Publications/PubMed
2015
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Gorini Alessandra, Mazzocco Ketti, Gandini Sara, Munzone Elisabetta, McVie Gordon, Pravettoni Gabriella:
Development and psychometric testing of a breast cancer patient profiling questionnaire
Breast Cancer: Targets and Therapy
2014
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Haridimos Kondylakis, Lefteris Koumakis, Stefan Rüping, Eleni Kazantzaki, Kostas Marias, Manolis Tsiknakis:
PMIR: A Personal Medical Information Recommender
Medical Informatics Europe (MIE 2014)
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J. Marés, L.Shamardin, G. Weiler, A. Anguita, S. Sfakianakis, E. Neri, S. J. Zasada, N. Graf, and P. V. Coveney:
p-medicine: A Medical Informatics Platform for Integrated Large Scale Heterogeneous Patient Data
AMIA 2014 Annual
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Haridimos Kondylakis, Vassilis Papakonstantinou, Giorgos Flouris, Irini Fundulak:
Securing Access to Sensitive RDF Data
Extended Semantic Web Conference (ESWC 2014)
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Gabriele Weiler, Gabriele Weiler1, Christina Schröder2, Fatima Schera1Matthias Dobkowicz, Stephan Kiefer, Karsten R Heidtke, Stefanie Hänold, Iheanyi Nwankwo, Nikolaus Forgó, Martin Stanulla, Cornelia Eckert and Norbert Graf:
p-BioSPRE—an information and communication technology framework for transnational biomaterial sharing and access
ecancermedicalscience, doi: 10.3332/ecancer.2014.401
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Haridimos Kondylakis, Eleni Kazantzaki, Lefteris Koumakis, Irini Genitsaridi, Kostas Marias, Alessandra Gorini, Ketti Mazzocco, Gabriella Pravettoni, Danny Burke, Gordon McVie and Manolis Tsiknakis:
Development of Interactive Empowerment services in support of personalized medicine
ecancermedicalscience, doi: 10.3332/ecancer.2014.400
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Marie-Luise Christ-Neumann, Ana Escrich, Alberto Anguita, Holger Stenzhorn, Marian Taylor, Hena Ramay, Stefan Rüping, Christian Krauth, Wolfgang Kuchinke, Norbert Graf and Simona Rossi:
Usability on the p-medicine infrastructure: an extended usability concept
ecancermedicalscience, doi: 10.3332/ecancer.2014.399
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Fatima Schera, Gabriele Weiler, Elias Neri, Stephan Kiefer and Norbert Graf:
The p-medicine portal - a collaboration platform for research in personalized medicine
ecancermedicalscience, doi: 10.3332/ecancer.2014.398
2013
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Irini Genitsaridi, Haridimos Kondylakis, Lefteris Koumakis, Kostas Marias, Manolis Tsiknakis:
Evaluation of personal health record systems through the lenses of EC research projects
Computers in Biology and Medicine, 10.1016/j.compbiomed.2013.11.004
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Irini Genitsaridi, Haridimos Kondylakis, Lefteris Koumakis, Kostas Marias, Manolis Tsiknakis:
Towards Intelligent Personal Health Record Systems: Review, Criteria and Extensions
Procedia Computer Science Volume 21, 2013, ages 327–334, 10.1016/j.procs.2013.09.043
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G.Stamatakos, D Dionysiou, A Lunzer, R Belleman, E Kolokotroni, E Georgiadi, M Erdt, J Pukacki, S Rueping, S Giatili, A d'Onofrio, S Sfakianakis, K Marias, C Desmedt, M Tsiknakis, N Graf:
The Technologically Integrated Oncosimulator: Combining Multiscale Cancer Modeling with Information Technology in the In Silico Oncology Context
IEEE Journal of Biomedical and Health Informatics.
