, Heraklion, Crete, Greece, 5th September, 2017.Hellenic Bioinformatics - Advanced RNA-Seq and ChIP-Seq data analysis – Hands-on, Heraklion, Crete, Greece, 5th September, 2017.

2. Hellenic Bioinformatics – Tutorials on Metagenomics and Phylogenomics Heraklion, Crete, Greece, 6th September, 2017.

3. Volos Summer School of Human Genetics, University of Thessaly - 29th - 31st May, 2017

4. Silvangs power user workshop at The Max Planck Institute for Marine Microbiology, Bremen, Germany – 28-30, September 2016

5. LifeWatch Data Analysis Workshop, Biodiversity data preparation and analysis using LifeWatch virtual labs and web services, Thursday 26th – Friday 27th November 2015; VLIZ, InnovOcean site, Wandelaarkaai 7, Oostende, Teaching: Data exploration, processing and analysis (LifeWatch Greece RvLab)

6. GSC 17, May 4-6, 2015 DOE JGI, Walnut Creek, California, USA and Satellite Workshop on Genomes to Secondary Metabolites (G2SM) workshop Date: May 7-8, 2015.

7. Micro B3 OSD Analysis Workshop 8 - 14 March 2015, ELIXIS building, EBI-EMBL, Hinxton, Cambridge, UK.

8. Micro B3 Marine Metagenomics Bioinformatics 24 - 28 March 2014, ELIXIS building, EBI-EMBL, Hinxton, Cambridge, UK.

9. COST action SeqAhead Workshop - Barcelona 2013, COST SeqAhead & AllBio, Wednesday, February 13, 2013 at 2:00 PM - Friday, February 15, 2013 at 5:30 PM (PST), Hospitalet de Llobregat, Spain

10. Workshop - Next-Generation Sequencing technologies and Informatics tools for studying Marine Biodiversity and Adaptation (HCMR-Crete). 1st-3rd, October, 2012, Contribution: organizing committee.

11. EMBRC - International Workshop on Marine E-Infrastructure - European Molecular Biology Laboratory (EMBL), Heidelberg - Wednesday, 28/03/12 - Friday, 30/03/12.

12. Microbial Diversity, Genomics and Metagenomics Workshop (HCMR Crete, 13th-16th, December 2011)

13. Introduction to Systems Biology Course (HCMR Crete, 17th-18th, November 2011)

14. Cancer Bioinformatics Workshop, Cambridge Research Institute 2nd - 4th September 2010. Poster spotlight talk titled: Development of a microRNA target prediction tool using hidden Markov models

15. Computational Biology Workshop, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia, July 25 – July 29, 2007.

16. 2nd International Advanced Research Workshop on In Silico Oncology, Kolympari, Chania, Greece, 25th and 26th September 2006, Talk titled: Prediction of novel miRNAs and their gene targets with implications in tumourigenesis, Anastasis Oulas , Martin Reczko, Panayiota Poirazi.

17. The Fifth BioSapiens European School in Bioinformatics held in Budapest (Hungary). Talk: Computational Prediction of MiRNA in Cancer, Sep 4-8 2006

18. Workshop in Bioinformatics, Jointly organized by The Department of Biology, University of Crete (UOC) The Institute of Molecular Biology and Biotechnology (IMBB) of the Foundation for Research and Technology (FORTH), Tutorial Presentation on Microarray Analysis Tools, Greece, Sep 2004.

TAUGHT COURSES

1. Cyprus School of Molecular Medicine Postgraduate course in Bioinformatics – Title: Computational Intelligence: Clustering, 4th November, 2017-present.

2. Cyprus School of Molecular Medicine Postgraduate course in Bioinformatics – Title: Omics Genomics, 16th October, 2017-present

3. Cyprus School of Molecular Medicine Postgraduate course in Bioinformatics – Title: Omics Genomics Tutorial, 16th October, 2017-present

4. Medical School of the University of Crete (UoC), tutorial on “Single-cell RNA-Seq” for students of the Postgraduate MSc Program in "Bioinformatics" Friday 26th November 2021.

5. The 4th OpenMultiMed Cost Training School in Systems Bioinformatics towards Network Medicine. May 29 – May 31, 2018. Tutor: Anastasis Oulas. Title: “Visualization of Network based approaches”.

6. Cost Workshop in Metagenomics of Bacterial 16sRNA Genes Analysis using QIIME Nicosia, Cyprus 2018. Tutor Anastasis Oulas, Title: “Microbiome Analysis Using R”.

7. Postgraduate Seminars Seminar Series 2018-2019 University of Cyprus, 17 October 2018. Tutor: Anastasis Oulas. Title: Tools for analysing high-throughput genetic variation data as a means for molecular diagnosis.

8. CING Bioinformatics workshop 1, Workshop on “Next Generation Sequencing and Human Variation Data Analysis”, Tutor: Anastasis Oulas. April 3rd, 2017 Thursday, 9:00-13:00 at CING’s Amphitheatre.

