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j43Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLAnika Oellrich, Terrence F. Meehan, Helen E. Parkinson, Sirarat Sarntivijai, Jacqueline K. White, Natasha A. Karp: Reporting phenotypes in mouse models when considering body size as a potential confounder. J. Biomedical Semantics 7: 2 (2016)
j42Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSirarat Sarntivijai, Drashtti Vasant, Simon Jupp, Gary Saunders, A. Patrícia Bento, Daniel Gonzalez, Joanna Betts, Samiul Hasan, Gautier Koscielny, Ian Dunham, Helen E. Parkinson, James Malone: Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. J. Biomedical Semantics 7: 8 (2016)
j41Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSimon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen E. Parkinson, James Malone: Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates. J. Biomedical Semantics 7: 17 (2016)
j40Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSimon Jupp, James Malone, Tony Burdett, Jean-Karim Hériché, Eleanor Williams, Jan Ellenberg, Helen E. Parkinson, Gabriella Rustici: The cellular microscopy phenotype ontology. J. Biomedical Semantics 7: 28 (2016)
j39Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSolomon Adebayo, Kenneth McLeod, Ilinca Tudose, David Osumi-Sutherland, Tony Burdett, Richard A. Baldock, Albert Burger, Helen E. Parkinson: PhenoImageShare: an image annotation and query infrastructure. J. Biomedical Semantics 7: 35 (2016)
j38Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLJon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak: Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research 44(Database-Issue): 38-47 (2016)
j37Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRobert Petryszak, Maria Keays, Y. Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Simon Jupp, Satu Koskinen, Oliver Mannion, Laura Huerta, Karine Megy, Catherine Snow, Eleanor Williams, Mitra Barzine, Emma Hastings, Hendrik Weisser, James Wright, Pankaj Jaiswal, Wolfgang Huber, Jyoti Choudhary, Helen E. Parkinson, Alvis Brazma: Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Research 44(Database-Issue): 746-752 (2016)
j36Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLMarcela K. Tello-Ruiz, Joshua C. Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule, Justin Elser, Bo Wang, James Thomason, Daniel M. Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A. Fonseca, Laura Huerta, Maria Keays, Y. Amy Tang, Helen E. Parkinson, Antonio Fabregat, Sheldon J. McKay, Joel Weiser, Peter D'Eustachio, Lincoln Stein, Robert Petryszak, Paul J. Kersey, Pankaj Jaiswal, Doreen Ware: Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Research 44(Database-Issue): 1133-1140 (2016)
j35Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLJames Malone, Robert Stevens, Simon Jupp, Tom Hancocks, Helen E. Parkinson, Catherine Brooksbank: Ten Simple Rules for Selecting a Bio-ontology. PLoS Computational Biology 12(2) (2016)
c16Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLOlga Vrousgou, Tony Burdett, Helen E. Parkinson, Simon Jupp: Biomedical Ontology Evolution in the EMBL-EBI Ontology Lookup Service. EDBT/ICDT Workshops 2016
c15Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSenay Kafkas, Ian Dunham, Helen E. Parkinson, Johanna R. McEntyre: Use of Text Mining for Experimental Factor Ontology Coverage Expansion in the Scope of Target Validation. ICBO/BioCreative 2016
c14Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLMélanie Courtot, Alex L. Mitchell, Maxim Scheremetjew, Janet Piñero, Laura I. Furlong, Robert D. Finn, Helen E. Parkinson: Slim-o-matic: a Semi-Automated Way to Generate Gene Ontology Slims. SWAT4LS 2016
