Publications
Title | Author(s) | Details |
|---|---|---|
Web-based Authoring and Secure Enactment of Bioinformatics Workflows | Stelios Sfakianakis, Lefteris Koumakis, George Zacharioudakis, Manolis Tsiknakis | Presentation of the workflow environment in the 4th International Workshop on Workflow Management (ICWM2009) in conjunction with the the 4th International Conference on Grid and Pervasive Computing (GPC 2009) that took place in 6 May 2009 |
Multilevel Cancer Modeling in the Clinical Environment: Simulating the Behavior of Wilms Tumor in the Context of the SIOP 2001/GPOH Clinical Trial and the ACGT Project. | Georgiadi ECh, Stamatakos GS, Graf NM, Kolokotroni EA, Dionysiou DD, Hoppe A, Uzunoglu NK, | IEEE BIBE (Bioinformatics and Bioengineering Conference), Athens, Greece, 8-10 October 2008 |
A significant proportion of elderly patients develop hormone-dependant "luminal-B" tumours associated with aggressive characteristics. | Durbecq V, Ameye L, Veys I, Paesmans M, Desmedt C, Sirtaine N, Sotiriou C, Bernard-Marty C, Nogaret JM, Piccart M, Larsimont D | Crit Rev Oncol Hematol 67:80-92, July 2008. |
A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? | Haibe-Kains B, Desmedt C, Sotiriou C, Bontempi G. | Bioinformatics. July 2008 |
Clinical relevance of mutations in the Wilms tumor suppressor 1 gene WT1 and the cadherin-associated protein Beta 1 gene CTNNB1 for patients with Wilms tumors. Results of long-term surveillance of 71 patients from International Society of Pediatric Oncology Study 9 | Royer-Pokora B, Weirich A, Schumacher V, Uschkereit C, Beier M, Leuschner I, Graf N, Autschbach F, Schneider D, von Harrach M | Society for Pediatric Oncology. Cancer accepted, July 2008 |
KIT, PDGFRa and EGFR Analysis in Nephroblastoma. | Wetli SC, Leuschner I, Harms D, Rufle A, Foerster A, Bihl M, Graf N, Furtwaengler R, Paulussen M, Briner J, Tornillo L, Mihatsch MJ, Zlobec I, Bruder E | Virchow Archiv 452:637-650, June 2008 |
Characteristics and survival of 750 children diagnosed with a renal tumor in the first seven months of life | Van den Heuvel-Eibrink MM, Grundy P, Graf N, Pritchard-Jones K, Bergeron C, Patte C, Peter E, van Tinteren H, Rey A, Hutton C, Anderson JR, de Kraker J | A collaborative study by the SIOP/GPOH/SFOP, NWTSG, and UKCCSG Wilms tumor study groups.. Pediatr Blood & Cancer 50:1130-1134, June 2008 |
Consultation within SIOP 2001/GPOH as part of the competence centre for nephroblastoma. | Zils K, Furtwangler R, Reinhard H, Alkassar M, Graf N | Klin Pediatr 220:183-188, June 2008 |
Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. | Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt AM, Gillet C, Ellis P, Ryder K, Reid JF, Daidone MG, Pierotti MA, Berns EM, Jansen MP, Foekens JA, Delorenzi M, Bontempi G, Piccart MJ, Sotiriou C. | BMC Genomics 9:239, May 2008. |
Role of MRI in the management of patients with nephroblastoma. | Schenk JP, Graf N, Gunther P, Ley S, Goppl M, Kulozik A, Rohrschneider WK, Troger J. | Eur Radiol 18:683-691, April 2008 |
"The cooperative and nonlinear dynamics of tumor-vasculature interaction suggests low-dose, time-dense antiangiogenic schedulings" | A. d'Onofrio, A. Gandolfi and A. Roccain | press on Cell Proliferation |
"A bi-parametric phenomenologic model for the tumor angiogenesis and anti-angiogenesis therapy". | A. d'Onofrio and P. Cerrai | In press on Mathematical and Computer Modelling (PDF available at Elsevier Website: dx.doi.org/10.1016/j.mcm.2008.05.001 ) |
Surgical Aspects in the treatment of patients with unilateral Wilms' tumor | Fuchs J, Kienecker K, Furtwangler R, Burger D, Thuroff JW, Hager J, Graf N | A report by the SIOP 93-01/ German Society of Pediatric Oncology and Hematology, Ann Surg accepted 2008 |
Das Nephroblastom und andere pediatrische Nierentumoren. | Furtwangler R, Schenk JP, Alkassar M, Leuschner I, Rube C, von Schweinitz D, Gessler M, Graf N | Padiat Prax 72:59-77, 2008 |
"Theory of risks and processing of medical data in Healthgrids in European Law" | J. HERVEG | J. HERVEG (ed.), La protection des données médicales. Les défis du XXIe siècle - The protection of medical data. Challenges of the 21st century , Anthemis et L.G.D.J., 2008, pp. 183-205. |
"Panorama des responsabilités liées aux services et produits de la santé en ligne en droit européen" | J. HERVEG | A.-M. DUGUET, I. FILIPPI et J. HERVEG (ed.), Evolution récente des actions en responsabilité médicale en France. Comparaison avec l'étranger , Bordeaux, Les éditions hospitalières, 2008, p. 69-118. |
Outcome of relapses of nephroblastoma in patients registered in the SIOP/GPOH trials and studies. | Reinhard H, Schmidt A, Furtwangler R, Leuschner I, Rube C, von Schweinitz D, Zoubek A, Niggli F, Graf N | Oncology Reports 20:463-467, 2008 |
Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment. | Smith B, Brochhausen M | Blobel B, Pharow P, Nerlich M (eds.): eHealth: Combining Health Telematics, Telemedicine, Biomedical Engineering and Bioinformatics on the Edge . IOS Press: Amsterdam, 219-34, 2008. |
A semantic grid infrastructure enabling integrated access and analysis of multilevel biomedical data in support of post-genomic clinical trials on Cancer. | Tsiknakis Manolis, Brochhausen Mathias, Nabrzyski J., Pucaski L, Potamias G., Desmedt C., Kafetzopoulos D | IEEE Trans Inf Technol Biomed. Mar;12(2):205-17, 2008 |
"Optimal Control for Combination Therapy in Cancer". | Urszula Ledzewicz, Heinz Schaettler and Alberto d'Onofrio | In press on Proceedings of the 47th IEEE Conference on Decision and Control |
Consultation within SIOP 2001/GPOH as part of the competence centre for nephroblastoma. | Zils K, Furtwangler R, Reinhard H, Alkassar M, Graf N | Klin Pediatr 220:183-188, 2008 |
The "Clinical Oncosimulator": a multilevel, "top-down", clinically oriented simulation system of tumor growth and organism response to therapeutic schemes. | G. Stamatakos | 3rd International CViT (NCI-ICBP) Workshop, Massachusetts General Hospital, Boston, USA https://www.cvit.org/node/247 [password controlled site] |
A semantic grid infrastructure enabling integrated access and knowledge discovery from multilevel data in post-genomic clinical trials | M.Tsiknakis, S.Sfakianakis, G.Potamias, G.Zacharioudakis, D.Kafetzopoulos | Akhgar, Babak (ed), ISBN: 978-1-84628-990-3 |
Semantic Data Integration in the European ACGT project | Martin L, AnguitaA, De la Calle G, Garcia-Remesal M, Crespo J, Tsiknakis M, Maojo V | Prodeedings of the American Medical Informatics Association (AMIA - Annual Symposium) 2007 - 11-14 Nov 2007, Chicago, IL (USA) |
An Ontology-based and Distributed KDD Model for Biomedical Sources | Perez-Rey, Anguita A, Crespo J, Maojo V | Prodeedings of the American Medical Informatics Association (AMIA - Annual Symposium) 2007 - 11-14 Nov 2007, Chicago, IL (USA) in press |
Clinical requirements of ''In Silico Oncology'' as part of the integrated project ACGT (Advancing Clinico-Genomic Trials on Cancer) | N. Graf, C. Desmedt, A. Hoppe, M. Tsiknakis, D. Dionysiou, G. Stamatakos, | European Journal of Cancer Supplements, Vol5 No 4, p. 83 and ECCO Conference September 2007, Barcelona |
Data Access and Management in ACGT: Tools to solve syntactic and semantic heterogeneities between clinical and image databases. | Martin L, Bonsma E, Potamias G, Anguita A, Brochhausen M, VrijnsenJ, Garcia-Remesal M, Crespo J, Tsiknakis M | First International Workshop on Conceptual Modelling for Life Sciences Applications (CMLSA 2007) [Accepted ] The paper describes how the problem of syntactic and semantic heterogeneity is tackled in ACGT using the Semantic Mediator (WP7) and the Data Access Wrappers (WP5) Submitted to [and accepted by]: CMLSA 2007, November 05-09 2007, Auckland, NewZealand, er2007.massey.ac.nz/cmlsa07/ |
Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinom as through genomic grade | Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, Ellis P, Harris A, Bergh J, Foekens JA, Klijn JG, Larsimont D, Buyse M, Bontempi G, Delorenzi M, Piccart MJ, Sotiriou C | J Clin Oncol. 2007 Apr 1;25(10):1239-46.Erratum in: J Clin Oncol. 2007 Aug20;25(24):3790 |
