Publications of the Sealife project

(Chronological order)

  1. Karen Sutherland, Kenneth McLeod, Gus Ferguson, Albert Burger, Knowledge-driven Enhancements for Task Composition in Bioinformatics (accepted for publication in the special issue of BMC Bioinformatics dedicated to the SWAT4LS workshop), 2009.
  2. Kenneth McLeod, Gus Ferguson, and Albert Burger, Using Argumentation to resolve conflict in Biological Databases, to appear Computational Models of Natural Argument (CMNA), 2009.
  3. Helen Oliver, Gayo Diallo, Ed de Quincey, Patty Kostkova, Gawesh Jawaheer, Dimitra Alexopoulou, Bianca Habermann, Robert Stevens, Simon Jupp, Khaled Khelif, Michael Schroeder, and Gemma Madle, A User-Centred Evaluation Framework for the SeaLife Semantic Web Browsers, (accepted for publication in the special issue of BMC Bioinformatics dedicated to the SWAT4LS workshop), 2009.
  4. Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder and Thomas Wächter, Biomedical word sense disambiguation with ontologies and meta-data: automation meets accuracy, BMC Bioinformatics, 2009.
  5. Bill Andreopoulos, Aijun An, Xiaogang Wang and Michael Schroeder, A Roadmap of Clustering Algorithms: Finding the Best Match for a Biomedical Application, Briefings in Bioinformatics, 2009.
  6. Ursula G. Sauer, Thomas Wächter, Barbara Grune, Andreas Doms, Michael R. Alvers, Horst Spielmann and Michael Schroeder, Go3R Semantic Internet Search Engine for Alternative Methods to Animal Testing, ALTEX, 2009.
  7. Christin Süss, Cornelia Czupalla, Christof Winter, Theresia Pursche, Klaus Knoch, Michael Schroeder, Bernard Hoflack and Michele Solimena, Rapid changes of mRNA binding protein levels following glucose and IBMX stimulation of insulinoma INS-1 cells, Molecular and Cellular Proteomics, 2009.
  8. Felix Rückert, Mario Hennig, Constantina D. Petraki, Diana Wehrum, Marius Distler, Axel Denz, Michael Schroeder, Gihan Dawelbait, Holger Kalthoff, Hans-Detlev Saeger, Eleftherios P. Diamandis, Christian Pilarsky and Robert Grützmann, Co-expression of KLK6 and KLK10 as prognostic factor for survival in pancreatic ductal adenocarcinoma, British Journal of Cancer, 2009.
  9. Heiko Dietze and Michael Schroeder, GoWeb: A semantic search engine for the life science web, in Proceedings of the Intl. Workshop on Semantic Web Applications and Tools for the Life Sciences SWAT4LS, Albert Burger, Adrian Paschke, Paolo Romano and Andrea Splendiani, editors, November 2008.
  10. G. Diallo, G. Madle, G. Jawaheer, P. Kostkova, D. Alexopoulou, R. Stevens, S. Jupp, K. Khelif, A User-Centred Evaluation Framework for the SeaLife Semantic Web Browsers, presented as poster at the Semantic Web Applications and Tools for Life Sciences (SWAT4LS) workshop, Edinburgh, November 2008.
  11. J. Boline, A. Burger, et al, The INCF Digital Brain Atlas Program: Building Community Consensus and Community Tools, presented as poster at INCF Workshop on Computational Developmental Neuroscience, Edinburgh, November 2008.
  12. Karen Sutherland and Albert Burger, Goal-Oriented Task Composition for Bioinformatics, presented as poster at the Semantic Web Applications and Tools for Life Sciences (SWAT4LS), Edinburgh, November 2008.
  13. Shevchenko A, Roguev A, Schaft D, Buchanan L, Habermann B, Sakalar C, Thomas H, Krogan NJ, Shevchenko A, Stewart AF, Chromatin Central: towards the comparative proteome by accurate mapping of the yeast proteomic environment, 2008, Genome Biology.
  14. Alan Rector and Robert Stevens, Barriers to the use of OWL in Knowledge Driven Applications, Fifth International workshop on OWL Experiences and Directions 2008 (OWLEd 2008) Co-located with ISWC 2008, Karlsruhe, Germany, 2008. Poster and short presentation.
  15. Alan Rector, Robert Stevens and Nick Drummond, What Causes Pneumonia? The Case for a Standard Semantics for "may" in OWL, Fifth International workshop on OWL Experiences and Directions 2008 (OWLEd 2008) Co-located with ISWC 2008, Karlsruhe, Germany, 2008. Poster and short presentation.
  16. Robert Stevens and Margaret Stevens, A Family History Knowledge Base Using OWL 2, Fifth International workshop on OWL Experiences and Directions 2008 (OWLEd 2008) Co-located with ISWC 2008, Karlsruhe, Germany, 2008. Poster and short presentation.
  17. Luigi Iannone, Mikel Egana, Alan Rector and Robert Stevens, Augmenting the Expressivity of the Ontology Pre-Processor Language, Fifth International workshop on OWL Experiences and Directions 2008 (OWLEd 2008) Co-located with ISWC 2008, Karlsruhe, Germany, 2008. Poster and short presentation.
  18. James Eales, John Pinney, Robert Stevens and David Robertson, Methodology capture: discriminating between the "best" and the rest of community practice, BMC Bioinformatics, 2008.
  19. Hammad Afzal, Robert Stevens and Goran Nenadic, Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary, 3rd International Symposium on Semantic Mining in Biomedicine, 2008.
  20. Mikel Egana, Alan Rector, Robert Stevens and Erick Antezana, Applying Ontology Design Patterns in Bio-ontologies, EKAW 2008, LNCS 5268, A. Gangemi and J. Euzenat editors, Springer-Verlag, p. 7-16
  21. Carole Goble, Robert Stevens, Duncan Hull, Katy Wolstencroft and Rodrigo Lopez, Data curation + process curation = data integration + science, Briefings in Bioinformatics, 2008.
  22. Simon Jupp, Sean Bechhofer, Robert Stevens, A Flexible API and Editor for SKOS, ISWC 2008 Karlsruhe, Germany, 2008. Poster and Demo session.
  23. Simon Jupp, Robert Stevens, Sean Bechhofer, Yeliz Yesilada and Patty Kostkova, SKOS with OWL: Don’t be Full-ish, Fifth International workshop on OWL Experiences and Directions 2008 (OWLEd 2008), Co-located with ISWC 2008, Karlsruhe, Germany, 2008. Poster and short presentation.
  24. Simon Jupp, Robert Stevens, Sean Bechhofer, Yeliz Yesilada and Patty Kostkova, Knowledge Representation for Web Navigation, SWAT4LS, 2008.
  25. Rainer Winnenburg, Thomas Wächter, Conrad Plake, Andreas Doms and Michael Schroeder, Facts from text: Can text mining help to scale-up high-quality manual curation of gene products with ontologies?, 2008, Briefings in Bioinformatics.
  26. Afzal, H., Stevens, R., Nenadic, G., Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary, Proc. of Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), 2-3 September, Turku, Finland, p. 5-12.
  27. James M Eales, John W Pinney, Robert D Stevens and David L Robertson, Discriminating between the "best" and the rest of community practice, BMC Bioinformatics 2008, 9:359
  28. S. Wiseman, G. Jawaheer, P. Kostkova and G. Madle, Editorial: Specialist Digital Libraries National Resource for Infection Control (NRIC) Informatic overlead or underload? British Journal of Infection Control 2008:9; 4, pages 4-6.
  29. Paschke, A.: Rule Responder HCLS eScience Infrastructure, 3rd International Conference on Pragmatic Web (ICPW 2009), Proc. ACM Press, Uppsala, Sweden, Sept. 2008.
  30. Khaled Khelif, Aroua Hedhili and Martine Collard, Semantic Patent Clustering for Biomedical Communities, In Proc. of the IEEE/WIC/ACM International Conference on Web Intelligence WI'08, 9-12 December 2008, Sydney, Australia.
  31. Gayo Diallo, Khaled Khelif, Olivier Corby, Patty Kostkova and Gemma Madle, Semantic Browsing of a Domain Related Resources: The Corese-NeLI Framework, In Proc. of the 2008 International Workshop on Web Information Retrieval Support Systems WIRSS 2008 held in collaboration with the IEEE/WIC/ACM International Conference on Web Intelligence WI'08, 9-12 December 2008, Sydney, Australia.
  32. Rainer Winnenburg, Conrad Plake and Michael Schroeder, Mutation tagging with gene identifiers applied to membrane protein stability prediction, ECCB Workshop 2008 Annotation, Interpretation and Management of Mutations, Bioinformatics.
  33. Karen Sutherland, Kenneth McLeod and Albert Burger, Semantically Linking Web Pages to Web Services in Bioinformatics, 3rd International Applications of Semantic Technologies Workshop, Munich, Germany, 9 September 2008.
  34. G. Madle, P. Kostkova, A. Roudsari, Impact-ED A New Model of Digital Library Impact Evaluation, In Proceedings of the ECDL 2008 confernece, Aarhus, Denmark, September 2008
  35. Bingding Huang and Michael Schroeder, Using protein binding site prediction to improve protein docking, Gene, 2008, in press.
  36. Schenck A, Goto-Silva L, Collinet C, Rhinn M, Giner A, Habermann B, Brand M, Zerial M. in Cell. 2008 May 2;133(3):486-97: The endosomal protein Appl1 mediates Akt substrate specificity and cell survival in vertebrate development.
  37. Kenneth McLeod and Albert Burger, Towards the use of Argumentation in Bioinformatics: A Gene Expression Case Study, 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, July, 2008. (also published in Bioinformatics, 1 July 2008; 24: i304 - i312)
  38. Karen Sutherland, Kenneth McLeod and Albert Burger, Semantically Linking Web Pages to Web Services in Bioinformatics, 3rd International Applications of Semantic Technologies Workshop, Munich, Germany, 9 September 2008.
  39. Gayo Diallo, Patty Kostkova, Gawesh Jawaheer, Simon Jupp, Robert Stevens, Process of Building a Vocabulary for the Infection Domain, cbms, pp. 308-313, 2008 21st IEEE International Symposium on Computer-Based Medical Systems, Jyvaskyla, Finland, 17-19th June 2008
  40. Patty Kostkova, Gayo Diallo, Gawesh Jawaheer, "User Profiling for Semantic Browsing in Medical Digital Libraries" Proceedings of ESWC 2008, The Semantic Web: Research and Applications, 5th European Semantic Web Conference, Tenerife, Canary Islands, Spain, June 1-5, 2008.
  41. Khaled Khelif and Fabien Gandon and Olivier Corby and Rose Dieng- Kuntz: Using the Intension of Classes and Properties definition in Ontologies for Word Sense Disambiguation, 6th International Conference on Knowledge Engineering and Knowledge Management Knowledge Patterns, EKAW 2008, Acitrezza, Catania, Italy, 2008.