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Alberto Anguita, Ana Escrich, Victor Maojo:
Fostering ontology alignment sharing: a general-purpose RDF mapping format
Stud Health Technol Inform - Medinfo 2013 192, 970, 10.3233/978-1-61499-289-9-970
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Alberto Anguita, Miguel Garcia-Remesal, Diana de la Iglesia, Victor Maojo:
NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases
BioMed Research International 983805, http://dx.doi.org/10.1155/2013/983805
Additional link
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Alberto Anguita, Luis Martin, Miguel Garcia-Remesal, Victor Maojo:
RDFBuilder: A tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources
Computer Methods and Programs in Biomedicine 111 (1), 220-227, 10.1016/j.cmpb.2013.04.009
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Haridimos Kondylakis, Lefteris Koumakis, Manolis Tsiknakis, Kostas Marias, Eirini Genitsaridi, Gabriella Pravettoni, Alessandra Gorini, Ketti Mazzocco:
Smart recommendation services in support of patient empowerment and personalized medicine
Multimedia Services in Intelligent Environments – Recommendation Services, 39-61, 10.1007/978-3-319-00375-7_4
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Benjamin Jefferys, Iheanyi Nwankwo, Elias Neri, David CW Chang, Lev Sharmardin, Stefanie Hänold, Norbert Graf, Nikolaus Forgó, Peter Coveney:
Navigating legal constraints in clinical data warehousing: a case study in personalized medicine
Interface Focus vol. 3 no.2, 10.1098/rsfs.2012.0088
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Peter Coveney, Vanessa Diaz-Zuccarini, Norbert Graf, Peter Hunter, Peter Kohl, Jesper Tegner, Marco Viceconti:
Integrative approaches to computational biomedicine
Interface Focus vol. 3 no. 2, 10.1098/rsfs.2013.0003
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Emilio M. Sanfilippo, Ulf Schwarz, Luc Schneider:
The Health Data Ontology Trunk (HDOT). Towards an ontological representation of cancer-related knowledge
Proceedings of the 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation, 57-60, ISBN: 978-618-80348-0-8
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Katerina D Argyri, Georgios Stamatakos, Dimitra Dionysiou:
Modeling the interplay between pathological angiogenesis and solid tumor growth: The anti-angiogenic treatment effect
Proceedings of the 2012 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The TUMOR Project Workshop (IARWISOCI) 2012, 1-4, Print ISBN (IEEE): 978-1-4673-5024-2; Open-access ISBN: 978-618-80348-0-8
Additional link
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Tzedakis, Georgios, Tzamali, Eleftheria; Sakkalis, Vangelis; Roniotis, Alexandros; Marias, Kostas :
Hybrid model for tumor spheroids with intratumoral oxygen supply heterogeneity
Proceedings of the 2012 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The TUMOR Project Workshop (IARWISOCI) 2012, 1-4, Print ISBN (IEEE): 978-1-4673-5024-2; Open-access ISBN: 978-618-80348-0-8
Additional link
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Giatili, Stavroula G, Stamatakos, Georgios:
The Continuous Mathematics Based Glioblastoma Oncosimulator: Application of an explicit three dimensional numerical treatment of the skull-glioblastoma Neumann boundary condition on real anatomical data
Proceedings of the 2012 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The TUMOR Project Workshop (IARWISOCI) 2012, 1-4, Print ISBN (IEEE): 978-1-4673-5024-2; Open-access ISBN: 978-618-80348-0-8
Additional link
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Georgiadi, Eleni Ch., Dionysiou, Dimitra D.; Graf, Norbert; Stamatakos, Georgios S. :
Modeling nephroblastoma treatment response cases with In-Silico scenarios
