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BIOINFORMATICS

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         Selections
1. Brief Description 6. Thesis
2. Research Interests 7. Photos
3. Personnel 8. Useful liks
4. Funded Research Projects 9. Contact
5. Puplications    

1. Brief Description:

 

The Bioinformatics Laboratory was created since 2010 and was founded with the FEK no. 511/3.4.2015.

2. Research Interests:

 

  • Protein phosphorylation. Quality control of High-throughput phosphoproteomic data and statistical analysis.
  • Recombination in viral genomes.
  • Evolution of the tRNA-synthetases superfamily.
  • Analysis of Next Generation Sequencing data (RNA-Seq, Bacterial Genome Assembly, Exome sequencing).
  • Evolution of gene regulation with a special interest on protein interaction networks and dimerization of transcription factors (bZIP, bHLH, Nuclear Receptors).
  • Gene/Genome duplications.


3. Personnel:

Students:

  • Panayotis Vlastaridis, PhD student: Organization and analysis of biological high-throughput data from multiple sources. In collaboration with Prof. Oliver, Cambridge University, UK, Prof. Van de Peer, VIB/UGent, Belgium, Dr Stratikos, Demokritos Research Center, Greece.
  • Anargyros Chaliotis, MSc student: Evolution of tRNA synthetases. In collaboration with Prof. Stathopoulos, University of Patra, Greece.
  • Michalis Tsimpidis, MSc student: Recombination in viral Genomes. In collaboration with Prof. Markoulatos, University of Thessaly, Greece.
  • Pelagia Kyriakidou, MSc student: Literature mining of high-throughput phosphoproteomic data.

In the Bioinformatics laboratory students learn to work primarily with Linux and Perl. Other programming languages may also be used, depending on the project and informatics expertise of the student, such as Java, Javascript, Visual Basic, SQL, PHP, Graph Databases, Matlab. Student projects vary from analyzing large and diverse biological data (phylogenetics, phylogenomics, genomic recombination, RNA-Seq, High-throughput phosphoproteomic data) to developing computational tools (viral genotyping and recombination tools, protein motif detection, databases, prediction of phosphorylation sites with machine learning) or a combination of data analysis and software development.

 

4. Funded Research Projects: 

  • Filtering, Annotation and Bioinformatics analyses of high-throughput Phosphoproteomic data (FAB-PHOS). Principal Investigator: GD Amoutzias. Funded by Aristeia II - GSRT.
  • Bioinformatic analysis of human genomic and phosphoproteomic data. Principal Investigator: GD Amoutzias. Funded by The Research Committee of the University of Thessaly.


5. Puplications:

29) Katsiani, A.T., Maliogka, V.I., Amoutzias, G.D., Efthimiou, K.E., Katis, N.I. Insights into the genetic diversity and evolution of Little cherry virus 1.

Plant Pathology 2015, 64 (4), pp. 817-824

28) Kyriakopoulou Z, Bletsa M, Tsakogiannis D, Dimitriou TG, Amoutzias GD, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Molecular epidemiology and evolutionary dynamics of Echovirus 3 serotype. Infect Genet Evol. 2015 Jun;32:305-12.

27) Kyriakopoulou Z, Pliaka V, Amoutzias GD, Markoulatos P. Recombination among human non-polio enteroviruses: implications for epidemiology and evolution. Virus Genes. 2015 Apr;50(2):177-88

26) Tsakogiannis D, Kyriakopoulou Z, Ruether IG, Amoutzias GD, Dimitriou TG, Diamantidou V, Kotsovassilis C, Markoulatos P. Determination of HPV16 physical status through E1/E6 and E2/E6 ratio analysis. J Med Microbiol. 2014 Sep 11. pii: jmm.0.076810-0.

25) Ruether IG, Dimitriou TG, Tsakogiannis D, Kyriakopoulou Z, Amoutzias GD, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Characterization of novel intergenogroup and intergenotype recombinant noroviruses from central Greece. Mol Cell Probes. 2014 Aug;28(4):204-10.

24) Tsakogiannis D, Darmis F, Gortsilas P, Ruether IG, Kyriakopoulou Z, Dimitriou TG, Amoutzias G, Markoulatos P. Nucleotide polymorphisms of the human papillomavirus 16 E1 gene. Arch Virol. 2014 Jan;159(1):51-63.

23) Tsakogiannis D, Kyriakopoulou Z, Amoutzias G, Ruether IG, Dimitriou TG, Panotopoulou E, Markoulatos P. Identification of novel E6-E7 sequence variants of human papillomavirus 16. Arch Virol. 2013 Apr;158(4):821-8.

22) Stagos D, Amoutzias GD, Matakos A, Spyrou A, Tsatsakis AM, Kouretas D. Chemoprevention of liver cancer by plant polyphenols. Food Chem Toxicol. 2012 Jun;50(6):2155-70.

21) Cock MJ, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, et al. The Ectocarpus Genome and Brown Algal Genomics. The Ectocarpus Genome Consortium. Advances in Botanical Research. 2012. Volume 64, 2012, Pages 141-184

20) Amoutzias GD, He Y, Lilley KS, Van de Peer Y, Oliver SG. Evaluation and properties of the budding yeast phosphoproteome. Mol Cell Proteomics. 2012 Jun;11(6):M111.009555.

