Publications

PONTE Publications

  • "Using EHRs to design drug repositioning trials: a devolved approach to data protection"
    Marc Stauch, Nikolaus Forgó and Tina Krügel
    International Review of Law, Computers and Technology submitted and accepted for next issue 2013
  • "Temporal Classifiers for Predicting the Expansion of Medical Subject Headings"
    G. Tsatsaronis, I. Varlamis, N. Kanhabua and K. Nørvåg
    The 14th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing 2013), March 2013, Samos, Greece.
  • "Prevalence of thyroid dysfunction and effect of contrast medium on thyroid metabolism in cardiac patients undergoing coronary angiography"
    Marraccini P, Bianchi M, Bottoni A, Mazzarisi A, Coceani M, Molinaro S, Lorenzoni V, Landi P, Iervasi G
    Acta Radiol. 2013 Feb 1; 54(1):42-7. doi: 10.1258/ar.2012.120326. Epub 2012 Nov 2.
  • "Thyroid and brain natriuretic Peptide response in children undergoing cardiac surgery for congenital heart disease"
    Cantinotti M, Lorenzoni V, Storti S, Moschetti R, Murzi B, Marotta M, Crocetti M, Molinaro S, Clerico A, Portman M, Iervasi G., Circ J.
    2012 Dec 25; 77(1):188-97. Epub 2012 Sep 27.
  • "Fatigue in Patients With Coronary Artery Disease: Association With Thyroid Axis Hormones and Cortisol"
    Adomas Bunevicius, Md, Vilte Gintauskiene, Md, Aurelija Podlipskyte, Phd, Remigijus Zaliunas, Md, Phd, Julija Brozaitiene, Md, Phd, Arthur J. Prange, Jr, Md, And Robertas Bunevicius, Md, Phd
    Psychosomatic Medicine 74:848Y853 (2012)
  • "Endocrine associations with health-related quality of life in coronary artery disease patients"
    Robertas Bunevicius, Margarita Staniute, Vilte Gintauskiene , Juste Buneviciute , Charles B. Nemeroff , Julija Brozaitiene
    Int J Cardiol (2012), doi:10.1016/j.ijcard.2012.06.076
  • "Mining Potential Research Synergies from Co-Authorship Graphs using Power Graph Analysis"
    Iraklis Varlamis, and George Tsatsaronis
    International Journal of Web Engineering and Technology (IJWET), 2012, vol. 7(3), pp. 250-272.
  • "SemaFor: Semantic Document Indexing using Semantic Forests"
    G. Tsatsaronis, I. Varlamis and K. Nørvåg
    The 21st ACM International Conference on Information and Knowledge Management (CIKM 2012), November 2012, Maui Hawaii, USA.
  • "PONTE: Decision Support Making for Clinical Trial Protocol Design", Tsatsaronis, G., Mourtzoukos, K., Andronikou, V., Tagaris, A., Varlamis, I.,Schroeder, M., Varvarigou, T., Koutsouris, D., Matskanis, N.  (2012)  38th International Conference on Very Large Databases, VLDB-2012
  • "Hypothesis Evaluation in Clinical Trial Design and Strategic Portfolio Analysis", Liebman, M.N. and Molinaro, S., International Journal of Data Mining and Bioinformatics, 2012
  • "Hypothesis Generation and Evaluation in Clinical Trial Design", Liebman, M. N. and Molinaro, S., IEEE Transactions on Bioengineering and Biomedical Informatics, 2012
  • "A novel Query Rewriting Mechanism for Semantically interlinking Clinical Research with Electronic Health Records"
    Chondrogiannis, T., Andronikou, V., Mourtzoukos, K., Tagaris, T., Varvarigou, T.
