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EBINET ProjectPublications

Selected publications in chronological order - NET projects

2009:

Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA. (2009). Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics. 27;10:125. [CiteXplore] [PDF]

Harttig U, Travis AJ, Rocca-Serra P, Renkema M, van Ommen B, Boeing H. (2009). Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network. Genes Nutr. Apr 30. [Epub ahead of print]

Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L, Battaglia C, Cavalieri D. Using pathway signatures as means of identifying similarities among microarray experiments. (2009) PLoS ONE, 4(1):e4128. Epub 2009 Jan 6. [Link]

2008:

Chris F Taylor, Dawn Field, Susanna-Assunta Sansone, Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A Ball, Pierre-Alain Binz, Molly Bogue, Tim Booth, Alvis Brazma, Ryan R Brinkman, Adam Michael Clark, Eric W Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Frank Gibson, Tanya Gray, Graeme Grimes, John M Hancock, Nigel W Hardy, Henning Hermjakob, Randall K Julian, Matthew Kane, Carsten Kettner, Christopher Kinsinger, Eugene Kolker, Martin Kuiper, Nicolas Le Novère, Jim Leebens-Mack, Suzanna E Lewis, Phillip Lord, Ann-Marie Mallon, Nishanth Marthandan, Hiroshi Masuya, Ruth McNally, Alexander Mehrle, Norman Morrison, Sandra Orchard, John Quackenbush, James M Reecy, Donald G Robertson, Philippe Rocca-Serra, Henry Rodriguez, Heiko Rosenfelder, Javier Santoyo-Lopez, Richard H Scheuermann, Daniel Schober, Barry Smith, Jason Snape, Christian J Stoeckert, Keith Tipton, Peter Sterk, Andreas Untergasser, Jo Vandesompele, Stefan Wiemann.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
(2008). Nat Biotech 26: 889-896.
[CiteXplore] [PDF]

Mathieu Vinken, Tatyana Doktorova, Heidrun Ellinger-Ziegelbauer, Hans-Jurgen Ahr, Edward Lock, Paul Carmichael, Erwin Roggen, Joost van Delft, Jos Kleinjans, Jose Castell, Roque Bort, Teresa Donato, Michael Ryan, Raffaella Corvi, Hector Keun, Timothy Ebbels, Toby Athersuch, Susanna-Assunta Sansone, Philippe Rocca-Serra, Rob Stierum, Paul Jennings, Walter Pfaller, Hans Gmuender, Tamara Vanhaecke, Vera Rogiers.

The carcinoGENOMICS project: critical selection of model compounds for the development of omics-based in vitro carcinogenicity screening assays.
(2008). Mutat. Res. 659(3): 202-10.
[CiteXplore] [PDF]

Field D, Sansone SA, Garrity GM. Foreword to the special issue on the fifth genomic standards consortium workshop. OMICS. 2008 Jun;12(2):99. [Link]

Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D, White O. Toward a standards-compliant genomic and metagenomic publication record. OMICS. 2008 Jun;12(2):157-60. [Link]

Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S; and Members of the RSBI Working Group. The First RSBI (ISA-TAB) Workshop: "Can a Simple Format Work for Complex Studies?". OMICS. 2008 Jun;12(2):143-9.[Link]

Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A. The minimum information about a genome sequence (MIGS) specification. Nat Biotech. 2008 May;26(5):541-7. [Link]

Spasi? I, Schober D, Sansone SA, Rebholz-Schuhmann D, Kell DB, Paton NW. Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S5. [Link]

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). (2008) Nat Biotech. 6(3):305-12. [Link]

2007:

Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel and Suzanna Lewis.

