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• Conference paper
  Stougiannis A, Tauheed F, Heinis T, Ailamaki Aet al., 2013,

  Accelerating spatial range queries

  , Pages: 713-716
  • Publisher Web Link
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• Conference paper
  Tauheed F, Nobari S, Biveinis L, Heinis T, Ailamaki Aet al., 2013,

  Computational Neuroscience Breakthroughs through Innovative Data Management

  , Pages: 14-27
  • Publisher Web Link
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• Journal article
  Dalby AR, Emam I, Franke R, 2012,

  Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level

  , PLOS ONE, Vol: 7, ISSN: 1932-6203
  • Author Web Link
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  • Citations: 1
• Journal article
  Yang X, Han R, Guo Y, Bradley J, Cox B, Dickinson R, Kitney Ret al., 2012,

  Modelling and performance analysis of clinical pathways using the stochastic process algebra PEPA

  , Bmc Bioinformatics, Vol: 13, ISSN: 1471-2105
  • Publisher Web Link
  • Open Access Link
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• Conference paper
  Holehouse A, Yang X, Adcock I, Guo Yet al., 2012,

  Developing a novel integrated model of p38 MAPK and glucocorticoid signalling pathways

  , Pages: 69-76
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• Journal article
  Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma Aet al., 2011,

  ArrayExpress update-an archive of microarray and high-throughput sequencing-based functional genomics experiments

  , NUCLEIC ACIDS RESEARCH, Vol: 39, Pages: D1002-D1004, ISSN: 0305-1048
  • Author Web Link
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  • Citations: 241
• Journal article
  Huntley DM, Pandis I, Butcher SA, Ackers JPet al., 2010,

  Bioinformatic analysis of <i>Entamoeba histolytica</i> SINE1 elements

  , BMC GENOMICS, Vol: 11, ISSN: 1471-2164
  • Author Web Link
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  • Citations: 11
• Journal article
  Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma Aet al., 2010,

  Gene Expression Atlas at the European Bioinformatics Institute

  , NUCLEIC ACIDS RESEARCH, Vol: 38, Pages: D690-D698, ISSN: 0305-1048
  • Author Web Link
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  • Citations: 163
• Journal article
  Curcin V, Ghanem M, Guo Y, 2010,

  Polymorphic type framework for scientific workflows with relational data model

  , International Journal of Business Process Integration and Management, Vol: 5, Pages: 45+-45+, ISSN: 1741-8763
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• Journal article
  Curcin V, Ghanem M, Guo Y, 2010,

  The design and implementation of a workflow analysis tool

  , Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol: 368, Pages: 4193-4208
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• Journal article
  Wang FZ, Helian N, Wu S, Guo Y, Deng DY, Meng L, Zhang W, Crowcroft J, Bacon J, Parker MAet al., 2009,

  Eight Times Acceleration of Geospatial Data Archiving and Distribution on the Grids (vol 47, pg 1444, 2009)

  , IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING, Vol: 47, Pages: 2988-2988, ISSN: 0196-2892
  • Author Web Link
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• Journal article
  Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone S-A, Sklyar N, Zhao M, Sarkans U, Brazma Aet al., 2009,

  ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression

  , NUCLEIC ACIDS RESEARCH, Vol: 37, Pages: D868-D872, ISSN: 0305-1048
  • Author Web Link
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  • Citations: 313
• Journal article
  Curcin V, Ghanem M, Guo Y, 2009,

  Analysing scientific workflows with Computational Tree Logic. Journal of Cluster Computing

  , Journal of Cluster Computing: Special Issue of Recent Advances in e-Science, ISSN: 1386-7857

  Motivated by the widespread use of workflow systems in e-Science applications, this article introduces a formal analysis framework for the verification and profiling of the control flow aspects of scientific workflows. The framework relies on process algebras that characterise each workflow component with a process behaviour, which is then used to build a CTL state model that can be reasoned about. We demonstrate the benefits of the approach by modelling the control flow behaviour of the Discovery Net system, one of the earliest workflow-based e-Science systems, and present how some key properties of workflows and individual service utilisation can be queried at design time. Our approach is generic and can be applied easily to modelling workflows developed in any other system. It also provides a formal basis for the comparison of control aspects of e-Science workflow systems and a design method for future systems.

  • Abstract
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• Conference paper
  Curcin V, Ghanem M, Guo Y, Darlington Jet al., 2008,

  Mining adverse drug reactions with e-science workflows.

  , Proceedings of the 4th Cairo International Biomedical Engineering Conference, 2008. CIBEC 2008
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• Book chapter
  Ghanem M, Curcin V, Wendel P, Guo Yet al., 2008,

  Building and using analytical workflows in Discovery Net

  , Data Mining Techniques in Grid Environments. Dubitzky, Werner (Ed)., Publisher: Wiley-Blackwell, Pages: 119-140, ISBN: 9780470512586

  The Discovery Net platform is built around a workflow model for integrating distributed data sources and analytical tools. The platform was originally designed to support the design and execution of distributed data mining tasks within a grid-based environment. However, over the years it has evolved into a generic data analysis platform with applications in such diverse areas as bioinformatics, cheminformatics, text mining and business intelligence. In this work we present our experience in designing the platform and map out the evolution paths for a workflow language, and its architecture, that need to address the requirements of different scientific domains.

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