Ontology Based Data Management Systems for post-genomic clinical Trials within an European Grid Infrastructure for Cancer Research | Weiler G, Brochhausen M, Graf N, Hoppe A, Schera F, Kiefer S | 29th Annual International Conference or IEEE Engineering in Medicine and Biology Society in conjunction with the biennial Conference of the French Society of Biological and Medical Engineering (SFGBM), August 23-26, 2007 [accepted] |
The "Oncosimulator": a multilevel, clinically oriented simulation system of tumour growth and response to therapeutic schemes. Towards clinical evaluation of in silico oncology | Stamatakos GS, Dionysiou DD, Graf N, Sofra NA, Desmedt C, Hoppe A, Uzunoglu NK, Tsiknakis M | Proceedings of the 29th Annual International Conference of the IEEE EMBS Cité Internationale, Lyon, France August 23-26, 2007, pp.6628-6631 |
Data protection issues with regard to research in genetic data | Marian Arning/ NikolausForgo/ Tina Krugel | For the 2nd Workshop on Personalisation for E-Health, held on the 11th international conference on User Modelling 2007 conference on the 26th of June 2007 in Corfu. [accepted] |
An interaction framework for VR and AR applications | M. Scarpa, R.G. Belleman | Proc. Of the 13th Advanced School for Computing and Imaging (ASCI) Conference, June 13-15, 2007, Heijen, the Netherlands. |
Strong time dependence of the 76-gene prognostic signature for breast cancer patients in the TRANSBIG multi center independent validation series | Desmedt C, Piette F, LoiS, Wang Y, Lallemand F, Haibe-Kains B, Viale G, Delorenzi M, Zhang Y, d'Assignies MS, Bergh J, Lidereau R, Ellis P, HarrisAL, Klijn JG, Foekens JA, Cardoso F, Piccart MJ, Buyse M, Sotiriou C;TRANSBIG Consortium | Clin Cancer Resp. 2007 June 1;13 (11):3207-14 |
Solving semantic heterogeneities and integration between clinical and image databases in post-genomic clinical trials | Anguita A, MartinCresp J, TsiknakisMaojo V | 4th pHealth Conference 2007. Porto Carras, Chalkidiki, Greece, June 20-22, 2007-07-20[Accepted]Invited Speaker, HealthGrid, "A new approach to pHealth", Y. Legré, HG |
Relation of a hypoxia metagene derived from head and neck cancer to prognosis of multiple cancers. | Winter SC, Buffa FM, Silva P, Miller C, Valentine HR, Turley H, Shah KA, Cox GJ, Corbridge RJ, Homer JJ, Musgrove B, Slevin N, Sloan P, Price P, West CM, Harris AL | Cancer Res. 2007 apr 1; 67 (7):33441-9 PMID: 17409455 [PubMed - indexed ] |
Towards Virtual Oncology | G. Stamatakos | ERCIM NEWS No 69, April 2007, Special on the Digital Patient, pp.21-22. |
A patient-specific in vivo tumor and normal tissue model for prediction of the response to radiotherapy: a computer simulation approach | V.P.Antipas, G.S.Stamatakos, N.K.Uzunoglu | Methods Inf. Med., 46, pp.367-375, 2007. |
A Platform for Understanding Cancer Behavior and Optimizing Radiation Therapy Treatment | G.S.Stamatakos, D.D.Dionysiou, N.K.Uzunoglu | Book chapter in M.Akay (Ed) "Genomics and Proteomics Engineering in Medicine and Biology", Wiley/IEEE Press, Hoboken, NJ, 2007. |
Multi-level analysis and information extraction considerations for validating 4D models of human function | K.Marias, D.Dionysiou, G.S. Stamatakos, F.Zacharopoulou, E.Georgiadi, T.G.Maris, I.Tollis | Lecture Notes in Computer Science vol. 4561, pp. 703-709, 2007 |
Simulating cancer radiotherapy on a multi-level basis: biology, oncology and image processing" | D.D.Dionysiou, G.S.Stamatakos, K.Marias | Lecture Notes in Computer Science vol. 4561, pp. 569-575, 2007. |
Autonomie et Droit au respect de la vie privée. | J. Herveg, FUND | In Revista de Direito Medico e da Saude and Editions hospitalières. |
Panorama des responsabilités liées aux services et aux produits de la santé en ligne en droit européen. | J. Herveg, FUND | In Revista de Direito Medico e da Saude and Editions Hospitalières. Article turned in for publication / foreseen for next year. |
