Publications
BioMart has been featured in peer reviewed publications for over 10 years
The list below showcases publications featuring BioMart, including Nature Methods' Technology Feature and the DATABASE Special Issue Dedicated to BioMart which documents the impressive achievements of the BioMart Community over the last ten years.
Citing BioMart
When citing BioMart, refer to this paper:
BioMart: driving a paradigm change in biological data management. Database (Oxford). 2011 Nov 13;2011:bar049. Print 2011. PubMed PMID: 22083790;|
Nature Methods' Technology Feature Quantitative data: learning to share. Nature Methods 9, 39–41 (2012) doi:10.1038/nmeth.1815DATABASE Special Issue Dedicated to BioMart This issue recognizes BioMart's outstanding contributions to bioinformatics and documents the achievements of the BioMart community. DATABASE Special Issue Dedicated to BioMart |
featured in nature methods and database |
Publications by the BioMart Team
| Title | Author | Read Online |
|---|---|---|
| BioMart: driving a paradigm change in biological data management | Kasprzyk A | Database Vol. 2011, doi:10.1093/database/bar049 |
| BioMart Central Portal: An Open Database Network for Biological Community | Jonathan M. Guberman, J. Ai, O. Arnaiz, Joachim Baran, Andrew Blake, Richard Baldock, Claude Chelala, David Croft, Anthony Cros, Rosalind J. Cutts, A. Di Génova, Simon Forbes, T. Fujisawa, E. Gadaleta, D. M. Goodstein, Gunes Gundem, Bernard Haggarty, Syed Haider, Matthew Hall, Todd Harris, Robin Haw, S. Hu, Simon Hubbard, Jack Hsu, Vivek Iyer, Philip Jones, Toshiaki Katayama, R. Kinsella, Lei Kong, Daniel Lawson, Yong Liang, Nuria Lopez-Bigas, J. Luo, Michael Lush, Jeremy Mason, Francois Moreews, Nelson Ndegwa, