James Malone

James Malone, Robert Stevens: Measuring the level of activity in community built bio-ontologies. Journal of Biomedical Informatics 46(1): 5-14 (2013)

Gabriella Rustici, Nikolay Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Jon Ison, Maria Keays, Natalja Kurbatova, James Malone, Roby Mani, Annalisa Mupo, Rui Pedro Pereira, Ekaterina Pilicheva, Johan Rung, Anjan Sharma, Y. Amy Tang, Tobias Ternent, Andrew Tikhonov, Danielle Welter, Eleanor Williams, Alvis Brazma, Helen E. Parkinson, Ugis Sarkans: ArrayExpress update - trends in database growth and links to data analysis tools. Nucleic Acids Research 41(Database-Issue): 987-990 (2013)

Helena F. Deus, Eric Prud'hommeaux, Michael Miller, Jun Zhao, James Malone, Tomasz Adamusiak, Jim McCusker, Sudeshna Das, Philippe Rocca-Serra, Ronan Fox, M. Scott Marshall: Translating standards into practice - One Semantic Web API for Gene Expression. Journal of Biomedical Informatics 45(4): 782-794 (2012)

Misha Kapushesky, Tomasz Adamusiak, Tony Burdett, Aedín C. Culhane, Anna Farne, Alexey Filippov, Ele Holloway, Andrey Klebanov, Nataliya Kryvych, Natalja Kurbatova, Pavel Kurnosov, James Malone, Olga Melnichuk, Robert Petryszak, Nikolay Pultsin, Gabriella Rustici, Andrew Tikhonov, Ravensara S. Travillian, Eleanor Williams, Andrey Zorin, Helen E. Parkinson, Alvis Brazma: Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments. Nucleic Acids Research 40(Database-Issue): 1077-1081 (2012)

Maria Copeland, Andy Brown, Helen E. Parkinson, Robert Stevens, James Malone: The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies. ICBO 2012

Simon Jupp, Andrew Gibson, James Malone, Robert Stevens: Taking a view on bio-ontologies. ICBO 2012

Simon Jupp, Helen E. Parkinson, James Malone: Semantic Web Atlas: Putting Gene Expression Data into Biological Context. SWAT4LS 2012

Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, Alan Ruttenberg: MIREOT: The minimum information to reference an external ontology term. Applied Ontology 6(1): 23-33 (2011)

Helen E. Parkinson, Ugis Sarkans, Nikolay Kolesnikov, Niran Abeygunawardena, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Ele Holloway, Natalja Kurbatova, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Gabriella Rustici, Anjan Sharma, Eleanor Williams, Tomasz Adamusiak, Marco Brandizi, Nataliya Sklyar, Alvis Brazma: ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Research 39(Database-Issue): 1002-1004 (2011)

Chao Pang, Tomasz Adamusiak, Helen E. Parkinson, James Malone: Rapid Development of an Ontology of Coriell Cell Lines. ICBO 2011

Sirarat Sarntivijai, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Brian D. Athey, Yongqun He: Cell Line Ontology: Redesigning the Cell Line Knowledgebase to Aid Integrative Translational Informatics. ICBO 2011

Ravensara S. Travillian, James Malone, Chao Pang, John M. Hancock, Peter W. H. Holland, Paul N. Schofield, Helen E. Parkinson: The Vertebrate Bridging Ontology (VBO). ICBO 2011

Helena F. Deus, Jun Zhao, Jim McCusker, Ronan Fox, Eric Prud'hommeaux, James Malone, Sudeshna Das, Michael Miller, Tomasz Adamusiak, Philippe Rocca-Serra, M. Scott Marshall: Translating standards into practice: one semantic web API for gene expression. SWAT4LS 2011: 6-7

James Malone, Ele Holloway, Tomasz Adamusiak, Misha Kapushesky, Jie Zheng, Nikolay Kolesnikov, Anna Zhukova, Alvis Brazma, Helen E. Parkinson: Modeling sample variables with an Experimental Factor Ontology. Bioinformatics 26(8): 1112-1118 (2010)

Misha Kapushesky, Ibrahim Emam, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen E. Parkinson, Alvis Brazma: Gene Expression Atlas at the European Bioinformatics Institute. Nucleic Acids Research 38(Database-Issue): 690-698 (2010)

Tim F. Rayner, Faisal Ibne Rezwan, Margus Lukk, Xiangqun Zheng Bradley, Anna Farne, Ele Holloway, James Malone, Eleanor Williams, Helen E. Parkinson: MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB. Bioinformatics 25(2): 279-280 (2009)

Helen E. Parkinson, Misha Kapushesky, Nikolay Kolesnikov, Gabriella Rustici, Mohammadreza Shojatalab, Niran Abeygunawardena, Hugo Berube, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Ele Holloway, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Tim F. Rayner, Faisal Ibne Rezwan, Anjan Sharma, Eleanor Williams, Xiangqun Zheng Bradley, Tomasz Adamusiak, Marco Brandizi, Tony Burdett, Richard Coulson, Maria Krestyaninova, Pavel Kurnosov, Eamonn Maguire, Sudeshna Guha Neogi, Philippe Rocca-Serra, Susanna-Assunta Sansone, Nataliya Sklyar, Mengyao Zhao, Ugis Sarkans, Alvis Brazma: ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Research 37(Database-Issue): 868-872 (2009)

James Malone, Tomasz Adamusiak, Ele Holloway, Misha Kapushesky, Helen E. Parkinson: Developing an Ontology from the Application Up. OWLED 2009

Mélanie Courtot, William J. Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, Alan Ruttenberg: The OWL of Biomedical Investigations. OWLED 2008

James Malone: Soft Computing in Bioinformatics: Genomic and Proteomic Applications. Soft Computing Applications in Industry 2008: 135-150

Mukesh Doble, William Loging, James Malone, Vincent Shin-Mu Tseng (Eds.): International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics, BCBGC-08, Orlando, Florida, USA , July 7-10, 2008. ISRST 2008, isbn 978-1-60651-002-5

James Malone, Kenneth McGarry, Chris Bowerman: Automated trend analysis of proteomics data using an intelligent data mining architecture. Expert Syst. Appl. 30(1): 24-33 (2006)

James Malone, Kenneth McGarry, Stefan Wermter, Chris Bowerman: Data mining using rule extraction from Kohonen self-organising maps. Neural Computing and Applications 15(1): 9-17 (2006)

Gayathri Nadarajan, Yun-Heh Chen-Burger, James Malone: Semantic Grid Services for Video Analysis. IAT Workshops 2006: 121-124

Gayathri Nadarajan, Chuanjiang Yi, Yun-Heh Chen-Burger, Hai Jin, James Malone, Chengwei Wang: Dynamic Access Control Prediction for Ordered Service Sequence in Grid Environment. Web Intelligence 2006: 145-151