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Helen Parkinson
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19
Brazma, Alvis
12
Stoeckert, Christian
11
Sansone, Susanna-Assunta
11
Sarkans, Ugis
10
Causton, Helen
9
Rocca-Serra, Philippe
8
Holloway, Ele
8
Kapushesky, Misha
8
Quackenbush, John
8
Sherlock, Gavin
7
Spellman, Paul
7
Shojatalab, Mohammadreza
7
Hingamp, Pascal
7
Rayner, Tim
6
Farne, Anna
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Geonetwork of Helen Parkinson (preview)
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All Publications
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2009: Kauffmann Audrey; Rayner Tim F; Parkinson Helen; Kapushesky Misha; Lukk Margus; Brazma Alvis; Huber Wolfgang
Importing ArrayExpress datasets into R/Bioconductor.
Bioinformatics (Oxford, England) 2009;25(16):2092-4.
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2009: Rayner Tim F; Rezwan Faisal Ibne; Lukk Margus; Bradley Xiangqun Zheng; Farne Anna; Holloway Ele; Malone James; Williams Eleanor; Parkinson Helen
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.
Bioinformatics (Oxford, England) 2009;25(2):279-80.
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2008: Rustici Gabriella; Kapushesky Misha; Kolesnikov Nikolay; Parkinson Helen; Sarkans Ugis; Brazma Alvis
Data storage and analysis in ArrayExpress and Expression Profiler.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2008;Chapter 7():Unit 7.13.
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2007: Parkinson H; Kapushesky M; Shojatalab M; Abeygunawardena N; Coulson R; Farne A; Holloway E; Kolesnykov N; Lilja P; Lukk M; Mani R; Rayner T; Sharma A; William E; Sarkans U; Brazma A
ArrayExpress--a public database of microarray experiments and gene expression profiles.
Nucleic acids research 2007;35(Database issue):D747-50.
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2006: Brazma Alvis; Parkinson Helen;
ArrayExpress service for reviewers/editors of DNA microarray papers.
Nature biotechnology 2006;24(11):1321-2.
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2006: Whetzel Patricia L; Parkinson Helen; Causton Helen C; Fan Liju; Fostel Jennifer; Fragoso Gilberto; Game Laurence; Heiskanen Mervi; Morrison Norman; Rocca-Serra Philippe; Sansone Susanna-Assunta; Taylor Chris; White Joseph; Stoeckert Christian J
The MGED Ontology: a resource for semantics-based description of microarray experiments.
Bioinformatics (Oxford, England) 2006;22(7):866-73.
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2006: Stoeckert Christian; Ball Catherine; Brazma Alvis; Brinkman Ryan; Causton Helen; Fan Liju; Fostel Jennifer; Fragoso Gilberto; Heiskanen Mervi; Holstege Frank; Morrison Norman; Parkinson Helen; Quackenbush John; Rocca-Serra Philippe; Sansone Susanna-Assunta; Sarkans Ugis; Sherlock Gavin; Stevens Robert; Taylor Chris; Taylor Ronald; Whetzel Patricia; White Joseph
Wrestling with SUMO and bio-ontologies.
Nature biotechnology 2006;24(1):21-2; author reply 23.
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2006: Rayner Tim F; Rocca-Serra Philippe; Spellman Paul T; Causton Helen C; Farne Anna; Holloway Ele; Irizarry Rafael A; Liu Junmin; Maier Donald S; Miller Michael; Petersen Kjell; Quackenbush John; Sherlock Gavin; Stoeckert Christian J; White Joseph; Whetzel Patricia L; Wymore Farrell; Parkinson Helen; Sarkans Ugis; Ball Catherine A; Brazma Alvis
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC bioinformatics 2006;7():489.
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2006: Brazma Alvis; Kapushesky Misha; Parkinson Helen; Sarkans Ugis; Shojatalab Mohammad
Data storage and analysis in ArrayExpress.
Methods in enzymology 2006;411():370-86.
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2006: Whetzel Patricia L; Parkinson Helen; Stoeckert Christian J
Using ontologies to annotate microarray experiments.
Methods in enzymology 2006;411():325-39.
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2006: Whetzel Patricia L; Brinkman Ryan R; Causton Helen C; Fan Liju; Field Dawn; Fostel Jennifer; Fragoso Gilberto; Gray Tanya; Heiskanen Mervi; Hernandez-Boussard Tina; Morrison Norman; Parkinson Helen; Rocca-Serra Philippe; Sansone Susanna-Assunta; Schober Daniel; Smith Barry; Stevens Robert; Stoeckert Christian J; Taylor Chris; White Joe; Wood Andrew;
Development of FuGO: an ontology for functional genomics investigations.
