INSTITUTE OF BIOLOGY, MEDICINAL CHEMISTRY & BIOTECHNOLOGY
 
  Drug Discovery
  Molecular Analysis
  Organic and Organometallic Chemistry
  Medicinal Chemistry
  Structural Biology & Chemistry
  Molecular Endocrinology
  Signal Mediated Gene Expression
  Molecular & Cellular Ageing
  Biomedical Applications
  Holistic Approaches in Health
  Chemical Carcinogenesis and Genetic Toxicology
  Metabolic Engineering-Bioinformatics
  Biotechnology
  Enzyme and Synthetic Biotechnology
  Biomimetics & Nanobiotechnology

 

Metabolic Engineering - Bioinformatics

 

Research Team

Dr. Aristotelis Chatziioannou, Researcher B'
Prof. F.N Kolisis, Collaborating Professor

Dr. Olga Papadodima, Functional Scientist
Ioannis Valavanis, Postdoctoral researcher
Eleftherios Pilalis, Postdoctoral researcher

 

Metabolic engineering principles have produced great advances for bioprocess applications and for increasing the general understanding of biological systems. The DNA microarray technologies creates a new environment for metabolic engineering, although its focus and central components remain the same, new tools are required to take advantage of the opportunities arising from the availability of whole-genome sequence information, and the gene profiling experiments, which allow to derive abundant information concerning the interactions between the classes of biological molecules (genes, proteins, metabolites, transcription factors, cofactors, etc) underlying the cellular phenotype.

The group of metabolic engineering and bioinformatics of IBRB is based on relevant activities initiated by the Laboratory of Biotechnology (Prof. F.N. Kolisis) of the School of Chemical Engineering NTUA. The group focuses its research interest in the study of biological mechanisms through the use of a wide range of computational tools in order to overcome the issues of significant measurement variation and the overwhelming complexity which is inherent in the biological systems. Using the chain of causal relations between the gene, the protein and the metabolic pathway level as a hypothesis bedrock, it aims to expand the boundaries of biological knowledge in the respective fields (genomic, proteomic, metabolic) by perceiving these fields as supplementary mechanisms of the same phenomenon. To this end, it uses systemic quantitative approaches to describe, analyze and create simulation models to study functional characteristics of specific physiological/ pathological mechanisms.

 

Software Tools

GRISSOM
 
ARMADA
 
SrRAnGER
         
GOrevenge
       

http://www.grissom.gr/



Participation in Funded Projects and Research Networks

European /International Projects

  1. Collaborative Project (large scale integrating project), FP7- Call: KBBE-2010.3.5-04, Microbial diversity and metagenomic mining for biotechnological innovation, entitled « Systematic screening for novel hydrolases from hot environments (HotZyme)» (480.000,00 €, Group budget, 2011-2015).
  2. Medium-scale focused research project, EU FP7, Theme: Environment, including climate change, Sub-activity: Environment and Health, entitled Envirogenomarkers, which aims at the development and application of a new generation of biomarkers to study the role of environmental agents in human disease (474,000.00 €, Group budget, 2009-2013).
  3. FP7- ICT-2007.4.4 Intelligent Content and Semantics, entitled «e-Laboratory for Interdisciplinary Collaborative Research in Data Mining and Data-Intensive Sciences (e-LICO)» (contract no:231519) (369,308.00 €, Group budget, 2009-2012,).
  4. Franco-Hellenic Bilateral Research Program 2007-2008. Application of Metabolic Engineering and Stochastic Modelling Methodologies for the Optimization of Fatty Acid Biosynthesis in Plants (12,600.00 €, Group budget, 2007-2008).
  5. 12CHN 204 Entrepreneurial Program Competitiveness & Entrepreneurship & Districts in Transition, (Action Bilateral Research and Technology Cooperation between Greece and China)
    Personalization of melanoma therapeutic management through the fusion of systems biology and intelligent data mining methodologies-PROMISE” (523000,00 € total budget, 2013-2015, scientific coordinator).