    International Conference on Web Intelligence, Mining and Semantics, WIMS'12
  • "Semantically-assisted Hypothesis Validation in Clinical Research"
    Joseph Roumier, Michael Liebman, George Tsatsaronis, Nikolaos Matskanis, Anastasios Tagaris, Konstantinos Mourtzoukos, Efthymios Chondrogiannis, Vassiliki Andronikou, Philippe Massonet, Michael Schroeder,
    T. Varvarigou, e-Challenges e2012 Conference, October 2012, Portugal
  • "Analyzing the Role of Terms' Ambiguity in Biomedical Documents Annotation"
    G. Tsatsaronis, M. Kissa, J. Mönnlich, and M. Schroeder
    European Conference on Computational Biology (ECCB 2012), Poster paper, September 2012, Switzerland.
  • "Temporal Language Modelling of Biomedical Text: A Novel Text Mining Approach for Biomarkers Prediction"
    O. Gkorgkas, G. Tsatsaronis, I. Varlamis, and K. Nørvåg
    European Conference on Computational Biology (ECCB 2012), Poster paper, September 2012, Switzerland.
  • "Thyroid hormone and cardiac repair/regeneration: from Prometheus myth to reality"
    Pantos C, Mourouzis I, Cokkinos DV
    Can J Physiol Pharmacol. 2012 Aug 90(8):977-87
  • "PONTE: A Context-Aware Approach for Automated Clinical Trial Protocol Design"
    G. Tsatsaronis, K. Mourtzoukos, V. Andronikou, T. Tagaris, I. Varlamis, M. Schroeder, T. Varvarigou, D. Koutsouris and N. Matskanis
    6th International VLDB Workshop on Personalized Access, Profile Management, and Context Awareness in Databases (VLDB PersDB 2012), August 2012, Istanbul, Turkey.
  • "Word Sense Disambiguation as an Integer Linear Programming Problem"
    V. Panagiotopoulou, I. Varlamis, I. Androutsopoulos, and G. Tsatsaronis,
    Proceedings of the 7th Hellenic Conference on Artificial Intelligence (SETN 2012), May 2012, Greece, (accepted, to appear in Springer LNCS Proceedings).
  • "A Maximum Entropy Approach for Accurate Document Annotation"
    G. Tsatsaronis, N. Macari, S. Torge, H. Dietze, and M. Schroeder,
    Journal of Biomedical Semantics (JBMS), 2012, 3(Suppl 1):S2.
  • "Extending ontologies by finding siblings using set expansion techniques."
    G. Fabian, T. Wächter, M. Schroeder
    Bioinformatics, 2012 - accepted, to be published
  • "Semantic Interoperability between Clinical Research and Healthcare: the PONTE approach"
    Tassos Tagaris, Efthymios Chondrogiannis , Joseph Roumier, George Tsatsaronis, Vassiliki Andronikou, Nikolaos Matskanis, Konstantinos Mourtzoukos, Michael Schroeder, Philippe Massonet, Theodora Varvarigou,
    (SIMI2012) ESWC2012 Workshop, May 2012, Heraklion, Crete (to appear in LNCS proceedings - companion volume of the ESWC 2012 proceedings).
  • "Dose-dependent effects of thyroid hormone on post-ischemic cardiac performance: potential involvement of Akt ad ERK signalings"
    Mourouzis I, Mantzouratou P, Galanopoulos G, Kostakou E, Roukounakis N, Kokkinos AD, Cokkinos DV, Pantos C
    Molecular and Cellular Biochemistry 2012 Apr;363 (1-2):235-43
  • Persistence of mortality risk in patients with acute cardiac diseases and mild thyroid dysfunction.
    Molinaro S, Iervasi G, Lorenzoni V, Coceani M, Landi P, Srebot V, Mariani F, L'Abbate A, Pingitore A.
    Am J Med Sci. 2012 Jan;343(1):65-70.
    PMID: 21876429 [PubMed - indexed for MEDLINE]
  • "DOG4DAG: Semi-automated Ontology Generation in OBO-Edit and Protégé (demo)"
    Thomas Wächter, Götz Fabian and Michael Schroeder
    Proceedings of SWAT4LS December 2011, pp.119-120.
