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List of Publications


Conference Papers:

  • K.Marias, V. Sakkalis, A. Roniotis, C. Farmaki, G. Stamatakos, D. Dionysiou, S.Giatili, N. Uzunoglou, N. Graf, R. Bohle, E. Messe, P. V. Coveney, S. Manos, S. Wan, A. Folarin, S. Nagl, P. Büchler, T. Bardyn, M. Reyes, G. Clapworthy, N. Mcfarlane, E. Liu, T. Bily, M. Balek, M. Karasek, V. Bednar, J. Sabczynski, R. Opfer, S. Renisch, and I. C. Carlsen, Clinically Oriented Translational Cancer Multilevel Modeling: The ContraCancrum project, WC 2009 World Congress of Medical Physics and Biomedical Engineering, Sept 7-12, Munich.
  • C. Farmaki, K. Marias,V. Sakkalis, FORTH; N. Graf, USAAR, A spatially adaptive active contour method for improving semi-automatic medical image annotation Task, WC 2009 World Congress of Medical Physics and Biomedical Engineering, Sept 7-12, Munich.
  • A. Roniotis, K. Marias, V. Sakkalis, and G. Stamatakos "Mathematical guide for developing a heterogeneous, anisotropic and 3-dimensional glioma growth model using the diffusion equation", Information Technology Applications in Biomedicine (IEEE-ITAB 2009), Larnaca, Cyprus, 2009.
  • A. Roniotis, K. Marias, and V. Sakkalis, "A complete mathematical study of a 4D model of heterogeneous and anisotropic glioma evolution", 31st IEEE-EMBS, Engineering in Medicine and Biology Society (EMBC 2009), Minessota, USA, September 2-6, 2009.
  • V. Sakkalis, A. Roniotis, C. Farmaki, I. Karatzanis, and K. Marias, "Evaluation framework for the multilevel macroscopic models of solid tumor growth in the glioma case", 32nd IEEE-EMBS, Engineering in Medicine and Biology Society (EMBC 2010), Buenos Aires, Argentina, August 31-September 4, 2010 (Accepted).
  • V. Sakkalis, K. Marias, A. Roniotis, and E. Skounakis "Translating cancer research into clinical practice: A framework for analyzing and modeling cancer from imaging data", 9th International Conference on Intelligent Systems Design and Applications (ISDA 2009), Pisa, Italy, November, 2009.
  • Skounakis E, Sakkalis V, Marias K, Banitsas K, Graf N., DoctorEye: A multifunctional open platform for fast annotation and visualization of tumors in medical images. Conf Proc IEEE Eng Med Biol Soc. 2009;1:3759-62.
  • Roniotis, K. Marias, V. Sakkalis, and G. Stamatakos, "Comparing Finite Element and Finite Difference Techniques as Applied to the Development of Diffusive Models of Glioblastoma Multiforme Growth", 32nd IEEE-EMBS, Engineering in Medicine and Biology Society (EMBC 2010), Buenos Aires, Argentina, August 31-September 4, 2010 (Accepted).
  • A. Roniotis, K. Panourgias, J. Ekaterinaris, K. Marias, and V. Sakkalis, "Approximating the diffusion – reaction equation for developing glioma models for the ContraCancrum Project: a showcase", 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation, Athens, Greece, September 8-9, 2010 (Accepted).
  • K. Marias, V. Sakkalis, et al., "Clinically Oriented Translational Cancer Multilevel Modelling", 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation, Athens, Greece, September 8-9, 2010 (Accepted).
  • A. Roniotis, K. Marias, V. Sakkalis, E. Skounakis, and M. Zervakis, "Incorporating different proliferation rates in glioma modeling using vectorization operators", 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation, Athens, Greece, September 8-9, 2010 (Accepted).
  • C. Farmaki, K. Mavrigiannakis, K. Marias, M. Zervakis, and V. Sakkalis, “Assessment of automated brain structures segmentation based on the mean-shift algorithm: Application in brain tumor”, Submitted to 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), Corfu, Greece, November 2010 (under review).
  • G. S. Stamatakos, D. Dionysiou, S. Giatili, E. Kolokotroni, Ε. Georgiadi, A. Roniotis,V. Sakkalis, P. Coveney, S. Wan, S. Manos, S. Zasada, A. Folarin, P. Büchler, T. Bardyn, S. Bauer, M. Reyes, T. Bily, V. Bednar, M. Karasek, N. Graf, R. Bohle, E. Meese, Y.-J. Kim, H. Stenzhorn, G. Clapworthy, E. Liu, J. Sabczynski, and K. Marias, “The ContraCancrum Oncosimulator: Integrating Biomechanisms Across Scales in the Clinical Context”, 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation, Athens, Greece, September 8-9, 2010.