 

International Scientific Networks

  1. COST Action BM0901 “European systems genetics network for the study of complex genetic human diseases using mouse genetic reference populations (SYSGENET) (WG3 Bionformatics (2010-2013).
  2.  COST Action FA1006. “Plant Metabolic Engineering for High Value Products (Working Group 3)(2012-2015).
  3. ERA-Instruments consortium (16 members), for a pan-european coordination of the funding actions regarding large research infrastructures, in the field of Life Sciences. (http://www.era-instruments.eu/) (2008-2011)

 

National Projects

  1. Operational Program “Education and Lifelong Learning” Action “Excellence II”, “Targeting tumor stroma and cancer cell metabolic co-operation for Lung Cancer Therapy  (Metaboli-CA)” (53,000 €, Group budget,  2014-2015)
  2. 09ΣΥΝ-11-675 Cooperation Research Program entitled “Development of novel Angiogenesis-Modulating Pharmaceuticals by screening of natural compounds and synthetic analogues-DAMP” (duration 2010-2014), sponsored by the Program “Competitiveness and Entrepreneurship” ΕΠΑΝ-ΙΙ Act 1 of the Peripheral Entrepreneurial Program of Attiki, with co-funding by the European Fund of Regional Development and National Funds. (297,000.00 €, Group budget, 2011-2015).
  3. Operational Program “Education and Lifelong Training” Action “Thalis”, “MODELLING THE DYNAMIC PROGRESSION OF CELLULAR AGING THROUGH THE DEVELOPMENT OF SYSTEMS BIOLOGY AND BIOINFORMATICS TOOLS - MAESTRO” (250,200.00 €, Group budget, 2012-2015).
  4. 09ΣΥΝ-11-675 Cooperation Research Program entitled “PIK3CA Oncogenic Mutations in Breast and Colon Cancers: Develop-ment of Targeted Anticancer Drugs and Diagnostics -POM” (duration 2010-2014), sponsored by the Program “Competitiveness and Entrepreneurship” ΕΠΑΝ-ΙΙ Act 1 of the Peripheral Entrepreneurial Program of Attiki, with co-funding by the European Fund of Regional Development and National Funds (332,100.00 €, Group budget, 2011-2015, team responsible for omic analysis activities).
  5. Entrepreneurial Program Competitiveness & Entrepreneurship & Districts in Transition, (Action Developmental Proposals of Research Institutions –KRIPIS) “ Targeted therapeutic Approaches against Degenerative Diseases with emphasis in Cancer and Ageing” (1500000,00 € total budget, 2012-2015,  team responsible for the bioinformatic activities).
  6. G.S.R.T./ Development of pilot grid applications for the exploitation of the National Grid Infrastructure (GRID-APP)- “Processing of Distributed Genetic Information from virtualized Bioinformatic Databases (54,000.00 €, Group budget, 2006-2007, technical coordinator)
  7. Operational Program “Competitiveness” Action “Excellence in the Research Centers of the GSRT 2nd round”, “Application/ Development of Bionformatic Tools for Systems Biology Research” (885,106.00 €, 2006-2009, principal investigator)

 

Economic Valorisation
  1. ACT 119153 3rd Phase ”Open Access Repositories and Electronic Journals” supervised by the Greek Information Society /FP6 Subtask 6  Development of an integrated DNA microarray data processing and meta-analysis platform plus a microarray experimental data repository, in Grid. (365,243.00 €, Group budget, 2007-2008, technical coordinator).