  42. Joerg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser, and Michael Schroeder. Gene mention normalization and interaction extraction with context models and sentence motifs, Genome Biology, 9(2):S14, 2008
  43. Joerg Hakenberg, Conrad Plake, Robert Leaman, Michael Schroeder, and Graciela Gonzalez. Inter- species normalization of gene mentions. Bioinformatics, 2008
  44. Loic Royer, Matthias Reimann, William Andreopoulos, and Michael Schroeder. Unravelling the molecular nature of protein interaction networks with powergraphs. Plos Computational Biology, 4(7):e1000108, 2008.
  45. Dimitra Alexopoulou, Thomas Wächter, Laura Pickersgill, Cecilia Eyre, and Michael Schroeder,
    Terminologies for text-mining; an experiment in the lipoprotein metabolism domain.
    BMC Bioinformatics, 2008 Apr 25;9 Suppl 4:S2.
  46. Albert Burger, Duncan Davidson, and Richard Baldock, editors.
    Anatomy Ontologies for Bioinformatics: Principles and Practice.
    Springer, 2008
  47. Heiko Dietze, Dimitra Alexopoulou, Michael R. Alvers, Liliana Barrio-Alvers, Bill Andreopoulos, Andreas Doms, Jörg Hakenberg, Jan Mönnich, Conrad Plake, Andreas Reischuck, Loic Royer, Thomas Wächter, Matthias Zschunke, and Michael Schroeder.
    Bioinformatics for Systems Biology.
    chapter GoPubMed: Exploring PubMed with Ontological Background Knowledge. The Human Press, 2008
  48. Nizar Ghoula, Khaled Khelif, and Rose Dieng-Kuntz.
    Vers une fouille semantique des brevets : Application au domaine biomedical.
    In Accepted at 8emes journees francophones Extraction et Gestion des Connaissances, INRIA Sophia Antipolis - Mediterranee, 2008
  49. Jörg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser, and Michael Schroeder.
    Gene mention normalization and interaction extraction with context models and sentence motifs.
    Genome Biology, 2008
  50. Alexander Andreopoulos, Bill Andreopoulos, Aijun An, and Xiaogang Wang.
    Translation and Rotation Invariant Mining of Frequent Trajectories: Application to Protein Unfolding Pathways.
    In PAKDD workshop on data mining for biomedical applications (BioDM 2007), Springer LNAI/LNCS, 2007
  51. Bill Andreopoulos, Dimitra Alexopoulou, and Michael Schroeder.
    Word Sense Disambiguation in Biomedical Ontologies with Term Co-occurrence Analysis and Document Clustering.
    International Journal of Data Mining and Bioinformatics, Special Issue on Biomedical Text Retrieval and Mining, 2008, Vol. 2, No.3 pp. 193 - 215.
  52. Bill Andreopoulos, Aijun An, and Xiaogang Wang.
    Hierarchical Density-based Clustering of Categorical Data and a Simplification.
    In Proceedings of the 11th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2007), volume 4426 of Springer LNAI, pages 11--22, 2007
  53. Bill Andreopoulos, Aijun An, Xiaogang Wang, Michalis Faloutsos, and Michael Schroeder.
    Clustering by Common Friends Finds Locally Significant Proteins Mediating Modules..
    Bioinformatics, 23(9):1124--1131, 2007
  54. Sean Bechhofer, Yeliz Yesilada, Robert Stevens, Simon Jupp, and Bernard Horan.
    Using Ontologies and Vocabularies for Dynamic Linking.
    Internet Computing, 2007
  55. Sean Bechhofer, Yeliz Yesilada, Robert Stevens, Simon Jupp, and Bernard Horan.
    Using Ontologies and Vocabularies for Dynamic Linking.
    IEEE Internet Computing, 2007, Accepted for publication
  56. Rachel Brenchley, Humera Tariq, Helen McElhinney, Balazs Szoor, Robert Stevens, Keith Matthews, and Lydia Tabernero.
    The TriTryp Phosphatome analysis of the protein phosphatase catalytic domains.
    BMC Genome, 8(434), 2007
  57. Albert Burger.
    Agent Technologies in the Life Sciences.
    In Christopher Baker and Kei-Hoi Cheung, editors, Semantic Web: Revolutionizing Knowledge and Discovery in the Life Sciences. Springer, 2007
  58. Gihan Dawelbait, Christof Winter, Yanju Zhang, Chrisitian Pilarky, Robert Grutzmann, Joerg-Chrisitan Heinrich, and Michael Schroeder.
    Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data..
    In Bioinformatics, Intelligent Systems for Molecular Biology, 2007
  59. David De Roure, Carole Goble, and Robert Stevens.
    DESIGNING THE MYEXPERIMENT VIRTUAL RESEARCH ENVIRONMENT FOR THE SOCIAL SHARING OF WORKFLOWS.
    In e-Science 2007 - Third IEEE International Conference on e-Science and Grid Computing, pages 603--610, 2007
  60. David De Roure, Carole Goble, and Robert Stevens.
    Designing the myexperiment virtual research environment for the social sharing of workflows.
    In 2nd International Workshop on Scientific Workflows and Business Workflow Standards in e-Science (SWBWS), 2007
  61. Frank Dressel, Annalisa Marsico, Anne Tuukkanen, Michael Schroeder, and Dirk Labudde.
    Understanding of SMFS barriers by means of energy profiles.
