Journal Articles

Journal articles published from 2006 onwards

Tsagrasoulis D, Danos V, Kissa M, Trimpalis P, Koumandou V L, Karagouni A D, Tsakalidis A, Kossida S, SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis Evolutionary Bioinformatics. 2012, 8, 47-60    

     Vlachakis D, Brancale A, Berry C, Kossida S, A rapid assay for the biological evaluation of helicase activity Protocol Exchange. 2011,   DOI: 10.1038/protex.2011.275   

Moschopoulos CN, Pavlopoulos GA, Iacucci E, Aerts J, Likothanassis S, Schneider R, Kossida S., Which clustering algorithm is better for predicting protein complexes?, BMC Res Notes. 2011 Dec 20;4(1):549.

Ropodi A, Sakkos N, Moschopoulos C, Magklaras G, Kossida S, Superclusteroid: a Web tool dedicated to data processing of protein-protein interaction networks, EMBnet.journal, vol 17, nr 2,  2011, 10-15

Arhondakis S, Frousios F, Iliopoulos CS, Pissis SP, Tischler G, Kossida S, Transcriptome map of mouse isochores, BMC Genomics 2011, 12:511

Moschopoulos CN, Pavlopoulos GA, Likothanassis S, Kossida S, Analyzing Protein-Protein Interaction Networks with Web Tools, Current Bioinformatics, 2011 6:389-397

Dimitriadis D, Koumandou VL, Trimpalis P, Kossida S, Protein functional links in Trypanosoma brucei, identified by gene fusion analysis, BMC Evolutionary Biology, 2011 11:193

Tsliki G, Kossida S, Fusion Methodologies for Biomedical Data, Journal of Proteomics, 2011, [Epub ahead of print]

Kritikos GD, Moschopoulos C, Vazirgiannis M, Kossida S, Noise reduction in protein-proteins interaction graphs by the implementation of a novel weighting scheme, BMC Bioinformatics ,2011 12: 239

Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG, Using graph theory to analyze biological networks, BioData Min., 2011 Apr 28;4(1):10.

Arhondakis S, Kossida S, Compositional perspective on human brain aging, BioSystems,2011 104: 94-98

Kastania AN, Loudos G, Sgouros NP, Constantinou I, Vavatsioula M, Boudoulas H, Kossida S, e-Herophilus: 24-hour personalised telecardiology services, Int J Electron Healthc. 2010 5(4):340-54

Kapasa M, Arhondakis S, Kossida S, Phylogenetic and regulatory region analysis of Wnt5 genes reveals conservation of a regulatory module with putative implication in pancreas development, Biol Direct. 2010 4;5:49

Logotheti S, Michalopoulos I, Sideridou M, Daskalos A, Kossida S, Spandidos DA, Field JK, Vojtesek B, Liloglou T, Gorgoulis V, Zoumpourlis V., Sp1 binds to the external promoter of the p73 gene and induces the expression of TAp73gamma in lung cancer, FEBS J. 2010 277(14):3014-3027

Makridakis M, Roubelakis MG, Bitsika V, Dimuccio V, Samiotaki M, Kossida S, Panayotou G, Coleman J, Candiano G, Anagnou NP, Vlahou A., Analysis of secreted proteins for the study of bladder cancer cell aggressiveness, J Proteome Res. 2010 4;9(6):3243-3259

D'Elia D, Gisel A, Eriksson NE, Kossida S, Mattila K, Klucar L,Bongcam-Rudloff E, The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community, BMC Bioinformatics 2009 10 Suppl 6:S1

Moschopoulos, CN, Pavlopoulos, GA, Schneider R, Likothanasis, SD, Kossida, S, GIBA: A clustering tool for detecting protein complexes, BMC Bioinformatics 2009 10 Suppl 6:S11

Tsagrasoulis D, Zerefos P, Loudos G, Vlahou A, Baumann M, Kossida S, Brukin2D: A 2D visualisation and comparison tool for LC-MS data, BMC Bioinformatics 2009 10 Suppl 6:S12

Theodosiou A, Arhondakis S, Baumann M, Kossida S, Evolutonary scenarios of Notch proteins, Mol Biol Evol. 2009 26:1631-1640

Pavlopoulos GA, Moschopoulos CN, Hooper SD, Schneider R, Kossida S, jClust: A clustering and visualization toolbox, Bioinformatics 2009 25:1994-1996

Moschopoulos C, Mavroudi S, Likothanasis S, Kossida S, Constructing and working with protein interaction graphs, EMBnet.news, vol 15, nr 2,  2009 30-36

Pavlopoulou A, Kossida S, Phylogenetic analysis of the Eukaryotic RNA (cytosine-5)-methyltransferases, Genomics 2009 93:350-357