  • J. Zepp, N. Graf, E. Skounakis, R. Bohle, E. Meese, H. Stenzhorn, Y.-J. Kim, C. Farmaki, V. Sakkalis, W. Reith, G. Stamatakos, K. Marias, “Tumor segmentation: The impact of standardized signal intensity histograms in glioblastoma”, 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation, Athens, Greece, September 8-9, 2010.
  • T.Bily, V.Bednar, M. Balek. Computational cell based framework for multi-scale description of biological processes. Accepted poster presentation on ESCS1-ECCB Sept. 26 2010 Ghent, Belgium.
  • T.Bily, V.Bednar, M.Karasek, T.Mikula. Computational cell based multi-scale multi-model framework for prediction of fates of cells in cancer biology. Accepted to be orally presented in the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation to held in Athens, Greece on Sept. 8-9 2010.
  • T.Bily, V.Bednar. Digital Biological Cell Approach – A unified Modeling platform for Biological Processes. Orally presented on YRF@MFCSL Aug. 21-22 2010, Brno, Czech Rep.
  • T.Bily, M.Balek, V.Bednar, M.Karasek. Microscopic tumor growth module for ContraCancrum project. IFMBE Proceedings 25 IFMBE (4), 2009.
  • B Liu, G J Clapworthy, E Kolokotroni and G Stamatakos, Using the GPU for Simulating Spatiotemporal Tumour Growth, to be presented in 4th International Advanced Research Workshop on in silico Oncology and Cancer Investigation, Athens, Sept 2010
  • B Liu, G J Clapworthy, F Dong and G Stamatakos, Improving the Efficiency of the Computational Modelling of Tumour Growth by Use of the GPU, to be presented in VPH2010 Conference, Brussels, Sept 2010
  • K Marias, V Sakkalakis, A Roniotis, S Wan, S Giatili, N Graf, R Bohle, E Messe, H Stenzhorn, Y J Kim, P V Coveney, S Zasada, A Folarin, P Büchler, T Bardyn, S Bauer, M Reyes, G J Clapworthy, E Liu, T Bily, V Bednar, Mkarasek, A Franz, R Grewer and D Dionysiou, ContraCancrum: Clinically Oriented Translational Cancer Multilevel Modelling, to be presented in VPH2010 Conference, Brussels, Sept 2010
  • T Wang, S Manos, E Liu, S Zasada, P V Coveney and G J Clapworthy, An ICT Environment for Patient-Specific Multiscale Cancer Modelling and Treatment, to be presented in VPH2010 Conference, Brussels, Sept 2010
  • X Zhao, T Wang, E Liu and G J Clapworthy, Web Services in Distributed Information Systems: Availability, Performance and Composition, Int. Jnl Distributed Systems & Technologies, Vol 1, No 1, pp. 1-16, 2010
  • T Wang, Y Zhao, E Liu, G J Clapworthy, X Zhao, H Wei and F Dong, Using Web Services as Functional-Level Plug-ins for Interactive 3D Medical Visualisation, Proc 7th International Conference on Biomedical Visualisation (MediVis 10), pp 617-622, IEEE Computer Society, London, July 2010
  • X Zhang, F Dong, G J Clapworthy, Y Zhao and L Jiao, Semi-Supervised Tissue Segmentation of 3D Brain MR Images, Proc 7th International Conference on Biomedical Visualisation (MediVis 10), pp 623-628, IEEE Computer Society, London, July 2010
  • T. Bardyn, M. Reyes, Philippe Büchler, Biomechanical model of tumour growth: application to the European ContraCancrum project, 4th International Advanced research Workshop on In Silico Oncology and Cancer Investigation, Athens, September 2010
  • S. Bauer, C. Seiler, T. Bardyn, P. Büchler, M. Reyes, Atlas-based segmentation of brain tumor images using a Markov Random Field-based tumor growth model and non-rigid registration, IEEE EMBC Conference, Buenos Aires, September 2010
  • S. Bauer, M. Reyes, A Markov Random Field-based biomechanical tumor growth model for atlas-based segmentation of brain tumor images, 4th International Advanced research Workshop on In Silico Oncology and Cancer Investigation, Athens, September 2010
  • S. Wan and P. V. Coveney, “Patient Specific Prediction of Drug Binding Affinities” Poster presentation “The World Congress on Medical Physics and Biomedical Engineering, Munich, Germany, 07/09/2009 – 12/09/2009”.
