Journal Articles

D'Elia D., Gisel A., Eriksson N.E., 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, C.N., Pavlopoulos, G.A., Schneider, R., Likothanasis, S.D., 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

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):3146-58. 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 428:349-67

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 Apr;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  

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 P.G., 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

Moschopoulos C., Likothanassis S., Stamatopoulos V.G., Kossida S. Applying graph theory on protein- protein interaction data, Conference proceedings, 2009, IWSSIP 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, 2008, IEEE BIBE, Athens, Greece

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

Kastania A., Boudoulas H., Kossida S., Evaluation aspects of the e-Herophilus Telecardiology Model, Conference proceedings, 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., Gavalas 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

Iakovidis D.K., 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

Kastania A., Gavala A., Loudos G. Kossida S., Telecardiology Systems Total Quality Management., Conference proceedings: ICICTH, International Conference on Information Communication Technologies in Health, 2006, Samos, 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 S.D., Zerefos P., Papadopoulou A, Vlahou A, Tamvakopoulos C, Kossida S, Diaz J, Pavlaki K, Tyritzis S, Vourekas S C C., 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

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

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

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

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

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

EMBnet Publications

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

Falquet L, , Herzog R., The EMBnet Annual General Meeting 2007, EMBnet.news, Vol13, nr3, 2007, 5-10

Falquet L., Course Report, Athens, Greece, 2007: EMBnet.news Vol13, nr4, Dec 2007, p5-6

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

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