  • "A Knowledge-based Semantic Kernel for Text Classification"
    Jamal Abdul Nasir, Asim Karim, G. Tsatsaronis, and I. Varlamis
    18th International Symposium on String Processing and Information Retrieval (SPIRE 2011), October 2011, Pisa, Italy, pp. 261-266, LNCS 7024,
  • "An Experimental Study on Syntactic and Semantic Annotations in Text Retrieval"
    G. Tsatsaronis
    CIKM ESAIR 2011, October 2011, Glasgow, UK, pp. 27-28, ACM.
  • "TRUMIT: A Tool to Support Large-Scale Mining of Text Association Rules"
    R. Neumayer, G. Tsatsaronis and K. Nørvåg
    Proceedings of the 2011 European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2011), September 2011, Athens, Greece, pp. 646-649, LNCS 6913.
  • "How to Become a Group Leader? or Modelling Author Types based on Graph Mining",
    G. Tsatsaronis, I. Varlamis, S. Torge, M. Reimann, K. Nørvåg, M. Schroeder and M. Zschunke,
    Proceedings of the International Conference on Theory and Practice of Digital Libraries (TPDL 2011), September 2011, Berlin, Germany, pp. 15-26, Springer LNCS 6966.
  • "A Maximum Entropy Approach for Accurate Document Annotation in the Biomedical Domain"br /> G. Tsatsaronis, N. Macari, S. Torge, H. Dietze and M. Schroeder ISMB/ECCB BioOntologies Special Interest Group 2011 (BioOntologies 2011), July 2011, Vienna, Austria
  • "Thyroid hormone and recovery of cardiac function in patients with acute myocardial infarction: a strong association?"
    Lymvaios I, Mourouzis I, Cokkinos DV, Dimopoulos MA, Toumanidis ST, Pantos C Eur J Endocrinol. 2011 Jul;165(1):107-14
  • Thyroid hormone and cardiac disease: from basic concepts to clinical application.
    Mourouzis I, Forini F, Pantos C, Iervasi G.
    J Thyroid Res. 2011;2011:958626. Epub 2011 Jun 19.
    PMID: 21765997 [PubMed] Free PMC Article
  • "Subclinical hyperthyroidism and the risk of coronary heart disease and mortality"
    Collet TH, Gussekloo J, Bauer DC, den Elzen WP, Cappola AR, Balmer P, Iervasi G, Åsvold BO, Sgarbi JA, Völzke H, Gencer B, Maciel RM, Molinaro S, Bremner A, Luben RN, Maisonneuve P, Cornuz J, Newman AB, Khaw KT, Westendorp RG, Franklyn JA, Vittinghoff E, Walsh JP, Rodondi N
    Thyroid Studies Collaboration., Arch Intern Med. 2012 May 28;172(10):799-809. doi: 10.1001/archinternmed.2012.402.
  • "The GNAT library for online and offline gene mention normalization."
    J. Hakenberg, M. Gerner, M. Haeussler, C. Plake, M. Schroeder, G. Gonzalez, G. Nenadic, C. M. Bergman,
    Bioinformatics, 27(19):2769--71, 2011.
  • Chondrogiannis, E., Matskanis, N., Roumier, J., Andronikou, V., Massonet, Ph., (2011) Enabling semantic interlinking of medical data sources and EHRs for clinical research purposes, eChallenges e-2011 Conference.
  • "Computational Polypharmacology with Text Mining and Ontologies"
    Conrad Plake, Michael Schroeder, TUD
    Current Pharmaceutical Biotechnology, 12(3):449-57 - 2011
    Impact factor 2009: 2.3
  • Semantically-enabled Intelligent Patient Recruitment in Clinical Trials
    Andronikou, V., Karanastasis, E., Chondrogiannis, T., Tserpes, K., Varvarigou, T.