Proceedings of the 2012 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The TUMOR Project Workshop (IARWISOCI) 2012, 1-4, Print ISBN (IEEE): 978-1-4673-5024-2; Open-access ISBN: 978-618-80348-0-8
Additional link
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Sfakianakis, Stelios, Sakkalis, Vangelis; Marias, Kostas :
Scientific workflows to support in silico modeling in cancer research
Proceedings of the 2012 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The TUMOR Project Workshop (IARWISOCI) 2012, 1-5, Print ISBN (IEEE): 978-1-4673-5024-2; Open-access ISBN: 978-618-80348-0-8
Additional link
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A. d'Onofrio, G. Caravagna, A. Graudenzi:
Distributed Delays in a Hybrid Model of Tumor-Immune System Interplay
MATHEMATICAL BIOSCIENCES AND ENGINEERING Vol 10, number 1, 37-57, 10.3934/mbe.2013.10.37
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Urszula Ledzewicz , Alberto d’Onofrio, Heinz Schättler:
Tumor Development Under Combination Treatments with Anti-angiogenic Therapies
Book Mathematical Methods and Models in Biomedicine volume of the series Lecture Notes on Mathematical Modelling in the Life Sciences 2013, 311-337, 10.1007/978-1-4614-4178-6
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Alberto d'Onofrio:
Multifaceted Kinetics of Immuno-Evasion from Tumor Dormancy
Advances in Experimental Medicine and Biology Volume 734, 111-143 , 10.1007/978-1-4614-1445-2_7
2012
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Georgios Stamatakos:
Top-Down Multiscale Simulation of Tumor Response to Treatment in the Context of In Silico Oncology.The Notion of Oncosimulator
New Challenges for Cancer Systems Biomedicine Part V, 355-375, 10.1007/978-88-470-2571-4_19
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Kostas Marias, Vangelis Sakkalis, Norbert Graf:
A framework for multi-modal imaging biomarker extraction with application to brain MRI
Springer Optimization and Its Applications Vol. 65: Data Mining for Biomarker Discovery , 91-116, 10.1007/978-1-4614-2107-8_6
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Favaro E, Bensaad K, Chong MG, Tennant DA, Ferguson DJ, Snell C, Steers G, Turley H, Li JL, Günther UL, Buffa FM, McIntyre A, Harris AL:
Glucose utilization via glycogen phosphorylase sustains proliferation and prevents premature senescence in cancer cells.
Cell Metabolism 16(6), 751-764, 10.1016/j.cmet.2012.10.017
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Haridimos Kondylakis, Manolis Tsiknakis, Kostas Marias, L. Koumakis, Gabriella Pravettoni, Alessandra Gorini, Ketti Mazzocco, et al.:
IEmS: A collaborative Environment for Patient Empowerment
IEEE 12th International Conference on Bioinformatics and BioEngineering (BIBE), 535–540, 10.1109/BIBE.2012.6399770
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Stelios Sfakianakis, Manolis Tsiknakis, Kostas Marias, Norbert Graf:
A technical infrastructure to support personalized medicine
IEEE 12th International Conference on Bioinformatics and BioEngineering (BIBE), 422–427, 10.1109/BIBE.2012.6399763
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Jonathan Zepp, Norbert Graf, Holger Stenzhorn, Wolfgang Reith, Ioannis Karatzanis, Georgios C. Manikis, Vangelis Sakkalis, Konstantinos Marias, Georgios Stamatakos:
An innovative mathematical analysis of routine MRI scans in patients with glioblastoma using DoctorEye
Proceeding of the 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE), 620-625, 10.1109/BIBE.2012.6399773
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Urszula Ledzewicz, Alberto d’Onofrio, Heinz Schättler:
On the Dynamics of Tumor-Immune System Interactions and Combined Chemo- and Immunotherapy
SIMAI Springer Series Vol.1 Vol. 1 2012, 249-266 , 10.1007/978-88-470-2571-4_13
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Eleftherios N. Ouzounoglou, Dimitra D. Dionysiou, Martin Stanulla, Georgios S. Stamatakos:
Towards patient personalization of an Acute Lymphoblastic Leukemia Model during the oral administration of prednisone in children: Initiating the ALL Oncosimulator
Proceedings of the 2012 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The TUMOR Project Workshop (IARWISOCI) , 1-4, Print ISBN (IEEE): 978-1-4673-5024-2; Open-access ISBN: 978-618-80348-0-8
Additional link
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Ruslan David, N.Graf, I. Karatzanis, H. Stenzhorn, G. Manikis, V. Sakkalis,G. Stamatakos, K. Marias:
Clinical Evaluation of DoctorEye Platform in Nephroblastoma
Proceedings of the 2012 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The TUMOR Project Workshop (IARWISOCI) , 1-4, Print ISBN: 978-1-4673-5024-2
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Wolfgang Kuchinke, Toeresin Karakoyun, Christian Ohmann:
Collaboration between Research Initiatives and Infrastructures for Personalized Medical Research: an Underestimated Challenge
eChallenges e-2012 Conference Proceedings, ISBN 978-1-905824-35-9
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Toeresin Karakoyun, Wolfgang Kuchinke, Christian Ohmann, Hans Jakob Auer:
A Scenario-Driven Approach to Enable Collaboration Among Research Infrastructures and Initiatives
eChallenges e-2012 Conference Proceedings, ISBN 978-1-905824-35-9
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Haridimos Kondylakis, D. Plexousakis:
Ontology Evolution, Assisting Query Migration
Lecture Notes in Computer Science Vol. 7532, 331–344, 10.1007/978-3-642-34002-4_26
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Alberto d'Onofrio, Mohannad Al-Tameemi, Mark Chaplain:
Evasion of tumours from the control of the immune system: consequences of brief encounters
Biology Direct Volume 7, art. n. 31, 10.1186/1745-6150-7-31
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Stefan Zasada, T. Wang, A. Haidar, E. Liu, N. Graf, G. Clapworthy, M. Steven, P. Coveney:
IMENSE: An e-infrastructure environment for patient specific multiscale data integration, modelling and clinical treatment
Journal of Computational Science 3:5, 314–327, 10.1016/j.jocs.2011.07.001
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Haridimos Kondylakis, Manolis Tsiknakis:
Computerized Clinical Guidelines: Current Status & Principles for Future Research
Studies in Health Technology and Informatics, Volume 180: Quality of Life through Quality of Information, 432–436, 10.3233/978-1-61499-101-4-432
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Stelios Sfakianakis, Vangelis Sakkalis, Kostas Marias, Georgios Stamatakos, Steve McKeever, Thomas S Deisboeck, Norbert Graf:
An architecture for integrating cancer model repositories
Engineering in Medicine and Biology Society (EMBC), 2012 Annual International Conference of the IEEE , 6628 - 6631, 10.1109/EMBC.2012.6347514
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V. Sakkalis, G. C. Manikis, N. Papanikolaou, I. Karatzanis, K. Marias:
A software prototype for the assessment of tumor treatment response using diffusion and perfusion MR imaging
Engineering in Medicine and Biology Society (EMBC), 2012 Annual International Conference of the IEEE , 388–391, 10.1109/EMBC.2012.6345950
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A. d'Onofrio, S. de Franciscis:
Spatiotemporal bounded noises and transitions induced by them in solutions of the real Ginzburg-Landau model
PHYSICAL REVIEW E Volume 86, art n. 021118, 10.1103/PhysRevE.86.021118
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Jana Schmitt, C. Backes, N. Nourkami-Tutdibi, P. Leidinger, S. Deutscher, M. Beier, M. Gessler, N. Graf, H.-P. Lenhof, A. Keller, E. Meese:
Treatment independent miRNA signature in blood of Wilms tumor patients
BMC Genomics 13, 10.1186/1471-2164-13-379
