Functional Genomics Production Team Publications

Functional Genomics Production Team papers and (from 2012) posters and conference presentations. Details of upcoming training courses are also available here.

2013 Papers

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2013 Presentations

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2012 Papers

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2012 Presentations

  • Simon Jupp, Helen Parkinson, James Malone
    Semantic Web Atlas: Putting Gene Expression Atals Data Into Biological Context
    Semantic Web Application and Tools for the Life Sciences (SWAT4LS), Paris, France 2012, accepted paper.
    full-text PDF
  • Helen Parkinson
    Integrating human and mouse phenotype data
    CBIIT Webinar on YouTube
  • Nathalie Conte, Lucia Banci, Paul Flicek, Gautier Koscielny, Christoph Lengger, Claudio Luchinat, Holger Maier, Terry Meehan, Heimo Mueller, Helen Parkinson, Michael Raess, Damian Smedley, Leonardo Tenori, Hendrik Tiedemann, Kurt Zatloukal
    PhenoBridge: Linking mouse model to human clinical data using Diabetes and Obesity as a framework
    Diabetes and Obesity Symposium, EMBL Heidelberg, September 2012
  • L.A. Hindorff, J.A.L. MacArthur, D. Welter, T. Burdett, P. Hall, H.A. Junkins. H. Parkinson
    Ontology, visual, and informatics enhancements to the NHGRI Genome-wide Association Study (GWAS) catalog
    American Society of Human Genetics Meeting, San Francisco, November 2012
  • Tony Burdett
    Zooma2 - A repository of annotation knowledge and curation API
    ISMB San Diego Technology Track
    Prezi download
  • Danielle Welter, Tony Burdett, Lucia Hindorff, Heather Junkins, Simon Jupp, Jacqueline MacArthur and Helen Parkinson
    Ontology-driven visualisation of NHGRI GWAS data
    ISMB San Diego BioOntologies Special Interest Group, accepted paper.
    Slides PDF
  • Amy Tang, Adam Faulconbridge, Marco Brandizi, Tony Burdett, Mike Gostev, Rui Pereira, Ugis Sarkans, Alvis Brazma and Helen Parkinson
    BioSamples Database at EMBL-EBI
    ISMB San Diego Poster Presentation
    Poster PDF
  • Maria Copeland, Andy Brown, Helen Parkinson, Robert Stevens and James Malone.
    The SWO Project: A Case Study for Applying Agile Ontology Engineering Methods for Community Driven Ontologies
    International Conference on BioOntologies, accepted paper.
    Paper PDF
  • Hastings, E., Williams, E., Farne, A., Tang, A., Ternent, T., Kurbatova, N., Burdett, T., Malone, J., Holloway, E., Faulconbridge, A., Welter, D., Keays, M., Jupp, S., Ison, J., Dylag, M., Emam, I., Kapushesky, M., Petryszak, R., Kolesnikov, N., Mani, R., Pilicheva, K., Brandizi, M., Brazma, A., Sarkans, U., Parkinson, H.
    ArrayExpress: Data submission and curation of functional genomics data
    Biocuration 2012 Washington D.C. Poster Presentation
    Poster PDF
  • Simon Jupp, Andrew Gibson, James Malone and Robert Stevens.
    Taking a view on bio-ontologies
    International Conference on BioOntologies, accepted paper.
    Paper PDF
  • Danielle Welter, Tony Burdett, Lucia Hindorff, Heather Junkins, Jacqueline MacArthur and Helen Parkinson
    GOCI: An Ontology-Driven Search and Curation Infrastructure for the NHGRI GWAS Catalog
    International Conference on BioOntologies, poster presentation.
    Abstract PDF Poster PDF
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2011

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2010

  • 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 A.
    ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.
    Nucleic Acids Res. 2010 Nov 10. [Epub ahead of print]
  • Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ Jr, Ball CA.
    Annotare -a tool for annotating high-throughput biomedical investigations and resulting data.
    Bioinformatics. 2010 Oct 1;26(19):2470-1. Epub 2010 Aug 23.
  • Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J;
    OBI consortium. Modeling biomedical experimental processes with OBI
    Journal of Biomedical Semantics 2010, 1(Suppl 1):S7
  • Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE;
    Coordination of Mouse Informatics Resources (CASIMIR); Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen (2010) A uniform and extensible data model and software platform for genotype and phenotype experiments (XGAP)
    Genome Biology. 11:R27
  • Malone, J, Holloway, E, Adamusiak, T, Kapushesky, M, Zheng, J, Kolesnikov, N, Zhukova, A, Brazma, A and Parkinson H,
    Modelling Sample Variables with an Experimental Factor Ontology
    Bioinformatics, 2010 26:8, 1112-1118
  • Lukk, M, Kapushesky, M, Nikkila, J, Parkinson, H, Goncalves, A, Huber, W, Ukkonen, E, and Brazma, A
    A Global Map of Human Gene Expression
    Nat Biotechnol 28, 322-324
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2009