    In Martin Vingron, editor, Proceedings of German Bioinformatics Conference GCB, 2007
  62. Paul Fisher, Cornelia Hedeler, Katherine Wolstencroft, Helen Hulme, Harry Noyes, Stephen Kemp, Robert Stevens, and Andrew Brass.
    A Systematic Strategy for Large-Scale Analysis of Genotype-Phenotype Correlations: Identification of candidate genes involved in African Trypanosomiasis.
    Nucleic Acids Research, 2007
  63. Paul Fisher, Cornelia Hedeler, Katherine Wolstencroft, Helen Hulme, Harry Noyes, Stephen Kemp, Robert Stevens, and Andrew Brass.
    A Systematic Strategy for Large-Scale Analysis of Genotype-Phenotype Correlations: Identification of candidate genes involved in African Trypanosomiasis.
    Nucleic Acids Research, 2007
  64. Nizar Ghoula, Khaled Khelif, and Rose Dieng-Kuntz.
    Supporting Patent Mining by using Ontology-based Semantic Annotations.
    In IEEE/WIC/ACM International Conference on Web Intelligence, 2007
  65. A Gibson, K Wolstencroft, and R Stevens.
    Promotion of ontological comprehension: Exposing terms and metadata with web 2.0.
    CKC 2007, Workshop on Social and Collaborative Construction of Structured Knowledge, 16th International World Wide Web Conference (WWW2007), 273, 2007, CEUR Workshop Proceedings (http://CEUR-WS.org)
  66. Carole Goble, Katy Wolstencroft, Antoon Goderis, Duncan Hull, Jun Zhao, Pinar Alper, Phillip Lord, Chris Wroe, Khalid Belhajjame, Daniele Turi, Robert Stevens, and David De Roure.
    Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences.
    Springer, 2007
  67. Joerg Hakenberg, Loic Royer, Conrad Plake, Hendrik Strobelt, and Michael Schroeder.
    Me and my friends: gene mention normalization with background knowledge.
    In Proceedings of the Second BioCreative Challenge Evaluation Workshop, 2007
  68. Joerg Hakenberg, Michael Schroeder, and Ulf Leser.
    Consensus pattern alignment to find protein-protein interactions in text.
    In Proceedings of the Second BioCreative Challenge Evaluation Workshop, 2007
  69. Jörg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser, and Michael Schroeder.
    Gene mention normalization and interaction extraction with context models and sentence motifs.
    Genome Biology, 2007, Submitted, [Bioinformatics (Textmining, ontologies, reasoning)]
  70. Andreas Henschel, Christof Winter, Wan Kyu Kim, and Michael Schroeder.
    Using multiple motif descriptors for sequence based binding site prediction.
    BMC Bioinformatics, 8(Suppl 4):S5, 2007
  71. Simon Jupp, Robert Stevens, Sean Bechhofer, Patty Kostkova, and Yeliz Yesilada.
    Document Navigation: Ontology or Knowledge Organization System?.
    In NETTAB, 2007
  72. Khaled Khelif, Rose Dieng-Kuntz, and Pascal Barbry.
    Mining Biomedical Texts to Generate Semantic Annotations.
    Technical report, INRIA Sophia-Antipolis, January 2007
  73. Khaled Khelif, Rose Dieng-Kuntz, and Pascal Barbry.
    An ontology-based approach to support text mining and information retrieval in the biological domain.
    Special Issue on Ontologies and their Applications of the Journal of Universal Computer Science (JUCS), (Accepted for publication), 2007
  74. Ralf Kittler, Laurence Pelletier, Anne-Kristine Heninger, Mikolaj Slabicki, Mirko Theis, Lukasz Miroslaw, Ina Poser, Steffen Lawo, Hannes Grabner, Karol Kozak, Jan Wagner, Vineeth Surendranath, Constance Richter, Wayne Bowen, Aimee Jackson, Bianca Habermann, Anthony Hyman, and Frank Buchholz.
    AOP: Genome-wide RNAi profiling of cell division in human tissue culture cells.
    Nature Cell Biology, 2007
  75. Ralf Kittler, Vineeth Surendranath, Anne-Kristin Heninger, Mikolaj Slabicki, Mirko Theis, Gabriele Putz, Kristin Franke, Antonio Caldareli, Hannes Grabner, Karol Kozak, Jan Wagner, Effi Rees, Bernd Korn, Christoph Sachse, Birte Soenichsen, Jie Guo, Janell Schelter, Julja Burchard, Peter S. Linsley, Aimee L. Jackson, Bianca Habermann, and Frank Buchholz.
    A Genome-wide Resource of Endoribonuclease-prepared short interfering RNA for specific loss-of-function studies in Human, Mouse and Rat.
    in Nature Methods, 4(4), 337-44, 2007
  76. Patty Kostkova, Gayo Diallo, and Gawesh Jawaheer.
    Application of User Profiling on Ontology Module Extraction for Medical portals.
    In MedSemWeb 2007 (MedInfo 2007 Workshop), Brisbane, Australia, 2007
  77. Paschke, A., Boley, H., Kozlenkov. A., Craig, B.: Rule Responder: RuleML-Based Agents for Distributed Collaboration on the Pragmatic Web, 2nd International Conference on the Pragmatic Web, Tilburg, Netherlands, 2007.
  78. Paschke, A., Schröder, M.: Inductive Logic Programming for Bio-Informatics in Prova, 2nd Workshop on Data Mining in Bioinformatics (DMB 2007), Vienna, Austria, 2007.