Does HealthGrid Present Specifics Risks with Regard to Data Protection? | J. Herveg, FUND | From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences, IOS Press, 2007, vol. 126, pp 219-228 |
L'information génétiques et le traitement des données - caractère personnel | J-M Van Gyseghem, FUND | Dossier médial et données médicales de santé, Bordeaux, Ed. Hospitalières, 2007, pp.243-258 |
"La protection des données médicales en droit européen" | J. Herveg, FUND | Dossier médical et données médicales de santé, Bordeaux, Ed. Hospitalières, 2007, pp.183-196 |
A family of models of angiogenesis and anti-angiogenesis anti-cancer therapy | A. d'Onofrio (corr. auth.)and A. Gandolfi | In review process on a ISI-indexed journal |
A bi-parametricgeneral model for the tumor angiogenesis and anti-angiogenesis therapy | P.Cerrai and A. d'Onofrio(corr. auth) | In review process on a ISI-indexed journal |
"Noisy Oncology": some Caveats inusing Gaussian Noise in Mathematical Models of Chemotherapy. | A. d'Onofrio | In press on the book "Aspects of Non linear Modelling" Birkauser Publishing (E.Venturino and R. Hodskings eds.) |
"Fuzzy Oncology": fuzzy noise induced bifurcations and their application to anti-tumour chemotherapy. | A. d'Onofrio | In press on "Applied Mathematics Letters" [ISIindexed journal] |
Rapidly acting anti tumoral anti angiogenic therapies | A. d'Onofrio | In press on "Physical Review E" [PubMed and ISI indexed journal] |
"Genetic data - new challenges for data protection" | Marian Arning, Nikolaus Forgo, Tina Krugel (LUH) | Article turned in for publication / foreseen for next year. |
Interactive Simulation and Visualization for Cancer Treatment Planning with Grid-Based Technology | R.G Belleman et al. | ERCIM News 69 Special on The Digital Patient, pp.22-24, 2007 |
The importance of anontology based clinical data management system (OCDMS) for clinico-genomic trials in ACGT | Graf N, Weiler G, Brochhausen M, Scherer F, Hoppe A, Tsiknakis M, Kiefer S | ECCO, Barcelona 2007, [accepted as Poster] |
Design of Individual Donor Feedback Processes in Biobank Research. | Luttenberger, N; Kollek, R. | Paper given at the workshop "Electronic Data Custodianship-Applications, Methods, Foundations", INFORMATIK 2006, Oct. 2 - 6, 2006, Dresden (Annual Conference of the Gesellschaft fur Informatik) in co-operation with the GI Special Interest Group "Privacy Enhancing Technologies". Paper will be published in the Informatik 2006 workshop proceedings, to appear in the GI series "Lecture Notes in Informatics (LNI)" |
Developing a European Biomedical GRID for post-genomic research on Cancer, | M. Tsiknakis, D. Kafetzopoulos, G. Potamias, A. Analyti, K. Marias, S. Sfakianakis | IEEE Information Technology and Applications in Biomedicine, 25-28 Oct 2006, Ioannina, Greece |
Established sciences and technologies as sources of inspiration and guidance for the emerging discipline of in silico oncology | N. Uzunoglou ICCS-NTUA, Athens, Greece | The ISOG/ICCS/NTUA approach accepted to be published in the Proc. of 2nd Advanced Research Workshop on In Silico Oncology, Kolymbari, Chania, Crete, Greece, Sept 25-26 2006 |
A four dimensional simulation model of the in vivo response of nephroblastoma to vincristine | N. Sofra1, G. Stamatakos1, N. Graf2, N. Uzunoglu1, 1ICCSNTUA, Athens, Greece, and 2University of Saarland, Saarbruecken, Germany | to be published in the Proc. of 2nd Advanced Research Workshop on In Silico Oncology, Kolymbari, Chania, Crete, Greece, Sept 25-26 2006 |
Intelligent client for integrating bioinformatics services | Ismael Navas-Delgado, Maria del Mar Rojano-Munoz, Sergio Ramierez, Antonio J. Perez, Eduardo Andrés Leon; Jose F. Aldana-Montes, and Oswaldo Trelles | Bioinformatics, vol.22 no.1 2006 pages 106-111 |
Designing new methodologies for integrating biomedical information in clinical trials | V. Maojo, M. Garcia-Remesal, H. Billhardt, R. Alonso-Calvo, D. Perez-Rey, F. Martin-Sanchz | Methods of Information in Medicine 2006 45 2:180-185. |
Patient Individualized Simulation Model of Solid Tumor Response to Chemotherapy in Vivo: The Paradigm of Glioblastoma Multiforme | G. S. Stamatakos, V. P. Antipas, N. K. Uzunoglu A Spatiotemporal | Temozolomide IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, VOL. 53, NO. 8, AUGUST 2006 1467 |
L'espace européen de la santé en ligne: vers un marché des données médicales | J. Herveg | Journal de médecine légale, droit médical, victimologie dommage corporel, abstracts of the 16th World Congress on Medical Law, August 2006, p. 130 |
Reflections on Biomedical Informatics: From Cybernetics to Genomic Medicine and Nanomedicine | V. Maojo, C.A. Kulikowski | Methods of Information in Medicine (in press). |
OntoDataClean: Ontology-based Integration and Preprocessing of Distributed Data | D. Perez-Rey, A. Anguita, J. Crespo | ISBMDA 06 - 7th International Symposium on Biological and Medical Data Analysis, Thessaloniki, Greece. |
Datenschutzrechtliche Aspekte der Forschung mit genetischen Daten | Marian Arning, Nikolaus Forgo, Tina Krugel | article, DuD (Journal) |
Towards a collaborative formulation of the Mathematical Principles of Natural Philosophy: Living Matter. The paradigm of In Silico Oncology | G.S. Stamatakos | DIMACS Workshop on Computational Tumor Modeling, August 3 - 4, 2006, DIMACS Center, CoRE Building, Rutgers University,Piscataway NJ, USA. |
Integrated analysis of gene expression by association rules discovery | Carmona-Saez P, Chagoyen M, Rodriguez A, Trelles O, Carazo JM, Pascual-Montano A | BMC Bioinformatics 2006, 7:54 |
Developing a European Biomedical Grid on Cancer: The ACGT Integrated Project | M. Tsiknakis, D. Kafetzopoulos, G. Potamias, C. Marias, A. Analyti, A. Manganas. | , HealthGRID 06 Conference, 6-8 June 2006,Valencia, Spain. |
Microarray-Based Analysis of Spinal versus Intracranial Meningiomas: Different Clinical, Biological, and Genetic Characteristics Associated with Distinct Patterns of Gene Expression | José Maria Sayagues, Maria Dolores Tabernero, Angel Maillo, Oswaldo Trelles, Ana Belen Espinosa, Maria Eugenia Sarasquete, Ana Rasillo, Marta Merino, Jaime Fernandez Vera, Angel Santos-Briz and Alberto Orfao | Journal of Neuropathology and Experimental Neurology, vol.65 No 5; May 2006; pp. 445-454 |
Programming Grid Applications with Gridge | J Pukacki, J. Nabrzyski et al. | Journal of Computational Methods in Science and Technology 12(1), Issue subtitled: Grid Applications, New Challenges for Computational Methods, pp. 47-68, Scientific Publishers OWN,2006. |
Paradoxes and politics of "personalized" medicine. | Kollek, R. | Paper given at the 1. International Conference on Ethics and Politics, 24.-28. May 2006, Heraklion, Crete (Greece). |
Requirements and architectural specifications of a European Biomedical Grid: The ACGT Integrated Project | M. Tsiknakis, D. Kafetzopoulos | Annual Conference of the Cancer Biomedical Informatics Grid (caBIG), April 2006, Washington. |
Open Grid Services for improving medical knowledge discovery on Cancer: The ACGT integrated project | M. Tsiknakis | Workshop on Clinical Decision Support Systems, Scientific and Technological Park of Epirus, Ioannina - 17 March 2006. |
Applying a 4D multiscale in vivo tumor growth model to the exploration of radiotherapy scheduling: the effects of week end treatment gaps and p53 gene status on the response of fast growing solid tumors | Applying a 4D multiscale in vivo tumor growth model to the exploration of radiotherapy scheduling: the effects of week end treatment gaps and p53 gene status on the response of fast growing solid tumors | Cancer Informatics, 2: pp.113-121, 2006 |
Automatic Generation of Integration and Preprocessing Ontologies for Distributed KDD | Anguita A, Perez-Rey D, Maojo V | 7th IEEE International Conference on Data Mining, Omaha, USA, October 28-31, 2001[submitted, pending accept] |