2015
j34Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLWarren A. Kibbe, Cesar Arze, Victor Felix, Elvira Mitraka, Evan Bolton, Gang Fu, Christopher J. Mungall, Janos X. Binder, James Malone, Drashtti Vasant, Helen E. Parkinson, Lynn M. Schriml: Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Research 43(Database-Issue): 1071-1078 (2015)
j33Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLNikolay Kolesnikov, Emma Hastings, Maria Keays, Olga Melnichuk, Y. Amy Tang, Eleanor Williams, Miroslaw Dylag, Natalja Kurbatova, Marco Brandizi, Tony Burdett, Karyn Megy, Ekaterina Pilicheva, Gabriella Rustici, Andrew Tikhonov, Helen E. Parkinson, Robert Petryszak, Ugis Sarkans, Alvis Brazma: ArrayExpress update - simplifying data submissions. Nucleic Acids Research 43(Database-Issue): 1113-1116 (2015)
c13Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDavid Osumi-Sutherland, Enrico Ponta, Mélanie Courtot, Helen E. Parkinson, Laura Badi: Cell, Chemical and Anatomical Views of the Gene Ontology: Mapping to a Roche Controlled Vocabulary. SWAT4LS 2015: 84-93
c12Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSimon Jupp, Tony Burdett, Catherine Leroy, Helen E. Parkinson: A new Ontology Lookup Service at EMBL-EBI. SWAT4LS 2015: 118-119
c11Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSimon Jupp, Danielle Welter, Tony Burdett, Helen E. Parkinson, James Malone: Collaborative Ontology Development Using the Webulous Architecture and Google App. SWAT4LS 2015: 120-121
2014
j32Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSimon Jupp, James Malone, Jerven T. Bolleman, Marco Brandizi, Mark Davies, Leyla J. Garcia, Anna Gaulton, Sebastien Gehant, Camille Laibe, Nicole Redaschi, Sarala M. Wimalaratne, Maria Jesus Martin, Nicolas Le Novère, Helen E. Parkinson, Ewan Birney, Andrew M. Jenkinson: The EBI RDF platform: linked open data for the life sciences. Bioinformatics 30(9): 1338-1339 (2014)
j31Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLJames Malone, Andy Brown, Allyson L. Lister, Jon C. Ison, Duncan Hull, Helen E. Parkinson, Robert Stevens: The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. J. Biomedical Semantics 5: 25 (2014)
j30Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma D. Vempati, Stephan C. Schürer, Chao Pang, James Malone, Helen E. Parkinson, Yue Liu, Terue Takatsuki, Kaoru Saijo, Hiroshi Masuya, Yukio Nakamura, Matthew H. Brush, Melissa Haendel, Jie Zheng, Christian J. Stoeckert Jr., Bjoern Peters, Christopher J. Mungall, Thomas E. Carey, David J. States, Brian D. Athey, Yongqun He: CLO: The cell line ontology. J. Biomedical Semantics 5: 37 (2014)
j29Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLAdam Faulconbridge, Tony Burdett, Marco Brandizi, Mikhail Gostev, Rui Pedro Pereira, Drashtti Vasant, Ugis Sarkans, Alvis Brazma, Helen E. Parkinson: Updates to BioSamples database at European Bioinformatics Institute. Nucleic Acids Research 42(Database-Issue): 50-52 (2014)
j28Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLGautier Koscielny, Gagarine Yaikhom, Vivek Iyer, Terrence F. Meehan, Hugh Morgan, Julian Atienza-Herrero, Andrew Blake, Chao-Kung Chen, Richard Easty, Armida Di Fenza, Tanja Fiegel, Mark Grifiths, Alan Horne, Natasha A. Karp, Natalja Kurbatova, Jeremy C. Mason, Peter Matthews, Darren J. Oakley, Asfand Qazi, Jack Regnart, Ahmad Retha, Luis A. Santos, Duncan J. Sneddon, Jonathan Warren, Henrik Westerberg, Robert J. Wilson, David G. Melvin, Damian Smedley, Steve D. M. Brown, Paul Flicek, William C. Skarnes, Ann-Marie Mallon, Helen E. Parkinson: The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Research 42(Database-Issue): 802-809 (2014)
