| Objective | ● BSc Biochemistry and Molecular Medicine (with honours) (project funded by Ministry of Defence UK) |
| ● MSc in Bioinformatics (European studying fund) |
| ● PhD Bioinformatics NTUA – BSRC Al. Fleming |
| General Information | Spoken Languages: English (Language Professor), Greek (Native Language), And German (Zertifikat). Basic level of Italian and French. |
| Year of birth : 1979 |
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| Current Work | Hospital “Attikon”- Hellenic National Diabetes Centre Greece ● Jan – May 2009 microarray analyst-experiment designer |
| Education related info | 2009-2010 Studies in University of Athens Department of Economics and Business, GR ● MSc Medicinal Statistics |
| 2005-2008 Work in Alexander Fleming – studies in Technological University of Athens Ath, GR |
| ● Microarray Analysis (Affymetrix and cDNA) |
| ● PhD Bioinformatics Candidate (officially finished laboratory work) |
| 2004-2005 Greek Army Service- Studies in University of Athens Department of Economics and Business, GR |
| ● March 2004 – March 2005 Army Service in Greece (Chemical Analyst on plane fuel) |
| ● October 2004 Start of MSc Medicinal Statistics |
| 2002-2003 Studies at the United Nations Research Centre: ICGEB Trieste Area Sc. Park TS, Italy |
| ● PhD Bioinformatics 1st year (4 yr scholarship) |
| 2001-2002 Studies in University of Crete – Abertay Dundee University Combined |
| ● 1yr MSc project in Biology Department - FORTH institute, of University of Crete Greece |
| 2000-2001 Studies in Abertay Dundee University Scotland UK |
| ● Postgraduate Diploma in Bioinformatics (taught MSc-Scholarship) |
| ● Continuation for 1yr MSc degree |
| 1996-2000 Studies in Essex University , Essex UK |
| ● BSc Honours Degree Biochemistry and Molecular Medicine |
| 1985-1996 School Studies in Greece , Athens, Greece |
| ● Graduation mark 18.4/20. |
| Scientific Publications | 1. Triantafillos Paparountas, Argyris Tzouvelekis, Vaggelis Harokopos, Nikos Oikonomou, Aristotelis Chatziioannou, George Vilaras, Evangelos Tsiambas,Andreas Karameris, Demosthenes Bouros and Aidinis V., 2007, "Comparative Expression Profiling in Pulmonary Fibrosis suggests a Role of Hypoxia Inducible Factor 1a in Disease Pathogenesis", Am J Respir Crit Care Med. 2007 Dec 1;176(11):1108-19. Epub 2007 Aug 29 : Biomarker Identification through comparative analysis of 10 different datasets of human and mice models of IPF. After finding orthologous genes the comparison identified 296 IPF related genes. IF 9.2 |
| 2. Vassilis Aidinis, Nikos Oikonomou, Artemis Thanassopoulou, Argyris Tzouvelekis, Vaggelis Harokopos, Triantafillos Paparountas, Ioanna Nikitopoulou, Walter Witke, Andreas Karameris, Anastasia Kotanidou, Demosthenes Bouros. Gelsolin expression is necessary for the development of pulmonary inflammation and fibrosis. Submitted for evaluation. Accepted for publication in THORAX journal 21_01_2009 IF 6.2 |
| 3. Triantafillos Paparountas, Maria Nefeli Nikolaidou-Katsaridou, Vassilis Aidinis Data mining and meta-analysis on DNA microarray data. Submitted for evaluation |
| 4. Nikolaos Maniatis, Triantafillos Paparountas, Vassilis Aidinis. Microarray experiment with data from human patients that have developed Acute Respiratory Disease Syndrome. In preparation. |
| 5. Vassilis Aidinis, Triantafillos Paparountas, Stella Fotopoulou. Role of Autotaxin. In preparation. |
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| PhD Bioinformatics Related information | NTUA – Alex. Fleming Institute Athens Greece |
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| Second Supervisor Dr. V. Aidinis Email: v.aidinis<at>fleming.gr |
| ● Analysis of 17 microarray datasets. (human, mouse samples) Affymetrix and cDNA microarray data using R-bioconductor, Partek ® and Genespring® and the in-house (team of F.Kolisis) software. For each experiment statistics and analytical data mining approaches were utilized related to Gene Ontology, miRNA, transcription factor and pathway analysis. |
| ● Design and Evaluation of microarray experiment and data that will be used for microarray BSRC Al. Fleming database. |
| ● Exploration of alternative technologies for microarray design |
| ● Creation of Microarray Database for BSRC Al. Fleming |
| ● Creation of BSRC Al. Fleming’s Microarray Unit-Web site (www.expressionprofiling.eu) |