9. CING Bioinformatics workshop 2, Workshop on “Mass Spectrometry-based omics: Data production, analysis and perspectives”, Tutor: Anastasis Oulas. July 6, 2017 Thursday, 9:00-13:00 at CING’s Amphitheatre.

10. Hands-on Tutorial on Whole Exome Sequencing and Panel Data Analysis. CING, Tutor: Anastasis Oulas. Dates: 9/2/2018

11. Cyprus School of Molecular Medicine Postgraduate course in Bioinformatics – Title: Computational Intelligence: Clustering, 2 October, 2017.

12. Cyprus School of Molecular Medicine Postgraduate course in Bioinformatics – Title: Omics Genomics, 16 November, 2017

13. Cyprus School of Molecular Medicine Postgraduate course in Bioinformatics – Title: Omics Genomics Tutorial, 24 November, 2017

14. Genomics Standards Consortium (GSC) ­18, June 12­-15, 2016, HCMR, Heraklion, Crete. Tutor: Anastasis Oulas. Talk 1: Ecosystems physiology of the Kolumbo submerged volcano in the Hellenic volcanic arc. Talk 2: LifeWatch Greece ­ Greek Biodiversity portal: Analysis and Visualization tools

15. Introductory Course to the Principles of Coalescent Theory and Applications, 20th - 24th of February 2012, HCMR-Crete.

16. Teaching: "Introduction to Programming Using Python" - https://sites.google.com/site/pythoncompbio/ HCMR June 2011, Heraklion, Crete, Greece. (in collaboration with Dr. Evangelos Pafilis and Jacques Lagnel)

17. Workshop - Literature Mining for Biologists, March 19th, 2011, University of Cyprus. Talk title: “Biomedical textmining - applications in miRNA target prediction”.

18. LifeWatch Data Analysis Workshop, Biodiversity data preparation and analysis using LifeWatch virtual labs and web services, Thursday 26th – Friday 27th November 2015; VLIZ, InnovOcean site, Wandelaarkaai 7, Oostende, Teaching: Data exploration, processing and analysis (LifeWatch Greece RvLab).

19. Micro B3 summer school Crete: From sampling to analyzing microbial diversity & function, May 26 - June 7, 2014. Tutor: Anastais Oulas, Title: “Environmental and marine bioinformatics for biologists”

20. Workshop - Next-Generation Sequencing technologies and Informatics tools for studying Marine Biodiversity and Adaptation (HCMR-Crete). 1st-3rd, October, 2012, Contribution: organizing committee and tutor 

MOST IMPORTANT SOURCES OF FUNDING, HONOURS AND AWARDS

1. ELIXIR-CONVERGE (HO2020) project funded by the European Commission to help standardise life science data management across Europe. End: July 2023

2. Research Innovation Foundation (RIF) funded project environ​Ment​Al microbioloGy aNd biotEchnology uniT (MAGNET - https://magnet.moa.gov.cy/). End: June 2023

3. COST action CA16120 as a representative for Cyprus, which aims to establish a European Epitranscriptomics Network. End: September 2021

4. BIORISE project (HO2020) establishment of Bioinformatics ERA Chair at the Cyprus Institute of Neurology and Genetics (http://biorisecyprus.com/en/cing-home).

5. LifeWatchGreece infrastructure (MIS 384676), funded by the Greek Government under the General Secretariat of Research and Technology (GSRT), ESFRI Projects, National Strategic Reference Framework (NSRF). Coordinator Dr. Christos Arvanitidis.

6. MARBIGEN “Supporting research potential for MARine BIodiversity and GENomics in the Eastern Mediterranean” project (FP7-REGPOT-2010-1). P.Is. Dr. Antonios Magoulas, Dr Georgios Kotoulas.

7. PENED “Development of computational methods for genomic data analysis”, Funding:General Secretary of Research and Technology, Hellas. 2005-2008, €228.000. P.I. Dr. Panayiota Poirazi

8. A.G. Leventis Foundation Grant for postgraduate studies, based on academic excellence (2004-2006).

9. PROGNOCHIP: “Development and Establishment of DNA Microarray Technology in Greece: Identification and Validation of Classification and Prognosis Molecular Markers for Breast Cancer”, Funding: General Secretary of Research and Technology, Hellas. 12/2003-12/2006, €350.000. P.I. George Thireos, Panayiota Poirazi Partner.

REFERENCE

• Dr. Giorgos Spyrou, georges@cing.ac.cy, CING

• Dr. Yiota Poirazi, poirazi@imbb.forth.gr, IMBB, FORTH.

• Dr. Ioannis Iliopoulos, ioannis@iti.gr University of Crete, Medical Department. 

• Dr. Kriton Kalantidis, kriton@imbb.forth.gr, University of Crete, Biology Department.

• Dr. Georgios Kotoulas, kotoulas@hcmr.gr, IMBBC, HCMR

• Dr. Christos Arvanitidis, arvanitidis@hcmr.gr, IMBBC, HCMR