j27Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRobert Petryszak, Tony Burdett, Benedetto Fiorelli, Nuno A. Fonseca, Mar Gonzalez-Porta, Emma Hastings, Wolfgang Huber, Simon Jupp, Maria Keays, Nataliya Kryvych, Julie McMurry, John C. Marioni, James Malone, Karine Megy, Gabriella Rustici, Y. Amy Tang, Jan Taubert, Eleanor Williams, Oliver Mannion, Helen E. Parkinson, Alvis Brazma: Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Research 42(Database-Issue): 926-932 (2014)
j26Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDanielle Welter, Jacqueline A. L. MacArthur, Joannella Morales, Tony Burdett, Peggy Hall, Heather Junkins, Alan Klemm, Paul Flicek, Teri Manolio, Lucia Hindorff, Helen E. Parkinson: The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Research 42(Database-Issue): 1001-1006 (2014)
2013
j25Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLGabriella Rustici, Nikolay Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Jon C. 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)
c10Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLJames Malone, Tony Burdett, Jon C. Ison, Simon Jupp, Drashtti Vasant, Danielle Welter, Helen E. Parkinson: Putting OWL into Production at the European Bioinformatics Institute. OWLED 2013
2012
j24Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLVincent Xue, Tony Burdett, Margus Lukk, Julie Taylor, Alvis Brazma, Helen E. Parkinson: MageComet - web application for harmonizing existing large-scale experiment descriptions. Bioinformatics 28(10): 1402-1403 (2012)
j23Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLMikhail Gostev, Adam Faulconbridge, Marco Brandizi, Julio Fernandez-Banet, Ugis Sarkans, Alvis Brazma, Helen E. Parkinson: The BioSample Database (BioSD) at the European Bioinformatics Institute. Nucleic Acids Research 40(Database-Issue): 64-70 (2012)
j22Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLMisha 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)
c9Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLMaria 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
c8Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLDanielle Welter, Tony Burdett, Lucia Hindorff, Heather Junkins, Jackie MacArthur, Helen E. Parkinson: GOCI: An Ontology-Driven Search and Curation Infrastructure for the NHGRI GWAS Catalog. ICBO 2012
c7Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSimon Jupp, Helen E. Parkinson, James Malone: Semantic Web Atlas: Putting Gene Expression Data into Biological Context. SWAT4LS 2012
c6Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSören Auer, Theodore Dalamagas, Helen E. Parkinson, François Bancilhon, Giorgos Flouris, Dimitris Sacharidis, Peter Buneman, Dimitris Kotzinos, Yannis Stavrakas, Vassilis Christophides, George Papastefanatos, Kostas Thiveos: Diachronic linked data: towards long-term preservation of structured interrelated information. WOD 2012: 31-39
2011
j21Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRavensara S. Travillian, Tomasz Adamusiak, Tony Burdett, Michael Gruenberger, John M. Hancock, Ann-Marie Mallon, James Malone, Paul N. Schofield, Helen E. Parkinson: Anatomy ontologies and potential users: bridging the gap. J. Biomedical Semantics 2(S-4): S3 (2011)
j20Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLTomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K. Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen E. Parkinson, Morris A. Swertz: OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript. BMC Bioinformatics 12: 218 (2011)