| ● Complete Pipeline on Affymetrix microarray analysis (human and mice 3’ IVT and GENE 1.0ST arrays) |
| ● Article on Meta Analysis on Idiopathic Pulmonary Fibrosis (first author) (Am J Respir Crit Care Med. Impact Fact. 9.2) |
| ● Participation in article on Gelsolin Knockout (microarray analysis part) (accepted to journal THORAX impact factor 6.22) |
| ● Article on Data Mining and Meta-Analysis of microarray data(first author) (submitted) |
| | ICGEB Trieste Italy |
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| Supervisor Prof. S. Pongor Email: pongor<at>icgeb.org |
| Second Supervisor S. Harnad (cognitive sciences) Web site: http://www.ecs.soton.ac.uk/~harnad/ |
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| Until the end of 1st year (2003): |
| ● Computational biology work on Structural Biology |
| ● Analysis of web based protein predictor services and comparison with the inhouse software. |
| ● Evaluation of protein domain prediction methods based on weighted and non weighted matrixes of disulfide bridges. |
| ● Perl (bioperl) programming code for search and storage of protein sequence information found in remote databases. |
| ● Analysis of sequence alignment techniques based on disulfide bridge position. |
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| MSc Bioinformatics Education related | University of Crete Greece – University of Abertay Dundee Scotland |
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| Experience Gained: |
| ● Computational biology work on Structural Biology, Bioinformatics and Database design and implementation |
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| Practical Part: |
| Labs Supervisor Prof. M/ Kokkinidis Email: kokkinid<at>imbb.forth.gr |
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| Project Title: |
| Uncovering patterns of H-bonds in protein DNA combined structures. An atom-interaction analysis |
| ● 160 pdb DNA-protein structures were analysed in order to uncover the relative tendencies of amino acids to bind to certain nucleotides. |
| ● Extended use of MS database and SQL. Developing of ingenious queries in order to find complex interactions in the simplest way. |
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| Theoretical Part: |
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| ● Applications of Bioinformatics, |
| ● Database design, analysis, maintenance and interaction with the programming language VB 6. Relational Algorithms Theory |
| ● Programming with VB 6. |
| ● Theoretical background of statistical models |
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| MSc Medicinal Statistics Education related | Athens Business & Econ. Univ. Athens Greece |
| ● Study of Statistical procedures and applications of experimental design, and statistical analysis. Sampling, Clinical Trials and various other aspects |
| ● Statistical packages used include S-plus, SPSS |
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| BSc Final Year Project | Essex University, Computational Chemistry Labs Essex UK |
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| Final Year Project |
| ● Computational biology work on Structural Biology and molecular dynamics |
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| Project Title: |
| Protein-Ligand binding: Docking anticancer experimental drugs on NADPH P450 reductase |
| ● Automatic Docking program tested (autodock) |
| ● Small bioreductive agents were created with OXmol-Nemesis docked to NADPH P450 reductase using Autodock ver. 3 and WhatIF and tested against electro-gravitational field maps created with gOpenmol |
| ● Several Databases Used (Chemweb/Isis/Embl) |
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| Computer Experience | |
| Operating System: |
| Linux (Redhat-Suse-Mandriva), MS-Windows95/98/2000-NT |
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| Biostatistics -Microarrays Software |
| ● Statistical Programs- SPSS, SPLUS , R-language |
| ● Partek , Genespring , Bioconductor, SAM |
| ● Data mining software , Ingenuity, GeneCodis , Fatigo, Babelomics , GeneTools, Gepas |
| ● Workflow analysis software: Taverna |
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| General Programming languages and skills |
| ● Perl programming language |
| ● Visual basic 6 programming |