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
(2007). Nat Biotech 25, 1251 - 1255
[CiteXplore] [PDF]

Susanna-Assunta Sansone, Teresa Fan, Royston Goodacre, Julian L Griffin, Nigel W Hardy, Rima Kaddurah-Daouk, Bruce S Kristal, John Lindon, Pedro Mendes, Norman Morrison, Basil Nikolau, Don Robertson, Lloyd W Sumner, Chris Taylor, Mariët van der Werf, Ben van Ommen, Oliver Fiehn.
The Metabolomics Standards Initiative.
(2007). Nat Biotech 25, 846 - 848.
[CiteXplore] [PDF]

Oliver Fiehn, Don Robertson, Jules Griffin, Mariet van der Werf, Basil Nikolau, Norman Morrison, Lloyd W. Sumner, Roy Goodacre, Nigel W. Hardy, Chris Taylor, Jennifer Fostel, Bruce Kristal, Rima Kaddurah-Daouk, Pedro Mendes, Ben van Ommen, John C. Lindon, Susanna-Assunta Sansone

The metabolomics standards initiative (MSI)
(2007). Metabolomics 3, 175-178.
[Link] [PDF]

Julian L. Griffin, Andrew W. Nicholls, Clare A. Daykin, Sarah Heald, Hector C. Keun, Ina Schuppe-Koistinen, John R. Griffiths, Leo L. Cheng, Philippe Rocca-Serra, Denis V. Rubtsov, Donald Robertson
Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments
(2007). Metabolomics 3, 179-188.
[Link] [PDF]

Norman Morrison, Dan Bearden, Jacob G. Bundy, Tim Collette, Felicity Currie, Matthew P. Davey, Nathan S. Haigh, David Hancock, Oliver A. H. Jones, Simone Rochfort, Susanna-Assunta Sansone, Dalibor Štys, Quincy Teng, Dawn Field, Mark R. Viant
Standard reporting requirements for biological samples in metabolomics experiments: environmental context
(2007). Metabolomics 3, 203-210.
[Link] [PDF]

Nigel W. Hardy and Chris F. Taylor
A roadmap for the establishment of standard data exchange structures for metabolomics
(2007). Metabolomics 3, 243-248.
[Link] [PDF]

Susanna-Assunta Sansone, Daniel Schober, Helen J. Atherton, Oliver Fiehn, Helen Jenkins, Philippe Rocca-Serra, Denis V. Rubtsov, Irena Spasic, Larisa Soldatova, Chris Taylor, Andy Tseng, Mark R. Viant, Ontology Working Group Members
Metabolomics standards initiative: ontology working group work in progress
(2007). Metabolomics 3, 249-256.
[Link] [PDF]

Andrew R Jones, Michael Miller, Ruedi Aebersold, Rolf Apweiler, Catherine A Ball, Alvis Brazma, James DeGreef, Nigel Hardy, Henning Hermjakob, Simon J Hubbard, Peter Hussey, Mark Igra, Helen Jenkins, Randall K Julian, Kent Laursen, Stephen G Oliver, Norman W Paton, Susanna-Assunta Sansone, Ugis Sarkans, Christian J Stoeckert, Chris F Taylor, Patricia L Whetzel, Joseph A White, Paul Spellman, Angel Pizarro.
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
(2007). Nat Biotech 25, 1127-1133.
[CiteXplore] [PDF]

Chris F Taylor, Norman W Paton, Kathryn S Lilley, Pierre-Alain Binz, Randall K Julian, Andrew R Jones, Weimin Zhu, Rolf Apweiler, Ruedi Aebersold, Eric W Deutsch, Michael J Dunn, Albert J R Heck, Alexander Leitner, Marcus Macht, Matthias Mann, Lennart Martens, Thomas A Neubert, Scott D Patterson, Peipei Ping, Sean L Seymour, Puneet Souda, Akira Tsugita, Joel Vandekerckhove, Thomas M Vondriska, Julian P Whitelegge, Marc R Wilkins, Ioannnis Xenarios, John R Yates, Henning Hermjakob.
The minimum information about a proteomics experiment (MIAPE)
(2007). Nat Biotech 25, 887 - 893.
[CiteXplore] [PDF]