j19Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLHelen 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)
c5Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLChao Pang, Tomasz Adamusiak, Helen E. Parkinson, James Malone: Rapid Development of an Ontology of Coriell Cell Lines. ICBO 2011
c4Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLSirarat 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
c3Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRavensara 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
2010
j18Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLJames 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)
j17Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRavi Shankar, Helen E. Parkinson, Tony Burdett, Emma Hastings, Junmin Liu, Michael Miller, Rashmi Srinivasa, Joseph White, Alvis Brazma, Gavin Sherlock, Christian J. Stoeckert Jr., Catherine A. Ball: Annotare - a tool for annotating high-throughput biomedical investigations and resulting data. Bioinformatics 26(19): 2470-2471 (2010)
j16Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLRyan R. Brinkman, Mélanie Courtot, Dirk Derom, Jennifer Fostel, Yongqun He, Phillip W. Lord, James Malone, Helen E. Parkinson, Björn Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Larisa N. Soldatova, Christian J. Stoeckert Jr., Jessica A. Turner, Jie Zheng, et al.: Modeling biomedical experimental processes with OBI. J. Biomedical Semantics 1(S-1): S7 (2010)
j15Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLMorris A. Swertz, Martijn Dijkstra, Tomasz Adamusiak, K. Joeri van der Velde, Alexandros Kanterakis, Erik T. Roos, Joris Lops, Gudmundur A. Thorisson, Danny Arends, George Byelas, Juha Muilu, Anthony J. Brookes, Engbert O. de Brock, Ritsert C. Jansen, Helen E. Parkinson: The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. BMC Bioinformatics 11(S-12): S12 (2010)
j14Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLMisha 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)
2009
j13Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLTim 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)
j12Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLAudrey Kauffmann, Tim F. Rayner, Helen E. Parkinson, Misha Kapushesky, Margus Lukk, Alvis Brazma, Wolfgang Huber: Importing ArrayExpress datasets into R/Bioconductor. Bioinformatics 25(16): 2092-2094 (2009)
j11Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLHelen E. Parkinson, Misha Kapushesky, Nikolay Kolesnikov, Gabriella Rustici, Mohammadreza Shojatalab, Niran Abeygunawardena, Hugo Bérubé, 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)
c2Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLJames Malone, Tomasz Adamusiak, Ele Holloway, Misha Kapushesky, Helen E. Parkinson: Developing an Ontology from the Application Up. OWLED 2009
2007
j10Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLHelen E. Parkinson, Misha Kapushesky, Mohammadreza Shojatalab, Niran Abeygunawardena, Richard Coulson, Anna Farne, Ele Holloway, N. Kolesnykov, P. Lilja, Margus Lukk, Roby Mani, Tim F. Rayner, Anjan Sharma, E. William, Ugis Sarkans, Alvis Brazma: ArrayExpress - a public database of microarray experiments and gene expression profiles. Nucleic Acids Research 35(Database-Issue): 747-750 (2007)
2006