  79. Annalisa Marsico, Andreas Henschel, Gihan Dawelbait, Christof Winter, Anne Tuukkanen, and Michael Schroeder.
    Conserved hydrogen bond patterns reveal structural and functional motifs in transmembrane protein regions.
    In Automated Function Prediction, 2007
  80. Annalisa Marsico, Dirk Labudde, Tanuj Sapra, Daniel J. Muller, and Michael Schroeder.
    A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single molecule force spectroscopy.
    Bioinformatics, 23(2), 2007
  81. Kenneth McLeod and Albert Burger.
    Using argumentation to tackle inconsistency and incompleteness in online distributed life science resources.
    In Nuno Guimar aes and Pedro Isais, editors, Proceedings of IADIS International Conference Applied Computing 2007, pages 489--492, Salamanca, Spain, February 2007
  82. Yassine Mrabet, Khaled Khelif, and Rose Dieng-Kuntz.
    Recognising Professional-Activity Groups and Web Usage Mining for Web Browsing Personalisation.
    In IEEE/WIC/ACM International Conference on Web Intelligence, 2007
  83. Loic Royer, Matthias Reimann, Bill Andreopoulos, and Michael Schreder.
    Unravelling the molecular nature of protein interaction networks with powergraphs.
    Submitted, 2007, [Bioinformatics (Protein interactions and gene expression)]
  84. Felix Rueckert, Gihan Dawelbait, Arndt Hartmann, Axel Denz, Ole Ammerpohl, Michael Schroeder, Hans Konrad Schackert, Bence Sipos, Guenter Kloeppel, Holger Kalthoff, Hans-Detlev Saeger, Robert Gruetzmann, and Christian Pilarsky.
    Defects of the apoptosis network in pancreatic cancer.
    Submitted, 2007, [Bioinformatics (Protein interactions and gene expression)]
  85. Robert Stevens.
    Sightless In Science.
    The Biochemist, 2007
  86. Robert Stevens, Jun Zhao, and Carole Goble.
    Using Provenance to Manage Knowledge of In Silico Experiments.
    Briefings in bioinformatics, 8(3):183--194, 2007
  87. Jenny Ure, Rob Proctor, Maryann Martone, David Porteous, Sharon Lloyd, Stephen Lawrie, Dominic Job, Richard Baldock, Alistair Philp, Dave Liewald, Frank Rakebrand, Alan Blaikie, Clare McKay, Stuart Anderson, John Ainsworth, Jano van Hemert, Ignacio Blanquer, Richard Sinnott, Christian Barillot, Frank Bernard Gibaud, Alan Williams, Mark Hartswood, Paul Watson, Leslie Smith, Albert Burger, Jessie Kennedy, Horacio Gonzalez-Velez, Robert Stevens, Oscar Coecho, Robin Morton, Pamela Linksted, Mylene Deschenne, Mark McGilchrist, Paul Johnson, Alex Vossi, Renate Gertz, and Joanna Wardlaw.
    Data Integration in eHealth: A Domain/Disease Specific Roadmap.
    Studies Health Technol Inform, 126:144--53, 2007
  88. S Wiseman, P Kostkova, F Hansraj, and J Mani-Saada.
    National Resource for Infection Control (www.nric.org.uk): meeting a need?.
    In ECCMID 2007, Munich, Germany, 2007
  89. K Wolstencroft, P Alper, D Hull, C Wroe, PW Lord, RD Stevens, and CA Goble.
    The myGrid Ontology: Bioinformatics Service Discovery.
    International Journal of Bioinformatics Research and Applications, special issue on biomedical ontologies, 2007
  90. Khalid Belhajjame, Suzanne M Embury, Norman W Paton, Robert Stevens, and Carole A Goble.
    Automatic Annotation of Web Services based on Workflow Definitions.
    In In Fifth International Semantic Web conference ISWC'06, pages 116--129, Athens, Georgia, USA, 2006
  91. Olivier Bodenreider and Robert Stevens.
    Bio-ontologies: current trends and future directions.
    Brief Bioinform, 7(3):256--274, 2006
  92. Charles Richard Bradshaw, Vineeth Surendranath, and Bianca Habermann.
    ProFAT: A web-based Tool for the Functional Annotation of Protein Sequences.
    BMC Bioinformatics, 23(7):466, 2006
  93. Andreas Doms, Vaida Jakonien, Patrick Lambrix, Michael Schroeder, and Thomas Wächter.
    Ontologies and Text Mining as a Basis for a Semantic Web for the Life Sciences.
    In REWERSE Summerschool 2006. Springer, 2006
  94. Nick Drummond, Alan Rector, Robert Stevens, Georgina Moulton, Matthew Horridge, Hai Wang, and Julian Seidenberg.
    Putting OWL in Order: Patterns for Sequences in OWL.
    In Accepted for Second OWL Experiences and Directions Workshop, Athens, Georgia, USA, 2006
  95. Tom Gardiner, Dmitry Tsarkov, and Ian Horrocks.
    Framework for Automated Benchmarking of Description Logic Reasoners.
    In In fifth International Semantic Web conference ISWC'06, Athens, Georgia, USA, 2006
  96. A Gibson, RD Stevens, and M Pocock.
    The Semantics of Genome Mapping.