19) Cock MJ, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, et al. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature. 2010 Jun 3;465(7298):617-21.

18) Amoutzias GD, He Y, Gordon J, Mossialos D, Oliver SG, Van de Peer Y. Posttranslational regulation impacts the fate of duplicated genes. Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2967-71.

17) Mossialos D, Amoutzias GD. Role of siderophores in cystic fibrosis (CF) pathogenesis: foes or friends? Int J Med Microbiol. 2009 Feb;299(2):87-98.

16) Amoutzias GD, Robertson DL, Van de Peer Y, Oliver SG. Choose your partners: Dimerization in eukaryotic transcription factors. Trends Biochem Sci. 2008 May;33(5):220-9.

15) Amoutzias GD, Van de Peer Y, Mossialos D. Evolution and taxonomic distribution of non-ribosomal peptide and polyketide synthases. Future Microbiol. 2008 Jun;3:361-70.

14) Amoutzias G, Van de Peer Y. Together we stand: genes cluster to coordinate regulation. Dev Cell. 2008 May;14(5):640-2.

13) Pinney JW, Amoutzias GD, Rattray M, Robertson DL. Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20449-53

12) Pampalakis G, Arampatzidou M, Amoutzias G, Kossida S, Sotiropoulou G. Identification and analysis of mammalian KLK6 orthologue genes for prediction of physiological substrates. Comput Biol Chem. 2007 Nov 29

11) Mossialos D, Amoutzias G. Siderophores in fluorescent pseudomonads: new tricks from an old dog. Future Microbiol. 2007 Aug;2:387-95.

10) Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, Robinson-Rechavi M, Bornberg-Bauer E, Robertson DL, Oliver SG. A protein interaction atlas for the nuclear receptors: Properties and quality of a hub-based dimerisation network. BMC Syst Biol. 2007 Jul 31;1(1):34.

9) Holden BJ, Pinney JW, Lovell SC, Amoutzias GD & Robertson DL. An exploration of alternative visualizations of the basic helix-loop-helix protein interaction network. BMC Bioinformatics. 2007 Aug 6;8(1):289.

8) Amoutzias G, Veron A, Weiner A, Robinson-Rechavi M, Bornberg-Bauer E, Oliver S, Robertson D. One Billion Years of bZIP Transcription Factor Evolution: Conservation and Change in Dimerization, and DNA-Binding Site Specificity. Mol Biol Evol. 2006 Dec 28.

7) Amoutzias GD, Bornberg-Bauer E, Oliver SG, Robertson DL. The Reduction/oxidation-phosphorylation control of the DNA binding of the bZIP family is linked with its dimerization network. BMC Genomics 2006 May 4;7:107

6) Podowski RM, Cleary JG, Goncharoff NT, Amoutzias G, Hayes WS. Suregene, a scalable system for automated term disambiguation of gene and protein names. J Bioinform Comput Biol. 2005 Jun;3(3):743-70.

5) Amoutzias GD, Weiner J, Bornberg-Bauer E. Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs. Gene. 2005 Feb 23

4) Amoutzias GD, Robertson DL, Oliver SG, Bornberg-Bauer E. Convergent evolution of gene networks by single-gene duplications in higher eukaryotes.. EMBO Rep. 2004 Mar;5(3):274-9.

                   Commented in       http://www.nature.com/embor/journal/v5/n4/full/7400129.html

                                               http://www.corante.com/loom/archives/2004/02/

                   Awarded in            http://www.manchester.ac.uk/press/title,47250,en.htm

3) Amoutzias GD, Robertson DL, Bornberg-Bauer E. The evolution of protein interaction networks in regulatory proteins. Comp Func Genomics 2004; 5: 79-84

2) Podowski RM, Cleary JG, Goncharoff NT, Amoutzias G, Hayes WS. AZuRE, a scalable system for automated term disambiguation of gene and protein names. Proc IEEE Comput Syst Bioinform Conf. 2004;:415-24.

1) Imsiridou A, Hardy H, Maudling N, Amoutzias G, Zaldivar Comenges JM. Web database of molecular genetic data from fish stocks. J Hered. 2003 May-Jun;94(3):265-7.

 

6. Thesis: 

Undergraduate Theses completed:

  • Tsimpidis M. 2014. Genomic and evolutionary analysis of human Enteroviruses with Bioinformatics methods.
  • Chaliotis A. 2012. Detection of microbial tRNA-synthetases with bioinformatics methods.

 

Postgraduate Theses completed:

  • Tsouhlou P. 2015. Bioinformatics and evolutionary analysis of RNA-Sequencing data from Bivalvia.
  • Chalyvopoulou P. 2014. Bioinformatic analysis of microbial metagenomes from Next-Generation Sequencing data.
  • Sini C. 2013. Bioinformatics analysis of Human Exome data from Next-Generation Sequencing technologies.
  • Doxara A. 2012. Bioinformatics analysis of Mitochondrial gene networks and related diseases from Genomic and Systems Biology data.

7. Photos: 

     

 

8. Useful links:

9. Contact:

Assistant Pofessor Grigorios Amoutzias
University of Thessaly
Department of Biochemistry & Biotechnology
Viopolis
Larissa – 41500
Greece
Tel.: +302410-565289
Fax. +30 2410-565290
Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

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