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Jana Schmitt, S. Heisel, A. Keller, P. Leidinger, N. Ludwig, N. Habel, R. Furtwängler, N. Nourkami-Tutdibi, J. Wegert, P. Grundy, M. Gessler, N. Graf, H.P. Lenhof, E. Meese:
Multicenter study identified molecular blood-born protein signatures for Wilms tumor
International Journal of Cancer 131:3, 673–682, 10.1002/ijc.26419
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A. d'Onofrio, A. Gandolfi, S. gattoni:
The Norton–Simon hypothesis and the onset of non-genetic resistance to chemotherapy induced by stochastic fluctuations
Physica A volume 391, 6484–6496, 10.1016/j.physa.2012.07.025
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Jonas Sjöbergh, Micke Kuwahara, Yuzuru Tanaka:
Visualizing Clinical Trial Data Using Pluggable Components
Proceedings of the 16th International Conference on Information Visualization, 10.1109/IV.2012.56
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S. N. Deftereos, E. Dodou, C. Andronis, A. Persidis:
From depression to neurodegeneration and heart failure: re-examining the potential of MAO inhibitors
Expert Review of Clinical Pharmacology Vol. 5, No. 4, 413-425, 10.1586/ecp.12.29
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Eleni Ch. Georgiadi, Dimitra D. Dionysiou, Norbert Graf, Georgios S. Stamatakos:
Towards In Silico Oncology: Adapting a Four Dimensional Nephroblastoma Treatment Model to a Clinical Trial Case Based on Multi-Method Sensitivity Analysis.
Computers in Biology and Medicine Volume 42, Issue 11, 1064–1078, 10.1016/j.compbiomed.2012.08.008
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Stavroula G. Giatili, Georgios S. Stamatakos:
A Detailed Numerical Treatment of the Boundary Conditions Imposed by the Skull on a Diffusion-Reaction Model of Glioma Tumor Growth. Clinical Validation Aspects.
Applied Mathematics and Computation Volume 218, Issue 17, 8779–8799, 10.1016/j.amc.2012.02.036,
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Victor Maojo, M. Fritts, F. Martin-Sanchez, D. De la Iglesia, R.E. Cachau, M. Garcia-Remesal, J. Crespo, J.A. Mitchell, A. Anguita, N. Baker, J.M. Barreiro, S.E. Benitez, G. De la Calle, J.C. Facelli, P. Ghazal, A. Geissbuhler, F. Gonzalez-Nilo, N. Graf, P. Grangeat, I:
Nanoinformatics: developing new computing applications for nanomedicine
Computing in Science and Engineering 94:6 Issue 6, 521-539, 10.1007/s00607-012-0191-2
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Tim Beck, S. Gollapudi, S. Brunak, Norbert Graf, U.H. Lemke, D. Dash, I. Buchan, C. Diaz, F. Sanz, A.J. Brookes:
Knowledge engineering for health: A new discipline required to bridge the “ICT gap” between research and healthcare
Human Mutation 33:5, 797–802, 10.1002/humu.22066
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C. Andronis, A. Sharma, S. Deftereos, V.Virvilis, O.Konstanti, Andreas Persidis, Aris Persidis:
Mining scientific and clinical databases to identify novel uses for existing Drugs
Drug Repositioning: Bringing New Life to Shelved Assets and Existing Drugs , 10.1002/9781118274408.ch6
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A. Persidis, Elizabeth T. Starck:
Business development Strategies in the Repositioning Industry
Drug Repositioning: Bringing New Life to Shelved Assets and Existing Drugs , 10.1002/9781118274408.ch13
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Alberto d'Onofrio, G. Caravagna, R. Barbuti:
Fine-tuning anti-tumor immunotherapies via stochastic simulations
BMC Bioinformatics Volume 13, Issue 4,, Art. S8, 10.1186/1471-2105-13-S4-S8
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Antonio F. Di Narzo, Simona Rossi:
Unchain the code: how to ease quality control in research, tips or requirements
Biohelikon: Computational Biology 1(1)
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Stefan Bauer, Christian May, Dimitra D. Dionysiou, Georgios S. Stamatakos, Philippe Büchler, Mauricio Reyes:
