Pavlopoulos CV

Public ProfilesAcademic Experience, Academic Degrees, Additional Certificates, Foreign LanguagesAwardsTechnical Skills and Bioinformatics Skills





     
March 2018 - now: Head of Bioinformatics
Principal Investigator B' (Associate Professor level)
Biomedical Science Research Center "Alexander Fleming"
,
Vari (Athens), Greece
Research Areas: Bioinformatics, Integrative, Genome and Network Biology

 
 
 November 2015 - March 2018
Bioinformatics Researcher
Lawrence Berkeley National Laboratory 
DOE Joint Genome Institute
Berkeley, CA, USA
Research Areas: Genomics, Metagenomics
Lab: Dr. Nikos Kyrpides

   
 January 2014 - December 2015:
Elected Board Member (Executive Secretary)
Hellenic Society for Computational Biology and Bioinformatics (HSCBB)
Athens, Greece
President at the time: Prof. Stavros Hamodrakas

   
 January 2013 - June 2015:
Senior Post-Doctoral Researcher,
Faculty of Medicine, Division of Basic SciencesUniversity of Crete,
Heraklion, Crete, Greece
Research Areas: Text Mining, Network Analysis and Microarray Data Analysis
Labs: Dr. Ioannis Iliopoulos, Prof. Aristides Eliopoulos 

   
 March 2015 - July 2015:
External Collaborator
Hellenic Center for Marine Research (HCMR), 
Heraklion, Crete, Greece
Research Areas: Image Analysis and Metagenomics

   
 November 2014:
Visiting Researcher
The de Novo Nordisk Foundation, Center for Protein Research, Faculty of Health and Medical Sciences
University of Copenhagen, Copenhagen, Denmark
Research Areas: Text Mining and Data Integration 
Lab: Prof. Lars Juhl Jensen

   
 November 2013 - September 2015:
External Collaborator
Center for Immunology and Transplantation, Biomedical Research Foundation of the Academy of Athens (BRFAA),
Soranou Efesiou, Papagou, Athens, Greece
Research Areas: Microarray and MicroRNA Data Analysis
Lab: Dr. Vangelis Andreakos

   
February 2011 - December 2012:
Post-Doctoral Fellow
Faculty of Electrical Engineering, Katholieke Universiteit Leuven,
Kasteelpark Arenberg 10, Leuven, Belgium
Research Areas: Visualization of Genomic Data and Network Biology
Lab: Dr. Jan Aerts, Prof. Yves Moreau

   
 October 2010 - January 2011: Post-Doctoral Researcher
Biomedcode Hellas SA - BSRC Alexander Fleming,
Alexander Fleming street, Vari Athens, Greece
.
Research Area: Microarray Data Analysis and Data Integration for Immunology
Lab: Prof. George Kollias

 
 
 March 2010 - August 2010:
Adjunct Lecturer
Department of Computer Science and Biomedical Informatics,
University of Thessaly (former University of Central Greece),
Galaneika, Lamia, Greece.

 
 September 2009 - April 2010: Obligatory Greek Military Service
Department of Informatics Research
National Ministry of Defence
Athens, Greece

   
 March 2009 - September 2009: Short-term Post-Doctoral Research fellow,
European Molecular Biology Laboratory (EMBL),
Heidelberg, Germany
Research Area: Data Integration and Visualization Techniques in Systems Biology
Lab: Dr. Reinhard Schneider
 
 
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  November 2005 – May 2009:


Ph.D in Computational Biology and Bioinformatics
European Molecular Biology Laboratory (EMBL)
Department of Structural and Computational Biology.
Heidelberg, Baden Wuerttemberg, Germany.
(PhD awarded jointly with the Ruprecht-Karls-Universität Heidelberg
).
Thesis: Visualization and Data Integration techniques in Systems Biology
Supervised by Dr. Reinhard Schneider

 
 
  September 2004November 2005: M.Res in Bioinformatics and Computational Biology
Master of Research (MRes) - (Distinction)
University of Leeds, School of Biochemistry and Microbiology, UK.
Dissertation: A parallel algorithm for microarray data clustering, based on social networks.
Supervised by Prof. David Westhead

 http://www.leeds.ac.uk/  
   September 2000 – June 2004: B.Sc in Computer Science
National and Kapodestrian University of Athens, Greece.
School of Informatics and Telecommunications.
Dissertation: Computational Geometry in Molecular Biology
Supervised by Prof. Ioannis Emiris
 
www.uoa.gr
 
       
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Additional Certificates

September 2015 - January 2016: Genomic Data Science Specialization
Coursera certified 8-module online certificate
offered by the J
ohns Hopkins University

 
https://www.jhu.edu/

5 March 2012: Cytoscape introduction and Cytoscape plugin development
Cytoscape Development Team
EMBL-Heidelberg, Germany
 

 

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Foreign Languages

 Greek (Native)

 English (Fluent)

 German (Advanced)

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Awards

  • 2013: Leader of one of the 10 winning teams entitled BioLitMin of COSMOTE StartUp competition for the best business idea
  • 2011: 12 month Postdoctoral fellowship, Greek State Scholarship Foundation (I.K.Y)
  • 2009: 6 months bridging Postdoctoral fellowship, EMBL
  • 2005: 4 year PhD fellowship, EMBL
  • 2005: Distinction for the MRes Bioinformatics and Computational Biology (Leeds, UK)
  • 2004: Undergraduate Diploma Thesis award, University Of Athens Department of Informatics and Telecommunications
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Technical Skills

Proficient or familiar with a vast array of programming languages, concepts and technologies, including:


  • Java, Perl, C, C++, OpenGL, Python, Ruby, Java3D, Processing, MPI
  • PHP, CGI, HTML, XML, Servlets, SQL, JDBC, Javascript, D3
  • Windows, UNIX, MacOS, Android
  • R, Bioconductor, Matlab
  • Hadoop, Spark, Hive
  • SLURM, UGE
  • Hardware & network fundamentals
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Bioinformatics Skills

Proficient with a vast array of programming techniques and software related to:

  • Sequence Analysis 
  • Next Generation Sequencing
  • Expression Analysis
  • Biological Data Visualization 
  • Biological Databases 
  • Data Integration
  • Clustering Analysis
  • Machine Learning
  • Text Mining
  • Biological Network Analysis
  • Genomics
  • Metagenomics
  • Comparative Genomics
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