j9Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLPatricia L. Whetzel, Helen E. Parkinson, Helen C. Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Laurence Game, Mervi Heiskanen, Norman Morrison, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris F. Taylor, Joseph White, Christian J. Stoeckert Jr.: The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22(7): 866-873 (2006)
j8Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLTim F. Rayner, Philippe Rocca-Serra, Paul T. Spellman, Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert Jr., Joseph White, Patricia L. Whetzel, Farrell Wymore, Helen E. Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brazma: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7: 489 (2006)
2005
j7Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLUgis Sarkans, Helen E. Parkinson, Gonzalo Garcia Lara, Ahmet Oezcimen, Anjan Sharma, Niran Abeygunawardena, Sergio Contrino, Ele Holloway, Philippe Rocca-Serra, Gaurab Mukherjee, Mohammadreza Shojatalab, Misha Kapushesky, Susanna-Assunta Sansone, Anna Farne, Tim F. Rayner, Alvis Brazma: The ArrayExpress gene expression database: a software engineering and implementation perspective. Bioinformatics 21(8): 1495-1501 (2005)
j6Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLHelen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Niran Abeygunawardena, Sergio Contrino, Richard Coulson, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Misha Kapushesky, P. Lilja, Gaurab Mukherjee, Ahmet Oezcimen, Tim F. Rayner, Philippe Rocca-Serra, Anjan Sharma, Susanna-Assunta Sansone, Alvis Brazma: ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Research 33(Database-Issue): 553-555 (2005)
c1Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLKevin L. Garwood, Phillip W. Lord, Helen E. Parkinson, Norman W. Paton, Carole A. Goble: Pedro Ontology Services: A Framework for Rapid Ontology Markup. ESWC 2005: 578-591
2003
j5Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLCatherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola J. Mulder, Claire O'Donovan, Helen E. Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron: The European Bioinformatics Institute's data resources. Nucleic Acids Research 31(1): 43-50 (2003)
j4Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLAlvis Brazma, Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Jaak Vilo, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Philippe Rocca-Serra, Susanna-Assunta Sansone: ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Research 31(1): 68-71 (2003)
2002
j3Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLVincent Lombard, E. B. Camon, Helen E. Parkinson, Pascal Hingamp, Guenter Stoesser, Nicole Redaschi: EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database. Bioinformatics 18(5): 763-764 (2002)
j2Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLCatherine A. Ball, Gavin Sherlock, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald Taylor, Alvis Brazma, John Quackenbush: An open letter to the scientific journals. Bioinformatics 18(11): 1409 (2002)
2001
j1Electronic Edition pubzone.org CiteSeerX Google scholar BibTeX bibliographical record in XMLGuenter Stoesser, Wendy Baker, Alexandra van den Broek, Evelyn Camon, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Vincent Lombard, Rodrigo Lopez, Helen E. Parkinson, Nicole Redaschi, Peter Sterk, Peter Stoehr, Mary Ann Tuli: The EMBL nucleotide sequence database. Nucleic Acids Research 29(1): 17-21 (2001)

Coauthor Index

1Niran Abeygunawardena[j20] [j19] [j11] [j10] [j7] [j6] [j4]
2Tomasz Adamusiak[j22] [j21] [j20] [j19] [c5] [j18] [j15] [j11] [c2]
3Solomon Adebayo[j39]
4et al.[j16]
5Vindhya Amarasinghe[j36]
6Christian Anthon[j38]
7Despoina Antonakaki[j20]
8Rolf Apweiler[j5]