Chris F Taylor
Standards for reporting bioscience data: a forward look.
(2007). Drug Discov Today 12(13-14):527-33
[CiteXplore]

Chris F Taylor
Progress in standards for reporting omics data.
(2007). Curr Opin Drug Discov Devel 10(3):254-63
[CiteXplore]

Sandra Orchard, Philip Jones, Chris F Taylor, Weimin Zhu, Randall K Julian, Henning Hermjakob, Rolf Apweiler.
Proteomic data exchange and storage: the need for common standards and public repositories.
(2007). Methods Mol Biol 367:261-70
[CiteXplore]

2006:

A. Garcia Castro, P. Rocca-Serra, R. Stevens, C. Taylor, K. Nashar, M.A. Ragan, and S.A. Sansone.

The use of concept maps during knowledge elicitation in ontology development processes. The nutrigenomics use case.
2006. BMC Bioinformatics, 7(1), 267. [doi:10.1186/1471-2105-7-267].
[CiteXplore]

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. Development of FuGO: An Ontology for Functional Genomics Investigations (2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 199-204. [PDF]

Dawn Field and Susanna-Assunta Sansone A Special Issue on Data Standards (2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 84-93. [PDF]

Susanna-Assunta Sansone, Philippe Rocca-Serra, Weida Tong, Jennifer Fostel, Norman Morrison, Andrew R. Jones. A Strategy Capitalizing on Synergies: The Reporting Structure for Biological Investigation (RSBI) Working Group (2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 164-171. [PDF]

Oliver Fiehn, Bruce Kristal, Ben Van Ommen, Lloyd W. Sumner, Susanna-Assunta Sansone, Chris Taylor, Nigel Hardy, Rima Kaddurah-Daouk. Establishing Reporting Standards for Metabolomic and Metabonomic Studies: A Call for Participation (2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 158-163. [PDF]

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 (2006). OMICS: A Journal of Integrative Biology, Vol.10 No.2, 172-178. [PDF]

Sansone SA, Waters MD, Viant MR. Databases and reporting methods (2006). Chapter for the The Handbook of Metabonomics and Metabolomics' book, edited by Lindon JC, Nicholson JK and Holmes S. Elsevier publisher.

Philippe Rocca-Serra and Elliott RM. Data storage: bringing us a step closer to data sharing? (2006). Br J Nutr, 95(6), 1237-9.

2005:

J.C. Lindon, J.K. Nicholson, H. Holmes, H.C. Keun, A. Craig, J.T.M. Pearce, S.J. Bruce, N. Hardy, S.A. Sansone et al. Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotech, 2005, 23: 833-838. [Abstract] [PDF].

P Garosi, C De Filippo, M van Erk, P Rocca-Serra, SA Sansone and R Elliott. Defining best practice for microarray analyses in nutrigenomic studies. British Journal of Nutrition, 2005, Vol 93, No 4: 425–432;DOI: 10.1079/BJN20041385. [Abstract].

R. Corvi, H. Ahr, S. Albertini, D.H. Blakey, L. Clerici, S. Coecke, G.R. Douglas, L. Gribaldo, J.P. Groten, B. Haase, K. Hamernik, T. Hartung, T. Inoue, I. Indans, D. Maurici, G. Orphanides, D. Rembges, S. Sansone, J.R. Snape, E. Toda, W. Tong, J.H. Delft, B. Weis, and L.M. Schechtman. Validation of Toxicogenomics-Based Test Systems: ECVAM-ICCVAM/NICEATM Considerations for Regulatory Use. Environ Health Perspect., 2005, doi:10.1289/ehp.8247. [PDF - 518kb].

2004:

S.A. Sansone, N. Morrison, P. Rocca-Serra and J. Fostel. Standardization initiatives in the (eco)toxicogenomics domain: a review. (2004). Comp Funct Genom, 5, 633-641. [Abstract] [PDF]

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