Omics : a journal of integrative biology 2006;10(2):199-204.
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2006: Morrison Norman; Wood A Joseph; Hancock David; Shah Sonia; Hakes Luke; Gray Tanya; Tiwari Bela; Kille Peter; Cossins Andrew; Hegarty Matthew; Allen Michael J; Wilson William H; Olive Peter; Last Kim; Kramer Cas; Bailhache Thierry; Reeves Jonathan; Pallett Denise; Warne Justin; Nashar Karim; Parkinson Helen; Sansone Susanna-Assunta; Rocca-Serra Philippe; Stevens Robert; Snape Jason; Brass Andy; Field Dawn
Annotation of environmental OMICS data: application to the transcriptomics domain.
Omics : a journal of integrative biology 2006;10(2):172-8.
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2006: Zimmermann Philip; Schildknecht Beatrice; Craigon David; Garcia-Hernandez Margarita; Gruissem Wilhelm; May Sean; Mukherjee Gaurab; Parkinson Helen; Rhee Seung; Wagner Ulrich; Hennig Lars
MIAME/Plant - adding value to plant microarrray experiments.
Plant methods 2006;2():1.
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2005: Mukherjee Gaurab; Abeygunawardena Niran; Parkinson Helen; Contrino Sergio; Durinck Steffen; Farne Anna; Holloway Ele; Lilja Per; Moreau Yves; Oezcimen Ahmet; Rayner Tim; Sharma Anjan; Brazma Alvis; Sarkans Ugis; Shojatalab Mohammadreza
Plant-based microarray data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a submission tool for Arabidopsis gene expression data to ArrayExpress.
Plant physiology 2005;139(2):632-6.
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2005: Sarkans Ugis; Parkinson Helen; Lara Gonzalo Garcia; Oezcimen Ahmet; Sharma Anjan; Abeygunawardena Niran; Contrino Sergio; Holloway Ele; Rocca-Serra Philippe; Mukherjee Gaurab; Shojatalab Mohammadreza; Kapushesky Misha; Sansone Susanna-Assunta; Farne Anna; Rayner Tim; Brazma Alvis
The ArrayExpress gene expression database: a software engineering and implementation perspective.
Bioinformatics (Oxford, England) 2005;21(8):1495-501.
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2005: Parkinson H; Sarkans U; Shojatalab M; Abeygunawardena N; Contrino S; Coulson R; Farne A; Lara G Garcia; Holloway E; Kapushesky M; Lilja P; Mukherjee G; Oezcimen A; Rayner T; Rocca-Serra P; Sharma A; Sansone S; Brazma A
ArrayExpress--a public repository for microarray gene expression data at the EBI.
Nucleic acids research 2005;33(Database issue):D553-5.
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2004: Ball Catherine; Brazma Alvis; Causton Helen; Chervitz Steve; Edgar Ron; Hingamp Pascal; Matese John C; Icahn Carl; Parkinson Helen; Quackenbush John; Ringwald Martin; Sansone Susanna-Assunta; Sherlock Gavin; Spellman Paul; Stoeckert Christian; Tateno Yoshio; Taylor Ronald; White Joseph; Winegarden Neil;
An open letter on microarray data from the MGED Society.
Microbiology (Reading, England) 2004;150(Pt 11):3522-4.
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2004: Ball Catherine A; Brazma Alvis; Causton Helen; Chervitz Steve; Edgar Ron; Hingamp Pascal; Matese John C; Parkinson Helen; Quackenbush John; Ringwald Martin; Sansone Susanna-Assunta; Sherlock Gavin; Spellman Paul; Stoeckert Chris; Tateno Yoshio; Taylor Ronald; White Joseph; Winegarden Neil
Submission of microarray data to public repositories.
PLoS biology 2004;2(9):E317.
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2004: Ball Catherine; Brazma Alvis; Causton Helen; Chervitz Steve; Edgar Ron; Hingamp Pascal; Matese John C; Parkinson Helen; Quackenbush John; Ringwald Martin; Sansone Susanna-Assunta; Sherlock Gavin; Spellman Paul; Stoeckert Christian; Tateno Yoshio; Taylor Ronald; White Joseph; Winegarden Neil;
Standards for microarray data: an open letter.