9Danny Arends[j15]
10Cesar Arze[j34]
11Brian D. Athey[j30] [c4]
12Julian Atienza-Herrero[j28]
13Sören Auer[c6]
14Laura Badi[c13]
15Wendy Baker[j1]
16Richard A. Baldock[j39]
17Catherine A. Ball[j17] [j8] [j2]
18François Bancilhon[c6]
19Elisabet Barrera[j37]
20Mitra Barzine[j37]
21Niall Beard[j38]
22A. Patrícia Bento[j42]
23Karel Berka[j38]
24Hugo Bérubé[j11]
25Joanna Betts[j42]
26Janos X. Binder[j34]
27Ewan Birney[j32] [j5]
28Andrew Blake 0003[j28]
29Jerven T. Bolleman[j32]
30Dan M. Bolser
Daniel M. Bolser
[j38] [j36]
31Evan Bolton[j34]
32Tim Booth[j38]
33Xiangqun Zheng Bradley[j13] [j11]
34Marco Brandizi[j33] [j32] [j29] [j25] [j23] [j19] [j11]
35Alvis Brazma[j37] [j33] [j29] [j27] [j25] [j24] [j23] [j22] [j19] [j18] [j17] [j14] [j12] [j11] [j10] [j8] [j7] [j6] [j5] [j4] [j2]
36Anthony Bretaudeau[j38]
37Jan Brezovsky[j38]
38Ryan R. Brinkman[j16]
39Engbert O. de Brock[j15]
40Alexandra van den Broek[j1]
41Anthony J. Brookes[j15]
42Catherine Brooksbank[j35] [j5] [j2]
43Andy Brown[j31] [c9]
44Steve D. M. Brown[j28]
45Søren Brunak[j38]
46Matthew H. Brush[j30]
47Peter Buneman[c6]
48Tony Burdett[j41] [j40] [j39] [j37] [c16] [j33] [c12] [c11] [j29] [j27] [j26] [j25] [c10] [j24] [j22] [c8] [j21] [j20] [j19] [j17] [j11]
49Albert Burger[j39]
50George Byelas[j15]
51Graham Cameron[j5]
52E. B. Camon[j3]
53Evelyn Camon[j5] [j1]
54Thomas E. Carey[j30]
55Rita Casadio[j38]
56Helen C. Causton[j9] [j8] [j2]
57Duccio Cavalieri[j2]
58Gianni Cesareni[j38]
59Chao-Kung Chen[j28]
60Piotr Chmura[j38]
61Jyoti Choudhary[j37]
62Kapeel Chougule[j36]
63Vassilis Christophides[c6]
64Sergio Contrino[j7] [j6]
65Maria Copeland[c9]
66Frederik Coppens[j38]
67Michael Cornell[j38]
68Richard M. R. Coulson
Richard Coulson
[j11] [j10] [j6]
69Mélanie Courtot[c14] [c13] [j16]
70Gianmauro Cuccuru[j38]
71Aedín C. Culhane[j22]
72Theodore Dalamagas[c6]
73Kristian Davidsen[j38]
74Mark Davies[j32]
75Dirk Derom[j16]
76Peter D'Eustachio[j36]
77Palitha Dharmawardhana[j36]
78Alexander D. Diehl[j30] [c4]
79Martijn Dijkstra[j15]
80Tunca Dogan[j38]
81Olivia Doppelt-Azeroual[j38]
82Ian Dunham[j42] [c15]
83Miroslaw Dylag[j33] [j25] [j19] [j11]
84Richard Easty[j28]
85Jan Ellenberg[j40]
86Justin Elser[j36]
87Ibrahim Emam[j25] [j19] [j14] [j11]
88Laura Emery[j38]
89Antonio Fabregat[j36]
90Liju Fan[j9]
91Anna Farne[j25] [j22] [j19] [j13] [j11] [j10] [j8] [j7] [j6]
92Adam Faulconbridge[j29] [j23]
93Victor Felix[j34]
94Armida Di Fenza[j28]
95Julio Fernandez-Banet[j23]
96Tanja Fiegel[j28]
97Alexey Filippov[j22]
98Robert D. Finn[c14]
99Benedetto Fiorelli[j27]
100Paul Flicek[j28] [j26]
101Giorgos Flouris[c6]
102Nuno A. Fonseca[j37] [j36] [j27]
103Jennifer Fostel[j16] [j9]
104Gilberto Fragoso[j9]
105Rune Møllegaard Friborg[j38]
106Gang Fu[j34]
107Alfonso Muñoz-Pomer Fuentes[j37]
108Anja Füllgrabe[j37]
109Laura Inés Furlong
Laura I. Furlong
[c14]
110Terry Gaasterland[j2]
111Laurence Game[j9]
112Leyla Jael García-Castro
Leyla J. Garcia
[j32]
113Maria Garcia-Pastor[j1]
114Kevin L. Garwood[c1]
115Elisabeth Gasteiger[j38]
116Thomas Gatter[j38]
117Anna Gaulton[j32]
118Sebastien Gehant[j32]
119Carole A. Goble[c1]
120Tatyana Goldberg[j38]
121Daniel Gonzalez[j42]
122Mar Gonzalez-Porta[j27]
123Mikhail Gostev[j29] [j23]
124Mark Grifiths[j28]
125Marie Grosjean[j38]
126Michael Gruenberger[j21]
127Björn A. Grüning[j38]
128Melissa Haendel[j30]
129Peggy Hall[j26]
130John M. Hancock[j21] [c3]
131Tom Hancocks[j35]
132Midori A. Harris[j5]
133Samiul Hasan[j42]
134Emma Hastings[j37] [j33] [j27] [j25] [j19] [j17]
135Yongqun He[j30] [c4] [j16]
136Mervi Heiskanen[j9]
137Manuela Helmer-Citterich[j38]
138Kim Henrick[j5]
139Jean-Karim Hériché[j40]