 

Selected Publications of the Team
  1. Logotheti M, Papadodima O, Venizelos N, Chatziioannou A, Kolisis F: A comparative genomic study in schizophrenic and bipolar disorder patients, based on microarray expression profiling meta-analysis. Scientific World Journal 2013, Article ID 685917, http://dx.doi.org/10.1155/2013/685917
  2. Papadodima O, Sirsjö A, Kolisis FN, Chatziioannou A: Application of an integrative computational framework in trancriptomic data of atherosclerotic mice suggests numerous molecular players. Advances in Bioinformatics 2012, doi:10.1155/2012/453513.
  3. Pampalakis G, Obasuyi O, Papadodima O, Chatziioannou A, Zoumpourlis V, Sotiropoulou G: The KLK5 protease suppresses breast cancer by repressing the mevalonate pathway. Oncotarget 2013, 4(9).
  4. Papadodima O, Chatziioannou A, Patrinou-Georgoula M, Kolisis FN, Pletsa V, Guialis A: HuR-Regulated mRNAs Associated with Nuclear hnRNP A1-RNP Complexes. International Journal of Molecular Sciences 2013, 14(10), 20256-20281.
  5. Moutselos K, Maglogiannis I, Chatziioannou A: Integration of High-volume Molecular and Imaging Data for Composite Biomarker Discovery in the study of Melanoma, Biomed Res International 2013, (in press).
  6. Valavanis I, Maglogiannis I, Chatziioannou AA: Intelligent Utilization of Biomarkers for the Recognition of Obstructive Nephropathy. Intelligent Decision Technologies, 2013, 7(1):11-22.
  7. Maglogiannis I, Goudas T, Doukas C, Chatziioannou A: A Collaborative Biomedical Image Mining Framework: Application on the Image Analysis of Microscopic Kidney Biopsies. IEEE Trans Inf Technol Biomed 2013, 17(1): 82-91
  8. Valavanis I, Sifakis EG, Georgiadis P, Kyrtopoulos S, Chatziioannou AA. A Composite Framework for the Statistical Analysis of Epidemiological DNA Methylation Data with the Infinium Human Methylation 450K BeadChip, Journal of Biomedical and Health Informatics (former IEEE Trans on Inform Tech in Biomed) 2013, (in press).
  9. Chatziioannou AA, Moulos P: Exploiting Statistical Methodologies and Controlled Vocabularies for Prioritized Functional Analysis of Genomic Experiments: the StRAnGER Web Application. Front Neurosci 2011, 5:8.
  10. Pilalis E, Chatziioannou A, Thomasset B, Kolisis F: An in silico compartmentalized metabolic model of Brassica napus enables the systemic study of regulatory aspects of plant central metabolism. Biotechnol Bioeng 2011, 108(7):1673-1682.
  11. Moutselos K, Maglogiannis I, Chatziioannou A: GOrevenge: a novel generic reverse engineering method for the identification of critical molecular players, through the use of ontologies. IEEE Trans Biomed Eng 2011, 58(12):3522-3527.
  12. Rao NAS, McCalman MT, Moulos P, Francoijs KJ, Chatziioannou A, Kolisis FN, Alexis MN, Mitsiou DJ, Stunnenberg HG: Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes. Genome Research 2011, 21(9):1404-1416
  13. Argyropoulos C, Chatziioannou AA, Nikiforidis G, Moustakas A, Kollias G, Aidinis V: Operational criteria for selecting a cDNA microarray data normalization algorithm. Oncol Rep 2006, 15 Spec no.:983-996.
  14. Chatziioannou A, Palaiologos G, Kolisis FN: An in-silico model of the biosynthesis of neurotransmitter glutamate, elucidates the complex regulatory role of glucocorticoids in neurotransmitter glutamate release. Comput Biol Med 2009, 39(6):501-511.
  15. Tzouvelekis A, Harokopos V, Paparountas T, Oikonomou N, Chatziioannou A, Vilaras G, Tsiambas E, Karameris A, Bouros D, Aidinis V: Comparative expression profiling in pulmonary fibrosis suggests a role of hypoxia-inducible factor-1α in disease pathogenesis. American Journal of Respiratory and Critical Care Medicine 2007, 176(11):1108-1119.