Roubelakis M, Zotos P, Papachristoudis G, Michalopoulos I, Pappa K, Anagnou N, Kossida S, Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application, BMC bionformatics 2009 10:Suppl 6:S20

Rizos E, Siafakas N, Katsantoni E, Lazou B, Sakellaropoulos K, Kastania A, Kossida S, Chatzigeorgiou K-S, Arsenis G, Zerva L, Katsafouros K, Lykouras L, Association of the dopamine D₃ receptor Ser9Gly and of the serotonin 2C receptor gene polymorphisms with tardive dyskinesia in Greeks with chronic schizophrenic disorder, Psychiatric Genetics 2009 19:106-107

Kastania A, Loudos G, Demarias S, Konstantinou I, Sgouros N, Gavala A, Vavatsioula M, Stamatopoulos V, Tsipis A, Stafylas P, Dafoulas G, Davos C, Boudoulas H, Kossida S, Qualtity Models  and Certificates for Telecardiology Platforms, MED Review Cardiology 2008 13:34-37

Kapasa M, Serafimidis I, Gavalas A, Kossida S, Identification of phylogenetically conserved enhancer elements implicated in pancreas development in the WISP1 and CTGF orthologs Genomics 2008 92:301-308

Garbis SD, Tyritzis SI, Roumeliotis T, Zerefos P, Giannopoulou EG, Vlahou A, Kossida S, Diaz J, Vourekas S, Tamvakopoulos C, Pavlakis K, Sanoudou D, Constantinides CA, Search for potential markers for prostate cancer diagnosis, prognosis and treatment in clinical tissue specimens using amine-specific isobaric tagging (iTRAQ) with two-dimensional liquid chromatography and tandem mass spectrometry, J Proteome Res. 2008 7(8):3146-3158 Epub 2008 Jun 14

Vlahou A, Schanstra J, Frokiaer J, El Nahas M, Spasovski G, Mischak H, Domon B, Allmaier G, Bongcam-Rudloff E, Attwood T., European Kidney and Urine Proteomics Network., Establishment of a European Network for Urine and Kidney Proteomics, J Proteomics 2008 71:490-492

Paliakasis CD, Michalopoulos I, Kossida S, Web-based tools for protein classification, Methods Mol Biol. 2008 428:349-367

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. 2008 32(2):111-21 Epub 2007 Nov 29

Pavlopoulou A, Kossida S, Plant cytosine-5 DNA methyltransferases: structure, function, and molecular evolution, Genomics 2007  90:530-541

Mavroudi S, Papadimitriou S, Kossida S, Likothanassis S., Vlahou A, Computational Methods & Algorithms for Mass-Spectrometry based Differential Proteomics, Current Proteomics 2007  

Moschopoulos C, Theodosiou A, Kossida S, Protein interactions and drug targets EMBnet.news, vol 13, nr 4,  2007 25-31

Zerefos P, Prados J, Kossida S, Kalousis A, Vlahou A, Sample preparation and bioinformatics in MALDI profiling of urinary proteins, J Chromatogr B Analyt Technol Biomed Life Sci. 2007  853:20-30

Fountoulakis M, Kossida S, Proteomics-driven progress in neurodegeneration research, Electrophoresis 2006  27:1556-1573

Xixi E, Dimitraki P, Vougas K, Kossida S, Lubec G, Fountoulakis M, Proteomic analysis of the mouse brain following protein enrichment by preparative electrophoresis, Electrophoresis 2006  27:1424-1431

Zerefos PG, Vougas K, Dimitraki P, Kossida S, Petrolekas A, Stravodimos K, Giannopoulos A, Fountoulakis M, Vlahou A, Characterization of the human urine proteome by preparative electrophoresis in combination with 2-DE, Proteomics 2006  6:4346-4355

Conferences Proceedings

Myolona EA, Savelonas, M. A., Maroulis, D. and Kossida, S., A computer-based technique for automated spot detection in proteomics images IEEE Transactions on Information Technology in Biomedicine: 2011, 15, 661-667    

Moschopoulos C, Likothanassis S, Stamatopoulos VG, Kossida S, Applying graph theory on protein- protein interaction data, Conference proceedings IWSSIP 2009, 2009 Chalkida, Greece

Zotos P, Papachristoudis G, Roubelakis M, Michalopoulos I, Pappa K, Anagnou N, Kossida S, GOmir: a stand alone application for human microRNA target analysis and gene ontology clustering,Conference proceedings IEEE BIBE, 2008 Athens, Greece

Moschopoulos C, Pavlopoulos G, Likothanasis D, Kossida S, An Enhanced Markov Clustering Method for Detecting Protein Complexes,Conference proceedings  IEEE BIBE, 2008 Athens, Greece