    In In Health Care and Life Sciences Workshop, Athens, Georgia, USA, 2006
  97. Carole Goble, Katy Wolstencroft, Antoon Goderis, Duncan Hull, Jun Zhao, Pinar Alper, Phillip Lord, Chris Wroe, Khalid Belhajjame, Daniele Turi, Robert Stevens, and David De Roure.
    Knowledge Discovery for in silico Experiments with Taverna.
    In Christopher J. O. Baker and Kei-Hoi Cheung, editors, Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. Springer Verlag, 2006
  98. Andreas Henschel, Wan Kyu Kim, and Michael Schroeder.
    Equivalent binding sites reveal convergently evolved interaction motifs.
    Bioinformatics, 22:550--555, 2006
  99. Andreas Henschel, Christof Winter, Wan Kyu Kim, and Michael Schroeder.
    Function and Interaction Prediction using multiple motif descriptors for classified domain-domain interactions and ligand binding sites.
    Accepted for Automated Function Prediction., 2006
  100. Matthew Horridge, Nick Drummond, John Goodwin, Alan Rector, Robert Stevens, and Hai Wang.
    The Manchester OWL Syntax.
    In Accepted for Second OWL Experiences and Directions Workshop, Athens, Georgia, USA, 2006
  101. Matthew Horridge and Dmitry Tsarkov.
    Supporting Early Adoption of OWL 1.1 with Protege-OWL and FaCT++.
    In Accepted for Second OWL Experiences and Directions Workshop, Athens, Georgia, USA, 2006
  102. Bingding Huang and Michael Schroeder.
    LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation.
    BMC Structural Biology, 6(1), 2006.
  103. D Hull, K Wolstencroft, R Stevens, C Goble, MR Pocock, P Li, and T Oinn.
    Taverna: a tool for building and running workflows of services.
    Nucleic Acids Res, 34(Web Server issue):729--732, 2006
  104. Duncan Hull, Evgeny Zolin, Andrey Bovykin, Ian Horrocks, Ulrike Sattler, and Robert Stevens.
    Deciding matching of stateless services.
    In The Twenty-First National Conference on Artificial Intelligence and the Eighteenth Innovative Applications of Artificial Intelligence Conference, Boston, Massachusetts, USA, 2006
  105. Wan Kyu Kim, Andreas Henschel, Christof Winter, and Michael Schroeder.
    The Many Faces of Protein-protein Interactions: A Compendium of Interface Geometry.
    PLoS Computational Biology, 2(9):e124, 2006
  106. P Kostkova and S DeSouza.
    Experience with Agents in Internet Healthcare Digital Library Management of the National Resource for Infection Control and National electronic Library of Infection.
    Special Issue of the ACM Transactions on Autonomous and Adaptive Systems (TAAS), The Agentlink Perspective On Autonomous And Adaptive Systems, Ed. T. Payne and A Omicini, 2006
  107. Samatha Kottha and Michael Schroeder.
    Classifying permanent and transient protein interactions.
    In Oliver Kohlbacher and Andrei Lupas, editors, Proceedings of German Bioinformatics Conference GCB2006, 2006
  108. Alex Kozlenkov, Rafael Penaloza, Vivek, Nigam, Loic Royer, Gihan Dawelbait, and Michael Schroeder.
    Prova: Rule-based Java Scripting for Distributed Web Applications: A Case Study in Bioinformatics.
    In Sebastian Schaffert, editor, Proceedings of Workshop on Reactivity on the Web at the International Conference on Extending Database Technology (EDBT 2006). Springer, 2006
  109. Tobias Kuhn, Loic Royer, Norbert E. Fuchs, and Michael Schroeder.
    Improving text mining with controlled natural language: A case study for protein interactions.
    In Ulf Leser, Barbara Eckman, and Felix Naumann, editors, Proc. of 3rd International Workshop on Data Integration in the Life Sciences 2006 (DILS'06), volume LNBI. Springer, 2006
  110. Zoe Lacroix, Bertram Ludaescher, and Robert Stevens.
    Integrating Biological Databases.
    Wiley-VCH, 2006.
  111. Annalisa Marsico, Tanuj Sapra, Daniel J. Muller, Michael Schroeder, and Dirk Labudde.
    A structure-based analysis of Single Molecular Force Spectroscopy (SMFS) data for bacteriorhodopsin and four mutants.
    In Michael Berthold and Robert Glen, editors, Proceedings of the 2nd International Symposium on Computational Life Science. Springer, 2006
  112. Emanuela Merelli, Giuliano Armano, Nicola Cannata, Flavio Corradini, Mark d'Inverno, Andreas Doms, Phil Lord, Andrew Martin, Luciano Milanesi, Steffen Moeller, Michael Schroeder, and Michael Luck.
    Agents in bioinformatics, computational and systems biology.
    Briefings in Bioinformatics, 2006
  113. N Morrison, JA Wood, D Hancock, S Shah, L Hakes, T Gray, B Tiwari, P Kille, A Cossins, M Hegarty, MJ Allen, WH Wilson, P Olive, K Last, C Kramer, T Bailhache, J Reeves, D Pallett, J Warne, K Nashar, H Parkinson, SA Sansone, P Rocca-Serra, R Stevens, J Snape, D Field, and A Brass.
    Standard annotation of environmental 'omic data - Application to the transcriptomics domain.
    OMICS: A journal of integrative biology, 10(2):172 --178, 2006
  114. Tom Oinn, Mark Greenwood, Matthew Addis, Justin Ferris, Kevin Glover, Carole Goble, Duncan Hull, Darren Marvin, Peter Li, Phillip Lord, Matthew Pocock, Martin Senger, Anil Wipat, and Chris Wroe.
    Taverna: Lessons in creating a workflow environment for the Life Sciences.
    Concurrency and Computation:Practice and Experience, 2006
  115. J Robinson, S de Lusignan, P Kostkova, and B Madge.
    Using UMLS to map from a library to a clinical classifiction: Improving the functionality of a digital library.
    Studies in Health Technology and Informatics, 121:86--95, 2006
  116. J Robinson, S de Lusignan, P Kostkova, B Madge, and L Southgate.
    Specific classification of Elibrary Resources says more about Users' Preferences.
    In MIE 2006, Maastricht, the Netherlands, 2006
  117. Loic Royer, Benedikt Linse, Thomas Wächter, Francois Bry, and Michael Schroeder.
    Querying the semantic web: A case study.
    In Christopher Baker and Kei-Hoi Cheung, editors, Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. Springer, 2006
  118. M Schroeder, A Burger, P Kostkova, R Stevens, B Habermann, and R Dieng-Kuntz.
    From a Service-based eScience Infrastructure to a Semantic Web for the Life Sciences: The Sealife Project.
    In Workshop on Network Tools and Applications in Biology, NETTAB 2006, Sardinia, Italy, 2006
  119. Michael Schroeder, Albert Burger, Patty Kostkova, Robert Stevens, Bianca Habermann, and Rose Dieng-Kuntz.
    Sealife: A Semantic Grid Browser for the Life Sciences Applied to the Study of Infectious Diseases.
    Stud Health Technol Inform, 120:167--78, 2006, Proceedings of HealthGrid 2006
  120. Robert Stevens, Phil Lord, and Duncan Hull.
    Using Distributed Data and Tools in bioinformatics Applications.
    Wiley-VCH, 2006
  121. Robert Stevens, Phillip Lord, and Andrew Gibson.
    Something nasty in the woodshed: the public knowledge model.
    In Accepted for Second OWL Experiences and Directions Workshop, Athens, Georgia, USA, 2006
  122. Robert Stevens, Yeliz Yesilada, Michael Schroeder, Albert Burger, Patty Kostkova, Bianca Habermann, and Rose Dieng-Kuntz.
    A Semantic Browser for a Web of Biomedicine.
    In In Health Care and Life Sciences Workshop, Athens, Georgia, USA, 2006
  123. C Stoeckert, C Ball, A Brazma, R Brinkman, H Causton, L Fan, J Fostel, G Fragoso, M Heiskanen, F Holstege, N Morrison, H Parkinson, J Quackenbush, P Rocca-Serra, S.A. Sansone, U Sarkans, G Sherlock, R Stevens, C Taylor, R Taylor, P Whetzel, and J White.
    Wrestling with SUMO and bio-ontologies.
    Nature Biotechnology, 24:21--22, 2006
  124. Dmitry Tsarkov, Ian Horrocks, and Peter Patel-Schneider.
    Optimising Terminological Reasoning for Expressive Description Logics.
    Journal of Automated Reasoning, 2006
  125. Thomas Wächter, He Tan, Andre Wobst, Patrick Lambrix, and Michael Schroeder.
    A corpus-driven approach for the design, evolution, and alignment of ontologies.
    In Adelinde M. Uhrmacher, editor, Proceedings of the Winter Simulation Conference (Computational Systems Biology), 2006
  126. Yimin Wang, York Sure, Robert Stevens, and Alan Rector.
    Knowledge elicitation plug-in for protege: Card sorting and laddering.
    In Asian Semantic Web Conference, pages 552--565, Beijing, China, 2006
  127. PL Whetzel, RR Brinkman, HC Causton, L Fan, D Field, J Fostel, G Fragaso, T Gray, M Heiskanen, T Hernandez-Boussard, N Morrison, H Parkinson, P Rocca-Serra, SA Sansone, D Schober, B Smith, R Stevens, CJ Stoeckert, C Taylor, J White, A Wood, and the FuGO Working Group.
    Development of FuGO: An Ontology for Functional Genomics Investigations.
    OMICS: A journal of integrative biology, 10(2):199 --204, 2006
  128. Christof Winter, Thorsten Baust, Bernard Hoflack, and Michael Schroeder.
    A novel, comprehensive method to detect and predict protein-protein interactions applied to the study of vesicular trafficking.
    In Oliver Kohlbacher and Andrei Lupas, editors, Proceedings of German Bioinformatics Conference GCB2006, 2006
  129. Christof Winter, Andreas Henschel, Wan Kyu Kim, and Michael Schroeder.
    SCOPPI: a structural classification of protein-protein interfaces.
    Nucleic Acids Research, 34 (Database Issue), 2006
  130. K. Wolstencroft, P. Lord, L. Tabernero, A. Brass, and R. Stevens.
    Protein classification using ontology classification.
    Bioinformatics, 22(14), 2006
  131. Katy Wolstencroft, Robert Stevens, and Volker Haarslev.
    Applying OWL Reasoning to Genomic Data.
    In Christopher J. O. Baker and Kei-Hoi Cheung, editors, Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. Springer Verlag, 2006
  132. Jun Zhao, Carole Goble, and Robert Stevens.
    An Identity Crisis in The Life Sciences.
    In Proc. of the International Provenace and Annotation Workshops, Chicago, USA, May 2006
  133. A. Cooke, A. Gray, and W. Nutt.
    Stream Integration Techniques in Grid Monitoring.