  • S. Wan, D. Wright, S. K. Sadiq, S. J. Zasada and P. V. Coveney, “Personalised Drug Ranking in Clinical Decision Support” International VPH Conferences (VPH2010), Brussels, Belgium, 30/09/10-01/10/10, accepted
  • S. Wan and P. V. Coveney, “Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs” 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation, Athens, Greece, 8-9 September 2010, accepted
  • A. Folarin, “Molecular personalization of cancer treatment via a multiscale simulation model of tumor response to therapy. The paradigm of glioblastoma treated with Temozolomide” 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation, Athens, Greece, 8-9 September 2010, accepted.
  • G.S.Stamatakos, E.Kolokotroni, D.Dionysiou, E.Georgiadi, S.Giatili, “In silico oncology: a top-down multiscale simulator of cancer dynamics. Studying the effect of symmetric stem cell division on the cellular constitution of a tumour”. IFMBE Proceedings 25 IFMBE (4), pp. 1830-1833, 2009.
  • Aran Lunzer, Robert Belleman, Paul Melis, Juliusz Pukacki, Paweł Spychała, and Georgios Stamatakos, “Validating the ACGT Oncosimulator with a Grid-Supported Visualisation Environment,” accepted to be orally presented in the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation to held in Athens, Greece on Sept. 8-9 2010.
  • Dimitra D. Dionysiou, “The ISOG, NTUA Tumor Response to Treatment Discrete Simulation Models: a Review of Basic Concepts and Algorithms,” submitted to the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation to held in Athens, Greece on Sept. 8-9 2010.
  • Eleni Ch. Georgiadi, Dimitra D. Dionysiou, Eleni Kolokotroni, Nikolaos K. Uzunoglu, Norbert Graf, and Georgios S. Stamatakos, “Discrete Event Based Modeling of Nephroblastoma. Sensitivity Considerations.” Accepted to be orally presented in the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation to held in Athens, Greece on Sept. 8-9 2010.
  • Eleni A. Kolokotroni, Dimitra D. Dionysiou, Eleni Ch. Georgiadi, Nikolaos K. Uzunoglu, and Georgios S. Stamatakos, “Breast Cancer Modeling in the Clinical Context: Parametric Studies.” Accepted to be orally presented in the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation to held in Athens, Greece on Sept. 8-9 2010.
  • Georgios Stamatakos, Dimitra Dionysiou, Εleni Georgiadi, Eleni Kolokotroni, Stavroula Giatili, Alexander Hoppe, Christine Desmedt, Aran Lunzer, Marius Erdt, Julien Jacques, Juliusz Pukacki, Robert Belleman, Paul Melis, Alberto d’Onofrio, Francesca M. Buffa, Brecht Claerhout, Stefan Rueping, Konstantinos Marias, Manolis Tsiknakis and Norbert Graf, “The ACGT Oncosimulator: from Conceptualization to Development via Multiscale Cancer Modeling.” .” Accepted to be orally presented in the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation to held in Athens, Greece on Sept. 8-9 2010.
  • Georgios S. Stamatakos, “In Silico Oncology: A Hypermatrix–Operator Formulation of a Top-Down Multiscale Simulation Model of Tumor Response to Treatment. The Oncosimulator Concept.” Accepted to be orally presented in the 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation to held in Athens, Greece on Sept. 8-9 2010.
  • Georgios Stamatakos, Dimitra Dionysiou, Eleni Georgiadi, Eleni Kolokotroni, Stavroula Giatili, Norbert Graf, “In Silico Oncology: Multiscale Modelling of Clinical Tumour Response to Treatment Based on Discrete Entity - Discrete Event Simulation. The Oncosimulator concept.” Submitted to the First VPH (Virtual Physiological Human) Conference, Brussels 30 Sept-1 Oct. 2010.
  • A. Franz, R. Opfer, S. Renisch, R. Grewer, J. Sabczynski, Image Processing for in-silico Oncology and Lung Cancer, 4th Int. Advanced Research Workshop on In Silico Oncology and Cancer Investigation, Athens, Greece, September 2010.
  • R. Opfer, J. Sabczynski, S. Renisch, S. Kabus, I. C. Carlsen, Contra Cancrum: Segmentation of different tissue types in lung tumors from PET/CT follow-up scans, The World Congress on Medical Physics and Biomedical Engineering, Munich, Germany, 07/09/2009 – 12/09/2009
  • Hans Hofstraat, Virtual Physiological Human – Biomedical and IT industries providing tools for clinical decision taking, Oral presentation, eHealth 2010, Barcelona, Spain, March 2010

Journal Papers and Books:

  • E. Skounakis, C. Farmaki, V. Sakkalis, A. Roniotis, K. Banitsas, N. Graf, and K. Marias, “DoctorEye: A clinically driven multifunctional platform, for accurate processing of tumors in medical images”, The Open Medical Informatics Journal, Vol. 4, pp.105-115, 2010.