140Lucia Hindorff[j26] [c8]
141Pascal Hingamp[j3] [j2]
142Peter W. H. Holland[c3]
143Ele Holloway[j22] [j19] [j18] [j14] [j13] [j11] [c2] [j10] [j8] [j7] [j6] [j4]
144Frank Holstege[j2]
145Alan Horne[j28]
146Wolfgang Huber[j37] [j27] [j12]
147Laura Huerta[j37] [j36]
148Duncan Hull[j31]
149Hans Ienasescu[j38]
150Vassilios Ioannidis[j38]
151Rafael A. Irizarry[j8]
152Jon C. Ison[j38] [j31] [j25] [c10]
153Vivek Iyer[j28]
154Pankaj Jaiswal[j37] [j36]
155Ritsert C. Jansen[j15]
156Andrew M. Jenkinson[j32]
157Martin Closter Jespersen[j38]
158Yinping Jiao[j36]
159Rafael C. Jimenez[j38]
160Heather Junkins[j26] [c8]
161Simon Jupp[j42] [j41] [j40] [j37] [j35] [c16] [c12] [c11] [j32] [j27] [c10] [c7]
162Nick S. Juty[j38]
163Peter Juvan[j38]
164Senay Kafkas[c15]
165Matús Kalas[j38]
166Alexandros Kanterakis[j15]
167Carola Kanz[j1]
168Misha Kapushesky[j22] [j20] [j18] [j14] [j12] [j11] [c2] [j10] [j7] [j6] [j4]
169Natasha A. Karp[j43] [j28]
170Audrey Kauffmann[j12]
171Maria Keays[j37] [j36] [j33] [j27] [j25]
172Patrick Kemmeren[j4]
173Arnaud Kerhornou[j36]
174Paul J. Kersey[j36]
175Warren A. Kibbe[j34]
176Andrey Klebanov[j22]
177Alan Klemm[j26]
178Maximilian Koch[j38]
179Nikolay Kolesnikov[j33] [j25] [j19] [j18] [j11]
180N. Kolesnykov[j10]
181Gautier Koscielny[j42] [j28]
182Satu Koskinen[j37]
183Dimitris Kotzinos[c6]
184Maria Krestyaninova[j11]
185Nataliya Kryvych[j27] [j22]
186Tamara Kulikova[j1]
187Sunita Kumari[j36]
188Natalja Kurbatova[j33] [j28] [j25] [j22] [j20] [j19]
189Pavel Kurnosov[j22] [j14] [j11]
190Camille Laibe[j38] [j32]
191Gonzalo Garcia Lara[j7] [j6] [j4]
192Catherine Leroy[c12]
193Jing-Woei Li[j38]
194Luana Licata[j38]
195P. Lilja[j10] [j6]
196Yu Lin[j30]
197Allyson L. Lister[j31]
198Junmin Liu[j17] [j8]
199Yue Liu[j30]
200Vincent Lombard[j3] [j1]
201Peter Løngreen[j38]
202Rodrigo Lopez[j5] [j1]
203Joris Lops[j15]
204Phillip W. Lord[j16] [c1]
205Margus Lukk[j24] [j19] [j13] [j12] [j11] [j10]
206Jackie MacArthur[c8]
207Jacqueline A. L. MacArthur[j26]
208Michele Magrane[j5]
209Eamonn Maguire[j11]
210Donald Maier[j8]
211Ann-Marie Mallon[j28] [j21]
212James Malone[j42] [j41] [j40] [j35] [j34] [c11] [j32] [j31] [j30] [j27] [j25] [c10] [j22] [c9] [c7] [j21] [j19] [c5] [c4] [c3] [j18] [j16] [j14] [j13] [j11] [c2]
213Roby Mani[j25] [j19] [j11] [j10]
214Oliver Mannion[j37] [j27]
215Teri Manolio[j26]
216Fabien Mareuil[j38]
217John C. Marioni[j27]
218Maria Jesus Martin[j32] [j5]
219Jeremy C. Mason[j28]
220Hiroshi Masuya[j30]
221Peter Matthews[j28]
222Johanna R. McEntyre[c15]
223Sheldon J. McKay[j36]
224Kenneth McLeod[j39]
225Julie McMurry[j27]
226Terrence F. Meehan[j43] [j30] [j28] [c4]
227Karyn Megy
Karine Megy
[j37] [j33] [j27]
228Olga Melnichuk[j33] [j22]
229David G. Melvin[j28]
230Hervé Ménager[j38]
231Ivan Micetic[j38]
232Michael Miller[j17] [j8]
233Alex L. Mitchell[c14]
234Elvira Mitraka[j34]
235Steffen Möller[j38]
236Joannella Morales[j26]
237Sébastien Moretti[j38]
238Hugh Morgan[j28]
239Chris Morris[j38]
240Norman Morrison[j9]
241Juha Muilu[j15]
242Gaurab Mukherjee[j7] [j6]
243Nicola J. Mulder[j5]
244Joseph Mulvaney[j36]
245Chris Mungall
Christopher J. Mungall
[j34] [j30]
246Annalisa Mupo[j25]
247Sushma Naithani[j36]
248Yukio Nakamura[j30]
249Aleksandra Nenadic[j38]
250Sudeshna Guha Neogi[j11]
251Nicolas Le Novère[j32]
252Darren J. Oakley[j28]
253Claire O'Donovan[j5]
254Anika Oellrich[j43]
255Ahmet Oezcimen[j7] [j6] [j4]
256Andrew Olson[j36]
257David Osumi-Sutherland[j39] [c13]
258Chao Pang[j30] [c5] [c4] [c3]
259George Papastefanatos[c6]
260Norman W. Paton[c1]
261Rui Pedro Pereira[j29] [j25]
262Björn Peters
Bjoern Peters
[j30] [j16]
263Kjell Petersen[j8]