  • Kauffmann, A, Rayner, T F, Parkinson, H, Kapushesky, M, Lukk, M, Brazma, A Huber, W,
    Importing ArrayExpress datasets into R/Bioconductor
    Bioinformatics, 2009 25(16): pp 2092-4
  • Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H and Brazma, A
    Gene Expression Atlas at the European Bioinformatics Institute
    Nucleic Acids Res
  • Rayner TF, Rezwan FI, Lukk M, Bradley XZ, Farne A, Holloway E, Malone J, Williams E, Parkinson H.
    MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB
    Bioinformatics 25(2):279-280
  • Malone, J, Adamusiak T, Holloway E, Kapushesky M, Parkinson H
    Developing an Ontology from the Application Up
    OWLED 2009
  • 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 SA, Sklyar N, Zhao M, Sarkans U, Brazma A.
    ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
    Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72. Epub 2008 Nov 10.
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2008

  • Rayner TF, Rezwan FI, Lukk M, Bradley XZ, Farne, A, Holloway E, Malone J, Williams, and Parkinson, H
    MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB
    Bioinformatics DOI101093/bioinformatics/btn617
  • Johnathan Bard, James Malone, Tim Rayner and Helen Parkinson
    Minimal Information about Anatomy (MIAA): a species-independent terminology for anatomical mapping and retrieval Short Paper,
    Bio-Ontologies SIG, ISMB 2008
  • Malone, J, Zheng, H, Rayner, R and Parkinson, H
    Developing an application focused experimental factor ontology: embracing the OBO Community Short Paper,
    Bio-Ontologies SIG, ISMB 2008
  • Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.
    Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)
    Nature Biotech 26, 305 -312
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2007

  • ArrayExpress-a public database of microarray experiments and gene expression profiles
    Nucl Acids Res 2007 35: D747-D750; doi:101093/nar/gkl995
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2006

  • Patricia L Whetzel, Helen Parkinson, Helen Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Laurence Game, Mervi Heiskanen, Norman Morrison, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris Taylor, Joseph White, Christian J Stoeckert Jr
    The MGED Ontology: a resource for semantics-based description of microarray experiments
    Bioinformatics 22(7): 866-73, April 2006
  • Patricia L Whetzel, Helen Parkinson, and Christian J Stoeckert, Jr
    Using Ontologies to Annotate Microarray Experiments Methods in Enzymology Brian Oliver & Alan Kimmel (eds)
    Elsevier, Vol 411, 2006
  • Alvis Brazma, Misha Kapushesky, Helen Parkinson, Ugis Sarkans, and Mohammad Shojatalab
    Data Storage and Analysis in ArrayExpress Methods in Enzymology Brian Oliver & Alan Kimmel (Eds)
    Elsevier, Vol 411, 2006
  • Eric W Deutsch, Catherine A Ball, G Steven Bova GS, Alvis Brazma A, Roger E Bumgarner, Campbell D, Helen Causton, Jeff Christiansen, Duncan Davidso, Eichner LJ, Goo YA, Sean Grimmond, Thorsten Henrich, Johnson MH, Korb M, Mills JC, Asa J Oudes, Helen Parkinson, Laura E Pascal, John Quackenbush J, Mirana Ramialison, Martin Ringwald, Susanna-Assunta Sansone, Gavin Sherlock G, Christian J Stoeckert Jr, Jason Swedlow, Ronald C Taylor RC, Laura E Walashek, You Zhou, Alvin Y Liu, Laurence D True
    Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)
    OMICS 10(2): 205-8 2006
  • Norman Morrison, A Joseph Wood, David Hancock, Sonia Shah, Luke Hakes, Tanya Gray, Bela Tiwari, Peter Kille, Andrew Cossins, Matthew Hegarty, Michael J Allen, William H Wilson, Peter Olive, Kim Last, Cas Kramer, Thierry Bailhache, Jonathan Reeves, Denise Pallett, Justin Warne, Karim Nashar, Helen Parkinson, Susanna-Assunta Sansone, Philippe Rocca-Serra, Robert Stevens, Jason Snape, Andy Brass, Dawn Field
    Standard Annotation of Environmental OMICS Data: Application to the Transcriptomics Domain OMICS:
    A Journal of Integrative Biology 2006, 10(2): 172178
  • Patricia L Whetzel, Ryan R Brinkman, Helen C Causton, Liju Fan, Dawn Field, Jennifer Fostel, Gilberto Fragoso, Tanya Gray, Mervi Heiskanen, Tina Hernandez-Boussard, Norman Morrison, Helen Parkinson, Philippe Rocca-Serra, Susanna-Assunta Sansone, Daniel Schober, Barry Smith, Robert Stevens, Christian J Stoeckert Jr, Chris Taylor, Joe White, Andrew Wood, Fugo Working Group
    Development of FuGO: An Ontology for Functional Genomics Investigations OMICS:
    A Journal of Integrative Biology 2006, 10(2): 199-204
  • Tim F Rayner, Philippe Rocca-Serra, Paul T Spellman, Helen Causton, Anna Farne, Ele Holloway E, Rafael A Irizarry RA, Junmin Liu, Donald S Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J Stoeckert, Joseph White, Patricia L Whetzel, Farrell Wymore, Helen Parkinson, Ugis Sarkans, Catherine A Ball and Alvis Brazma
    A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB BMC
    Bioinformatics 2006, 7:489
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2005