Environmental health perspectives 2004;112(12):A666-7.
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2004: Harris Midori A; Parkinson Helen
Standards and ontologies for functional genomics 2.
Comparative and functional genomics 2004;5(8):618-22.
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2004: Parkinson Helen; Aitken Stuart; Baldock Richard A; Bard Jonathan B L; Burger Albert; Hayamizu Terry F; Rector Alan; Ringwald Martin; Rogers Jeremy; Rosse Cornelius; Stoeckert Christian J; Davidson Duncan
The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data.
Comparative and functional genomics 2004;5(6-7):521-7.
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2003: Rocca-Serra Philippe; Brazma Alvis; Parkinson Helen; Sarkans Ugis; Shojatalab Mohammadreza; Contrino Sergio; Vilo Jaak; Abeygunawardena Niran; Mukherjee Gaurab; Holloway Ele; Kapushesky Misha; Kemmeren Patrick; Lara Gonzalo Garcia; Oezcimen Ahmet; Sansone Susanna-Assunta
ArrayExpress: a public database of gene expression data at EBI.
Comptes rendus biologies 2003;326(10-11):1075-8.
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2003: Brazma Alvis; Parkinson Helen; Sarkans Ugis; Shojatalab Mohammadreza; Vilo Jaak; Abeygunawardena Niran; Holloway Ele; Kapushesky Misha; Kemmeren Patrick; Lara Gonzalo Garcia; Oezcimen Ahmet; Rocca-Serra Philippe; Sansone Susanna-Assunta
ArrayExpress--a public repository for microarray gene expression data at the EBI.
Nucleic acids research 2003;31(1):68-71.
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2003: Brooksbank Catherine; Camon Evelyn; Harris Midori A; Magrane Michele; Martin Maria Jesus; Mulder Nicola; O'Donovan Claire; Parkinson Helen; Tuli Mary Ann; Apweiler Rolf; Birney Ewan; Brazma Alvis; Henrick Kim; Lopez Rodrigo; Stoesser Guenter; Stoehr Peter; Cameron Graham
The European Bioinformatics Institute's data resources.
Nucleic acids research 2003;31(1):43-50.
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2003: Harris Midori A; Parkinson Helen
Standards and ontologies for functional genomics: towards unified ontologies for biology and biomedicine.
Comparative and functional genomics 2003;4(1):116-20.
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2002: Ball Catherine A; Sherlock Gavin; Parkinson Helen; Rocca-Sera Philippe; Brooksbank Catherine; Causton Helen C; Cavalieri Duccio; Gaasterland Terry; Hingamp Pascal; Holstege Frank; Ringwald Martin; Spellman Paul; Stoeckert Christian J; Stewart Jason E; Taylor Ronald; Brazma Alvis; Quackenbush John;
The underlying principles of scientific publication.
Bioinformatics (Oxford, England) 2002;18(11):1409.
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2002: Ball Catherine A; Sherlock Gavin; Parkinson Helen; Rocca-Sera Philippe; Brooksbank Catherine; Causton Helen C; Cavalieri Duccio; Gaasterland Terry; Hingamp Pascal; Holstege Frank; Ringwald Martin; Spellman Paul; Stoeckert Christian J; Stewart Jason E; Taylor Ronald; Brazma Alvis; Quackenbush John;
Standards for microarray data.
Science (New York, N.Y.) 2002;298(5593):539.
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2002: Lombard V; Camon E B; Parkinson H E; Hingamp P; Stoesser G; Redaschi N
EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.
Bioinformatics (Oxford, England) 2002;18(5):763-4.
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2001: Brazma A; Hingamp P; Quackenbush J; Sherlock G; Spellman P; Stoeckert C; Aach J; Ansorge W; Ball C A; Causton H C; Gaasterland T; Glenisson P; Holstege F C; Kim I F; Markowitz V; Matese J C; Parkinson H; Robinson A; Sarkans U; Schulze-Kremer S; Stewart J; Taylor R; Vilo J; Vingron M
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Nature genetics 2001;29(4):365-71.
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2001: Stoesser G; Baker W; van den Broek A; Camon E; Garcia-Pastor M; Kanz C; Kulikova T; Lombard V; Lopez R; Parkinson H; Redaschi N; Sterk P; Stoehr P; Tuli M A
The EMBL nucleotide sequence database.
Nucleic acids research 2001;29(1):17-21.
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