Kastania A, Boudoulas H, Kossida S, Evaluation aspects of the e-Herophilus Telecardiology Model, Conference proceedings XV Winter Course of the CATAIXX Image Analysis Course of the ULL, 2008 LaLAguna, Spain

Sgouros N, Constantinou I, Loudos G, Kossida S, Use of the MPEG-4 ALS Architecture and Inter-channel Prediction for Multi-channel ECG Coding, Conference proceedings IEEE ISSPIT-2007, 2007 Cairo, Egypt

Kastania A, Demarias S, Davos C, Boudoulas C, Kossida S, A Telecardiology service Quality Model, Conference proceedings  Med@Tel 2007, 2007 Luxemburg

Kastania A, Gavala A, Tsipis A, Loudos G, Kossida S, Telecardiology quality and reliability assurance, Conference proceedings  XV Winter Course of the CATAIXX Image Analysis Course of the ULL, 2007 LaLAguna, Spain

Kastania A, Gavala A, Loudos G, Kossida S, Telecardiology Systems Total Quality Management, Conference proceedings ICICTH, International Conference on Information Communication Technologies in Health, 2007 Samos, Greece

Iakovidis DK, Maroulis D, Zacharia E, Kossida S, A Genetic  Approach to Spot Detection in two-Dimensional Gel Electrophoresis images, Conference proceedings  Proc. International Conference on Information Technology in Biomedicine (ITAB), 2006 Ioannina, Greece

Kossida S, Falkou C, Vasileoiu I, Zervas C, Towards an Integrated Bioinformatics System: Using Integrins as Case Study to Dissect the Molecular Basis of Cell Adhesion, Conference proceedings ECML/PKDD-2006 Workshop on Data and Text Mining for Integrative Biology, 2006 Berlin, Germany

Bougioukos P, Cavouras D, Daskalakis A, Kossida S, Nikiforidis G, Bezerianos A, Feature Extraction and Analysis of Prostate Cancer Proteomic Mass Spectra for Biomarker Discovery, Conference proceedings Proc. International Conference on Information Technology in Biomedicine (ITAB), 2006 Ioannina, Greece

Garbis SD, Zerefos P, Papadopoulou A, Vlahou A, Tamvakopoulos C, Kossida S, Diaz J, Pavlaki K, Tyritzis S, Vourekas SC., Quantitative Proteomic Approaches for the Determination of Carcinogenesis Biomarkers in Prostate Tissue., Conference proceedings 54th Annual ASMS Conference on Mass Spectrometry and Allied Topics, 2006 Seattle Wa, USA

Book chapters

Arhondakis S, Tsiliki G, Kossida S, Monitoring the Transcriptome, in digital Forensics for the Health Sciences, Medical Information Science Reference, 2011, 89-107

Kastania A, Kossida S, Statistics in Telemedicine, in Advance in Telemedicine: Technologies, Enabling factors and Scenarios, InTech, 2011, 191-210

Stamatopoulos VG, Karagiannis GE, Rigby ML, Kossida S, Development and Evaluation of a Web-Based Personal Electronical Health Record (pEHR), in Web-Based Applications in Healthcare and Biomedicine, Annals of Information Systems, Springer, 2010, 1-12

Stamatopoulos VG, Karagiannis GE, Gatzoulis MA, Kastania A, Kossida S, Open Virtual Environment for Research Business and Public Reseources, in Handbook of Research on Biocomputation and Biomedical Informatics, Information Science Reference, 2009, 215-227

Theodosiou A, Moschopoulos C, Baumann M, Kossida S, Protein interactions and disease., in Handbook of Research on Systems Biology Applications in Medicine Idea Group Inc., 2009, 694-713

Giannopoulou E, Kossida S, Data Mining Applications in the Post-Genomic Era, Data Mining in Medical and Biological Research, in Data Mining in Medical and Biological Research, InTech, 2008, 237-252

Kastania A, Zimeras S, Kossida S, A Biosignal Classification Neural Modeling Methodology for Intelligent Hardware Construction, in New Directions in Intelligent Interactive Multimedia, Springer Berlin / Heidelberg, 2008, 489-495

Paliakasis C, Michalopoulos I, Kossida S, Web-based Tools for Protein Classification, in The Humana Press Inc., Clinical Proteomics, 2008, 349-367

Pavlopoulou A, Kossida S, Cytosine Methyltransferases as tumor markers, in Genes, Genomes & Genomics, Regency Publications, 2007, 1-18

Fountoulakis M, Kossida S, Lubec G, Proteomics in Alzheimer’s disease, in Proteomics in Drug Research, Wiley-VCH Verlag GmbH & Co. KGaA, 2006, 279-297

Quick guides

guideMATLAB.pdf

guideXcede.pdf