    5th International Conference on P2P, Parallel, Grid, Cloud and Internet Computing (3GPCIC 2010), November 4-6, 2010, Fukuoka Institute of Technology, Fukuoka, Japan, IEEE Conference Publishing Services.
  • "Recrutement efficace de patients pour effectuer des tests cliniques innovants pour le re-positionnement de mollécules existantes"
    Joseph Roumier, CETIC
    Newsletter CETIC - May 2010
  • "Acute Myocardial Infarction and Thyroid Function: New Pathophysiological and Therapeutic Perspectives"
    Pingitore Alessandro MD, PhD (Clinical Physiology Institute, CNR/Fondazione G. Monasterio CNR-Regione Toscana, Pisa e Massa, Italy), Chen Yuefeng MD, PhD (Department of Biomedical Sciences, New York College of Osteopathic Medicine at New York Institute of Technology, Old Westbury, NY), Gerdes Antony Martin PhD (Department of Biomedical Sciences, New York College of Osteopathic Medicine at New York Institute of Technology, Old Westbury, NY), and Iervasi Giorgio MD (Clinical Physiology Institute, CNR/Fondazione G. Monasterio CNR-Regione Toscana, Pisa e Massa, Italy)
    In press on ANNALS of MEDICINE - 2010
  • "Subclinical Hypothyroidism and the Risk of Coronary Heart Disease and Mortality"
    Nicolas Rodondi, MD, MAS; Wendy P. J. den Elzen, MSc; Douglas C. Bauer, MD; Anne R. Cappola, MD, ScM; Salman Razvi, MD, FRCP; John P. Walsh, MBBS, FRACP, PhD; Bjørn O. Åsvold, MD, PhD; Giorgio Iervasi, MD; Misa Imaizumi, MD, PhD; Tinh-Hai Collet, MD; Alexandra Bremner, PhD; Patrick Maisonneuve, Ing; José A. Sgarbi, MD; Kay-Tee Khaw, MD; Mark P. J. Vanderpump, MD, FRCP; Anne B. Newman, MD, MPH; Jacques Cornuz, MD, MPH; Jayne A. Franklyn, MD, PhD, FRCP; Rudi G. J. Westendorp, MD, PhD; Eric Vittinghoff, PhD; Jacobijn Gussekloo, MD, PhD
    Thyroid Studies Collaboration - 2010
  • "Semi-automated Ontology Generation within OBO-edit"
    Thomas Wächter, Michael Schroeder, TUD
    Bioinformatics, 26(12):i88--i96 - 2010
    Impact factor 2009: 4.9
  • "SuperCYP: a Comprehensive Database on Cytochrome P450 Enzymes Including a Tool for Analysis of CYP-drug Interactions"
    Saskia Preissner, Katharina Kroll, Mathias Dunkel, Christian Senger, Gady Goldsobel, Daniel Kuzman, Stefan Guenther, Rainer Winnenburg, Michael Schroeder, and Robert Preissner
    Nucleic Acids Research, 38(Database issue):D237--D243, 2010
    Impact factor 2009: 6.9
  • "Thyroid hormone as a therapeutic option for treating ischaemic heart disease: From
    early reperfusion to late remodelling
    "
    Constantinos Pantos, Iordanis Mourouzis, Dennis V. Cokkinos
    Vascular Pharmacology - 2010
  • "L’IT comme soutien à la conception d’essais cliniques"
    Philippe Massonet, CETIC
    Newsletter CETIC - September 2009
  • "A novel Query Rewriting Mechanism for Semantically interlinking Clinical Research with Electronic Health Records"
    Chondrogiannis, T., Andronikou, V., Mourtzoukos, K., Tagaris, T., Varvarigou, T.
    International Conference on Web Intelligence, Mining and Semantics (WIMS '12)

PONTE-related Publications