264Hedi Peterson[j38]
265Robert Petryszak[j37] [j36] [j33] [j27] [j22]
266Ekaterina Pilicheva[j33] [j25] [j19] [j11]
267Janet Piñero[c14]
268Enrico Ponta[c13]
269Justin Preece[j36]
270Giuseppe Profiti[j38]
271Nikolay Pultsin[j22]
272Asfand Qazi[j28]
273John Quackenbush[j8] [j2]
274Kristoffer Rapacki[j38]
275Tim F. Rayner[j13] [j12] [j11] [j10] [j8] [j7] [j6]
276Nicole Redaschi[j32] [j3] [j1]
277Jack Regnart[j28]
278Ahmad Retha[j28]
279Faisal Ibne Rezwan[j13] [j11]
280Peter M. Rice[j38]
281Martin Ringwald[j2]
282Philippe Rocca-Serra[j16] [j11] [j9] [j8] [j7] [j6] [j4] [j2]
283Paolo Romano[j38]
284Paola Roncaglia[j38]
285Erik T. Roos[j15]
286Burkhard Rost[j38]
287Johan Rung[j25]
288Gabriella Rustici[j40] [j33] [j27] [j25] [j22] [j19] [j14] [j11]
289Alan Ruttenberg[j16]
290Emil Rydza[j38]
291Dimitris Sacharidis[c6]
292Rabie Saidi[j38]
293Kaoru Saijo[j30]
294Susanna-Assunta Sansone[j16] [j11] [j9] [j7] [j6] [j4]
295Luis A. Santos[j28]
296Ugis Sarkans[j33] [j29] [j25] [j23] [j19] [j11] [j10] [j8] [j7] [j6] [j4]
297Sirarat Sarntivijai[j43] [j42] [j41] [j30] [c4]
298Gary Saunders[j42]
299Andrea Schafferhans[j38]
300Maxim Scheremetjew[c14]
301Paul N. Schofield[j21] [c3]
302Lynn M. Schriml[j34]
303Stephan C. Schürer[j30] [c4]
304Veit Schwämmle[j38]
305Ravi Shankar[j17]
306Anjan Sharma[j25] [j19] [j11] [j10] [j7] [j6]
307Gavin Sherlock[j17] [j8] [j2]
308Mohammadreza Shojatalab[j11] [j10] [j7] [j6] [j4]
309William C. Skarnes[j28]
310Nataliya Sklyar[j19] [j11]
311Damian Smedley[j28]
312Callum Smith[j38]
313Duncan J. Sneddon[j28]
314Catherine Snow[j37]
315Larisa N. Soldatova[j16]
316Paul T. Spellman[j8] [j2]
317Maria Sperotto
Maria Maddalena Sperotto
[j38]
318Rashmi Srinivasa[j17]
319David J. States[j30]
320Yannis Stavrakas[c6]
321Joshua C. Stein[j36]
322Lincoln Stein[j36]
323Peter Sterk[j1]
324Robert Stevens[j35] [j31] [c9]
325Jason E. Stewart[j2]
326Heinz Stockinger[j38]
327Christian J. Stoeckert Jr.[j30] [j17] [j16] [j9] [j8] [j2]
328Peter Stoehr[j5] [j1]
329Guenter Stoesser[j5] [j3] [j1]
330Morris A. Swertz[j20] [j15]
331Terue Takatsuki[j30]
332Y. Amy Tang[j37] [j36] [j33] [j27] [j25]
333Jan Taubert[j27]
334Chris F. Taylor[j9]
335Julie Taylor[j24]
336Ronald Taylor[j2]
337Marcela K. Tello-Ruiz[j36]
338Tobias Ternent[j25]
339Kostas Thiveos[c6]
340James Thomason[j36]
341Gudmundur A. Thorisson[j15]
342Andrew Tikhonov[j33] [j25] [j22]
343Victor de la Torre[j38]
344Silvio C. E. Tosatto[j38]
345Ravensara S. Travillian[j22] [j21] [c3]
346Ilinca Tudose[j39]
347Mary Ann Tuli[j5] [j1]
348Jessica A. Turner[j16]
349Paolo Uva[j38]
350Radka Svobodová Vareková[j38]
351Drashtti Vasant[j42] [j34] [j29] [c10]
352Gianluca Della Vedova[j38]
353K. Joeri van der Velde[j20] [j15]
354Uma Vempati
Uma D. Vempati
[j30] [c4]
355Allegra Via[j38]
356Jaak Vilo[j4]
357Gert Vriend[j38]
358Olga Vrousgou[c16]
359Brandon Walts[j36]
360Bo Wang[j36]
361Doreen Ware[j36]
362Jonathan Warren[j28]
363Sharon Wei[j36]
364Joel Weiser[j36]
365Hendrik Weisser[j37]
366Danielle Welter[j41] [c11] [j26] [j25] [c10] [c8]
367Henrik Westerberg[j28]
368Patricia L. Whetzel[j9] [j8]
369Jacqueline K. White[j43]
370Joseph White[j17] [j9] [j8]
371E. William[j10]
372Eleanor Williams[j40] [j37] [j33] [j27] [j25] [j22] [j19] [j14] [j13] [j11]
373Robert J. Wilson[j28]
374Sarala M. Wimalaratne[j32]
375James Wright[j37]
376Farrell Wymore[j8]
377Zuoshuang Xiang[j30] [c4]
378Vincent Xue[j24]
379Guy Yachdav[j38]
380Gagarine Yaikhom[j28]
381Federico Zambelli[j38]
382Mengyao Zhao[j11]
383Jie Zheng[j30] [j18] [j16]
384Anna Zhukova[j18]
385Andrey Zorin[j22] [j14]

 

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