| ● Web Page Design with Dreamweaver, Frontpage 2000, Flash |
| ● Web Design |
| http://www.athens-recycling.com http://www.bioinformatics.gr |
| http://www.expressionprofiling.eu |
| http://www.animalfacility.eu |
| ● Server Administrator over a small LAN |
| ● MySQL Database design and management |
| ● Experience in QuarkExpress, Publisher, Photoshop |
| ● Microsoft Office Suite Highly experienced user |
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| Crystallography/Molecular Modelling software |
| ● User of Amber Package |
| ● Autodock ver. 3 |
| ● WhatIF |
| ● Editing and usage of UNIX |
| ● O software package |
| ● Crystallographic packages – intermolecular interaction analysis (patterns of H-bonds in protein DNA combined structures) |
| ● CCP4 |
| ● Gopenmol Molecular/Atomical Charge allocation Package |
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| Work Experience | Hospital “Attikon” Greece ● 2009 Work at Hellenic National Diabetes Centre as microarray analyst-experiment designer |
| BSRC Al. Fleming Athens Greece |
| ● 2007 -2008 Teaching experience while giving Lectures on microarray technology to MSc Biology Univ. Of Athens Students ● 2005 founded and designed bioinformatics oriented academic web site http://www.bioinformatics.gr |
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| Greek Army |
| ● 2004 worked as plane fuel and lubricants chemical analyst in the air force bases of Eleusina, Limnos and Tanagra. |
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| Dundee Scotland UK |
| ● Winter 2000-2001 official interpreter/translator English Greek-Greek English Dundee City NHS and Library. Dundee Scotland. |
| Futher details on this contact Mr. Hamid Rasheed on h.rasheed<at>dundeecity.gov.uk |
| Central Library, The Wellgate, Dundee DD1 1DB Scotland UK |
| Essex UK |
| ● Summer 1999: Work in Essex University Molecular Design Group as summer job. |
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| N. Ionia, Athens, Greece |
| ● Summer 1998 & 1999 PC Hardware Assembling and Testing. |
| ● Summer 1999: Picture Processing and Enhancement. |
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| Interests | |
| Theatre, Photography, Tennis, Windsurf, Dance, Marketing, Psychology, Classical Music Concerts, Sports Training, Excursions, Computers, Further Education, Fantasy Art, Arts and Literature. |
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| Further Qualifications | |
| ● Voted and remained (1year) in the position of finance manager of school board. |
| ● Music education for 8 years - average learning of guitar playing. |
| ● Attended French language lessons for 3 years. |
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| Major course Attendance | |
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| ● Evolution of Structure and Function in Biology - 1week theoretical course ICGEB Trieste. 11/2002 |
| ● RNA structure & function 1week theoretical course SISSA Trieste 03/2003 |
| ● Bioinformatics 1week practical course ICGEB Trieste. 06/2003 |
| ● Medical Genetics for developing countries - 1week theoretical course ICGEB Trieste. 9/2003 |
| ● Gene Expression Profiling and Bioinformatics Milan 2006 |
| ● Casimir 2007 Corfu Greece Oct 2007 |
| ● SPSS Bio-Statistics Course 2008 |
| ● International Greek Biotechnology forum 1 (2004), 2 (2005) ,4(2008), 5 (2009) Athens Greece |
| ● WASOG-BAL 2008 Athens Greece |
| ● 8th IEEE international Conference on Bioinformatics and Bioengineering (BIBE) Athens Greece |
| ● PhD related 1 month full day seminars related to copywrite, scientific writing and breakthrough idea organization 2008 |
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| Major Conference Attendance | |
| ● Greek National Centre for Research on Diabetes T2 Diabetological Seminar 2009 |
| ● Stephen Hawking, Physicist Lecture in Athens University, Athens Greece Summer 1999 |
| ● Prof. Gavin Gibson- Heriot-Watt University Edinburgh- Department of Actuarial Mathematics and Statistics 'Stochastic Modelling' Dundee University 2000 |
| ● Dr. John Crawford (Astrophysicist-Theoretical Biologist-Mathematician) “Who cares about Biodiversity” Abertay Dundee 21/02/2000 |
| ● 11/2001 Gergeri Crete – Prof. Kokkinidis Crystallography Symposium |
| ● International Greek Biotechnology Forum 1-4 |
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