  • Helen Parkinson, Stuart Aitken, Richard Baldock, Johnathan BL Bard, Albert Burger, Terry F Hayamizu, Alan Rector, Martin Ringwald, Jeremy Rogers, Cornelius Rosse, Christian J Stoeckert Jr, and Duncan Davidson
    The SOFG Anatomy Entry List (SAEL); an annotation tool for functional genomics data
    Comparative and Functional Genomics 5(6-7): 521-527
  • Helen Parkinson, Ugis Sarkans, Shojatalab, M Niran Abeygunawardena, Sergio Contrino, Richard Coulson, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Misha Kapushesky, Per Lilja, Gaurab Mukherjee, Ahmet Oezcimen, Tim F Rayner, Philippe Rocca-Serra, Anjan Sharma, Susanna-Assunta Sansone and Alvis Brazma, A
    ArrayExpress--a public repository for microarray gene expression data at the EBI
    Nucleic Acids Res 33 Database Issue: D553-5
  • Kevin L Garwood, Phillip W Lord, Helen Parkinson, Norman W Paton, Carole A Goble
    Pedro Ontology Services: A Framework for Rapid Ontology Markup
    ESWC 2005: 578-591
  • Ugis Sarkans, Helen 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
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2004

  • Helen Parkinson
    Gene Expression Databases In Database Annotation in Molecular Biology: Principles and Practice
    Ed Arthur M Lesk Wiley, London
  • Arthur M Lesk, Helen Parkinson and John C Whisstock Classification of Protein Function
    In Database Annotation in Molecular Biology: Principles and Practice
    Ed Arthur M Lesk Wiley, London
  • Catherine A Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C Matese, JC, Helen Parkinson, John Quackenbush, Martin Ringwald, Sussana-Assunta Sansone, Gavin Sherlock, Paul Spellman, Christian J Stoeckert Jr, Yoshio Tateno, Ron Taylor, R, Joseph White, J and Neil Winegarden
    Submission of Microarray Data to Public Repositories
    PLoS Biology 2(e317): 1276-1277
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2003

  • Catherine Brooksbank, Evelyn Camon, Midori A Harris, Michele Magrane, Maria Jesus Martin, Nicola Mulder, Claire O'Donovan, Helen Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, and Graham Cameron
    The European Bioinformatics Institute's data resources
    Nucleic Acids Res 31(1): 43-50
  • Alvis Brazma, Helen Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Jaak Vilo, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Philippe Rocca-Serra, and Susanna-Assunta Sansone
    ArrayExpress--a public repository for microarray gene expression data at the EBI
    Nucleic Acids Res 31(1): 68-71
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2002

  • Stoeckert, C J and Parkinson H
    The MGED ontology: a framework for describing functional genomics experiments
    Comparative and Functional Genomics 4: 127-132
  • Vincent Lombard, Evelyn Camon, Helen Parkinson, Gunter Stoesser and Nicole Redaschi
    EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database
    Bioinformatics 18(5): 763-4
  • Catherine A Ball, Gavin Sherlock, Helen Parkinson, Philippe Rocca-Sera, Catherine Brooksbank, Helen C Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank Holstege, Martin Ringwald, Paul Spellman, Christian J Stoeckert, Jr, Jason E Stewart, Ronald Taylor, Alvis Brazma, and John Quackenbush
    The underlying principles of scientific publication
    Bioinformatics 18(11):1409
  • Catherine A Ball, Gavin Sherlock, Helen Parkinson, Philippe Rocca-Sera, Catherine Brooksbank, Helen C Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank Holstege, Martin Ringwald, Paul Spellman, Christian J Stoeckert Jr, Jason E Stewart, Ronald Taylor, Alvis Brazma, John Quackenbush
    Standards for microarray data
    Science 298(5593): 539
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2001

  • Alvis Brazma, Pascal Hingamp, John Quackenbush, Gavin Sherlock, Paul Spellman, Chris Stoeckert, John Aach, Wilhelm Ansorge, Catherine A Ball, Helen C Causton, Terry Gaasterland, Patrick Glenisson, Frank CP Holstege, Irene F Kim, Victor Markowitz, John C Matese, Helen Parkinson, Alan Robinson, Ugis Sarkans, Steffen Schulze-Kremer, Jason Stewart, Ronald Taylor, Jaak Vilo & Martin Vingron
    Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
    Nat Genet 29(4): 365-71
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1997

  • Lesley A Sawyer, J Michael Hennessy, Alexandre A Peixoto, Ezio Rosato, Helen Parkinson, Rodolfo Costa, Charalambos P Kyriacou
    Natural variation in a Drosophila clock gene and temperature compensation
    Science 278(5346): 2117-20
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FGPT Publications