  • A. Roniotis, K. Marias, V. Sakkalis and M. Zervakis, “Diffusive modelling of glioma evolution: a review”, Journal of Biomedical Science and Engineering, Scientific Research, Vol. 3, No 5, pp.501-508, May 2010.
  • V. Sakkalis, A. Roniotis, C. Farmaki, I. Karatzanis and K. Marias, "Translating predictive oncology research into clinical practice: An integrated framework for analyzing and modeling cancer from imaging data", Applied Soft Computing (under review).
  • A. Roniotis, V. Sakkalis, K. Marias, I. Karatzanis and M. Zervakis, "In-depth analysis and evaluation of diffusive glioma models", IEEE Trans. Inf. Tech. (under review).
  • Graf N, Hoppe A, Georgiadi E, Bellemann R, Desmedt C, Dionysiou D, Erdt M, Jacques J, Kolokotroni E, Lunzer A, Tsiknakis M, Stamatakos G: ‘In Silico’ oncology for clinical decision-making in the context of nephroblastoma, Klin Pädiatr 221:141-149, 2009
  • Ludwig N, Keller A, Heisel S, Leidinger P, Klein V, Rheinheimer S, Andres CU, Stephan B, Steudel WI, Graf NM, Burgeth B, Weickert J, Lenhof HP, Meese E: Improving seroreactivity based detection of glioma. Neoplasia 11:1383-1389, 2009
  • Graf N: Glioblastoma in Children with NF1: The need for basic research. Pediatr Blood Cancer 54:870-871, 2010
  • Fischer U, Leidinger P, Keller A, Folarin A, Ketter R, Graf N, Lenhof HP, Meese E. Amplicons on chromosome 12q13-21 in glioblastoma recurrences. Int J Cancer 126:2594-2602, 2010
  • Farmaki C, Marias K, Sakkalis V, Graf N: Spatially adaptive active contours: a semi-automatic tumor segmentation framework. Int J Comput Assist Radiol Surg 5:369-384, 2010
  • Thibaut Bardyn, Mauricio Reyes, Xabier Larrea and Philippe Büchler, Influence of Smoothing on Voxel-Based Mesh Accuracy in Micro-Finite Element, Computational Biomechanics for Medicine, Karol Miller, Poul M. F. Nielsen (Eds.), Springer Verlag, 1st edition, 2010, XII, ISBN: 978-1-4419-5873-0
  • G.S.Stamatakos, E.A.Kolokotroni, D.D.Dionysiou, E.Ch.Georgiadi, C.Desmedt, “ An advanced discrete state – discrete event multiscale simulation model of the response of a solid tumor to chemotherapy: Mimicking a clinical study. “ Journal of Theoretical Biology, Volume 266, Issue 1, 7 September 2010, Pages 124-139, (doi:10.1016/j.jtbi.2010.05.019)
  • T. Athanaileas, A.Menychtas, D.Dionysiou, D. Kyriazis, D.Kaklamani, T.Varvarigou, N.Uzunoglu and G.Stamatakos, “Exploiting Grid Technologies for the Simulation of Clinical Trials In Silico: the Paradigm of In Silico Radiation Oncology.” Simulation, Accepted. In press. 2010
  • G.S.Stamatakos, D.D. Dionysiou, “Introduction of Hypermatrix and Operator Notation into a Discrete Mathematics Simulation Model of Malignant Tumour Response to Therapeutic Schemes In Vivo. Some Operator Properties”, Cancer Informatics 2009:7 239–251.
  • T. S. Deisboeck and G. S. Stamatakos Eds, “Multiscale Cancer Modeling.” Chapman & Hall/CRC, Boca Raton, Florida, USA, 2010 (in press)
  • G.S. Stamatakos, “In Silico Oncology Part I: Clinically Oriented Cancer Multilevel Modeling Based on Discrete Event Simulation”. In T. S. Deisboeck and G. S. Stamatakos Eds, Multiscale Cancer Modeling. Chapman & Hall/CRC, Boca Raton, Florida, USA, 2010 (in press)

Refereed Articles:

  • A. Roniotis, K. Marias, and V. Sakkalis, "Glioma evolution could be predicted using diffusive modeling", European Research Consortium for Informatics and Mathematics ERCIM News, No. 81, pp. 21-22, 2010.