  16. Chatziioannou A, Moulos P, Kolisis FN: Gene ARMADA: An integrated multi-analysis platform for microarray data implemented in MATLAB. BMC Bioinformatics 2009, 10:354.
  17. Moutselos K, Kanaris I, Chatziioannou A, Maglogiannis I, Kolisis FN: KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database. BMC Bioinformatics 2009, 10:324.
  18. Moulos P, Papadodima O, Chatziioannou A, Loutrari H, Roussos C, Kolisis FN: A transcriptomic computational analysis of mastic oil-treated Lewis lung carcinomas reveals molecular mechanisms targeting tumor cell growth and survival. BMC Med Genomics 2009, 2:68.
  19. Tenta R, Katopodis H, Chatziioannou A, Pilalis E, Calvo E, Van L-T, Labrie F, Kolisis F, Koutsilieris M: Microarray analysis of survival pathways in human PC-3 prostate cancer cells. Cancer Genomics and Proteomics 2007, 4(4):309-317.
  20. Pilalis E, Grigoroudis AI, Chatziioannou A, Panagiotidis CA, Kolisis F, Kyriakidis D: E-coli genome-wide promoter analysis in search for potential AtoC target elements. FEBS JOURNAL 2008, 275(Suppl 1):286.
  21. Maglogiannis I, Sarimveis H, Kiranoudis CT, Chatziioannou AA, Oikonomou N, Aidinis V: Radial basis function neural networks classification for the recognition of idiopathic pulmonary fibrosis in microscopic images. IEEE Trans Inf Technol Biomed 2008, 12(1):42-54.
  22. Doukas CN, Maglogiannis I, Chatziioannou AA: Computer-supported angiogenesis quantification using image analysis and statistical averaging. IEEE Trans Inf Technol Biomed 2008, 12(5):650-657.
  23. Kanaris I, Mylonakis V, Chatziioannou A, Maglogiannis I, Soldatos J: HECTOR: Enabling microarray experiments over the hellenic grid infrastructure. Journal of Grid Computing 2009, 7(3):395-416.
  24. Grigoroudis AI, Panagiotidis CA, Pilalis E, Chatziioannou A, Kolisis F, Papadopoulos G, Kyriakidis DA: Identification of additional Escherichia coli AtoC binding target elements gives new insight to bacterial regulatory networks: molecular modeling of AtoC-DNA binding domain amino acids. . Amino Acids 2009, 37(Suppl 1):S102-S103.
  25. Chatziioannou AA, Kanaris I, Doukas C, Moulos P, Kolisis FN, Maglogiannis I: GRISSOM platform: Enabling distributed processing and management of biological data through fusion of grid and web technologies. IEEE Transactions on Information Technology in Biomedicine 2011, 15(1):83-92.
  26. Pilalis E, Chatziioannou AA, Grigoroudis AI, Panagiotidis CA, Kolisis FN, Kyriakidis DA: Escherichia coli genome-wide promoter analysis: Identification of additional AtoC binding target elements. BMC Genomics 2011, 12.
  27. Sifakis EG, Lambrou GI, Prentza A, Vlahopoulos S, Koutsouris D, Tzortzatou-Stathopoulou F, Chatziioannou AA: Elucidating the identity of resistance mechanisms to prednisolone exposure in acute lymphoblastic leukemia cells through transcriptomic analysis: A computational approach. J Clin Bioinforma 2011, 1:36.
  28. Lambrou GI, Chatziioannou A, Vlahopoulos S, Moschovi M, Chrousos GP: Evidence for Deterministic Chaos in Aperiodic Oscillations of Acute Lymphoblastic Leukemia Cells in Long-Term Culture. Chaotic Modeling and Simulation (CMSIM) 2011, 1:119-126.
  29. Sifakis EG, Prentza A, Koutsouris D, Chatziioannou AA: Evaluating the effect of various background correction methods regarding noise reduction, in two-channel microarray data. Computers in Biology and Medicine 2012, 42(1):19-29.
  30. Chatziioannou A, Palaiologos G, Kolisis FN: Metabolic flux analysis as a tool for the elucidation of the metabolism of neurotransmitter glutamate. Metab Eng 2003, 5(3):201-210. (5yr IF 5.911)

 

 

Software tools

 

 

   
       

 

 

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