Multiscale Modeling for Image Analysis of Brain Tumor Studies
IEEE Transactions on Biomedical Engineering vol. 59, issue 1, 25 - 29 , 10.1109/TBME.2011.2163406
2011
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P.V. Coveney, C. Sansom, M. Mendes:
Modelling the Virtual Physiological Human
Journal of Biotechnology, Computational Biology and Bionanotechnology 2011, 225-229
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Christos Andronis, Eftychia Lekka, Spyros N. Deftereos, Aris Persidis, Andreas Persidis:
Literature analysis for systematic drug repurposing: a case study from Biovista
Drug Discovery Today: Therapeutic Strategies vol. 8, issues 3-4, 103-108, 10.1016/j.ddstr.2011.06.005
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V. Virvilis, A. Sharma, M. Koutsokeras:
Drug Repositioning on the Cloud
IEEE 3rd International Conference on Cloud Computing Technology and Science, http://doi.ieeecomputersociety.org/10.1109/CloudCom.2011.88
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Dennis Wegener, Simona Rossi, Francesca Buffa, Mauro Delorenzi and Stefan Rüping:
Towards an Environment for Data Mining based Analysis Processes in Bioinformatics & Personalized Medicine
IEEE BIBM 2011 International Workshop on Biomedical and Health Informatics
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E. A. Kolokotroni, D. D. Dionysiou, N. K. Uzunoglu, G. S. Stamatakos:
Studying the growth kinetics of untreated clinical tumors by using an advanced discrete simulation model
Mathematical and Computer Modelling Volume 54, Issues 9–10, 1989–2006, 10.1016/j.mcm.2011.05.007
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Haridimos Kondylakis, Dimitris Plexousakis:
Ontology Evolution in Data Integration: Query Rewriting to the Rescue
Conceptual Modeling – ER 2011 Lecture Notes in Computer Science 2011, 393-401, 10.1007/978-3-642-24606-7_29
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A. d'Onofrio, A. Ciancio:
Simple biophysical model of tumor evasion from immune system control
PHYSICAL REVIEW E vol 84, Art n. 031910, 10.1103/PhysRevE.84.031910
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Simona Rossi, Marie L. Christ-Neumann2, Stefan Rüping2 , Francesca M. Buffa3, Dennis Wegener2, Gordon McVie4, Peter V. Coveney5, Norbert Graf6,§ , and Mauro Delorenzi1 on behalf of the p-medicine consortium:
p-medicine: From Data Sharing and Integration via VPH Models to Personalized Medicine
www.ecancermedicalscience.com, 10.3332/ecancer.2011.218
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Alberto Anguita, Norbert Graf, Manolis Tsiknakis, Mathias Brochhausen, Stefan Rüping, Anca Bucur, Stelios Sfakianakis, Thierry Sengstag, Francesca Buffa, Holger Stenzhorn:
ACGT: Advancing Clinico-genomic Trials on Cancer - Four Years of Experience
Studies in Health Technology and Informatics, Volume 169: User Centred Networked Health Care, 10.3233/978-1-60750-806-9-734
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Dennis Wegener, Alberto Anguita, Stefan Rüping:
Enabling the reuse of data mining processes in healthcare by integrating data semantics
3th International Workshop on Knowledge Representation for Health Care
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Andreas Persidis, C. Andronis, A. Sharma, V. Virvilis, S. Deftereos:
Literature mining, ontologies and information visualization for drug repurposing
Briefings in Bioinformatics 12 (4), 357-368, 10.1093/bib/bbr005
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Alessandra Gorini, Gabriella Pravettoni:
P5 medicine: a plus for a personalized approach to oncology
Nature Reviews Clinical Oncology vol. 8, no. 7, 10.1038/nrclinonc.2010.227-c1
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Pravettoni G., Gorini A.:
A P5 cancer medicine approach: why personalized medicine cannot ignore psychology
Journal of Evaluation in Clinical Practice 2011 - 17, 594-596