    Journal on Data Semantics, 2005, to appear
  134. R. Dieng-Kuntz.
    Corporate Semantic Webs.
    In David Schwartz, editor, Encyclopedia of Knowledge Management. Idea Publishing, 2005, to appear
  135. Andreas Doms and Michael Schroeder.
    GoPubMed: Exploring PubMed with the GeneOntology.
    Nucleic Acid Research, Web Server Issue, 2005
  136. Albert Burger, Duncan Davidson, and Richard Baldock.
    Formalization of mouse embryo anatomy.
    Bioinformatics, 20(2):259--67, 2004
  137. Albert Burger, Duncan Davidson, Yiya Yang, and Richard Baldock.
    Integrating partonomic hierarchies in anatomy ontologies.
    BMC Bioinformatics, 5(184), 2004
  138. Panos Dafas, Alexander Kozlenkov, Alan Robinson, and Michael Schroeder.
    Integrating gene expression data, protein interaction data, and ontology-based literature search.
    In Werner Dubitzky and Francisco Azuaje, editors, Artificial Intelligence and Systems Biology, pages 107--126. Springer, 2004
  139. B Habermann.
    The BAR-domain family of proteins: a case of bending and binding?.
    EMBO Rep., 5:250--5, 2004
  140. B Habermann, AG Bebin, S Herklotz, M Volkmer, K Eckelt, K Pehlke, HH Epperlein, HK Schackert, and EM Tanaka G Wiebe and.
    An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries.
    Genome Biol., 5(9), 2004
  141. A Henschel, F Buchholz, and B Habermann.
    DEQOR: a web-based tool for the design and quality control of siRNAs.
    Nucleic Acids Res, 32:W113--20, 2004
  142. Konstantinos Karasavvas, Richard Baldock, and Albert Burger.
    Criticality-Based Task Composition in Distributed Bioinformatics Systems.
    In 12th International Conference on Intelligent Systems for Molecular Biology, 2004, short paper: published on-line: www.iscb.org/ismbeccb2004/accepted_papers.html
  143. Alexander Kozlenkov and Michael Schroeder.
    PROVA: Rule-based Java-Scripting for a Bioinformatics Semantic Web.
    In E. Rahm, editor, International Workshop on Data Integration in the Life Sciences DILS, Leipzig, Germany, 2004. Springer
  144. Helen Parkinson, Stuart Aitken, Richard A. Baldock, Jonathan B.L. Bard, Albert Burger, Terry F. Hayamizu, Alan Rector, Martin Ringwald, Jeremy Rogers, Cornelius Rosse, Christian J. Stoeckert, and Duncan Davidson.
    The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data.
    Comparative and Functional Genomics, 5:521--7, 2004
  145. RD Stevens, HJ Tipney, CJ Wroe, TM Oinn, M Senger, PW Lord, CA Goble, A Brass, and M Tassabehji.
    Exploring Williams Beuren Syndrome Using myGrid.
    Bioinformatics, 20:i303--310, 2004, Intelligent Systems for Molecular Biology (ISMB) 2004
  146. Olivier Corby, Rose Dieng-Kuntz, and Catherine Faron-Zucker.
    Querying the Semantic Web with the CORESE search engine.
    In Lopez de Mantaras and L. Saitta, editors, Proc. of PAIS2004 at 16th European Conference on Artificial Intelligence (ECAI'2004), pages 705--709. IOS Press, 2003
  147. Patty Kostkova, Gemma Madle, Julius R. Weinberg, and Jane Mani-Saada.
    Agent-Based Up-to-date Data Management in National electronic Library for Communicable Disease.
    In J. Nealon and T. Moreno Ed, editors, Applications of intelligent agents in health care, pages 103--122. Whitestein Series in Software Agent Technologies, 2003
  148. Patty Kostkova, Jane Mani-Saada, Julius R Weinberg, and Gemma Madle.
    Knowledge Management and Communities of Practice around Healthcare Digital Libraries.
    In I Rudomin, J Vazquez-Salceda, and J L Diaz de Leon Santiago, editors, e-health: Application of Computing Science in Medicine and Health Care, volume 5, pages 86--99. Research on Computing Science, 2003
  149. G Madle, P Kostkova, J Mani-Saada, and JR Weinberg.
    Evaluating the changes in knowledge and attitudes of digital library users.
    In T. Koch and I.T. Solvberg, editors, Proc. of 7th European Conference on Digital Libraries, volume 2769 of Lecture Notes In Computer Science, pages 29--40. Springer-Verlag, 2003
  150. C Wroe, R Stevens, C Goble, A Roberts, and M Greenwood.
    A suite of DAML+OIL ontologies to describe bioinformatics web services and data..
    International Journal of Cooperative Information Systems, 12(2):197--224, 2003
  151. O Corby, R Dieng, and C Hebert.
    A Conceptual Graph Model for W3C Resource Description Framework.
    In Bernhard Ganter and Guy W. Mineau, editors, Conceptual Structures: Logical, Linguistic, and Computational Issues, 8th International Conference on Conceptual Structures, ICCS 2000, volume 1867 of Lecture Notes in Computer Science. Springer, 2000
  152. J. Rogers and A. Rector.
    GALEN's Model of Parts and Wholes: Experience and Comparisons.
    In Proc. of AMIA Annual Symposium 2000, 2000
  153. A Roy, P Kostkova, E Carson, and M Catchpole.
    Web-based provision of information on infectious diseases: a systems study.
    Health Informatics Journal

 
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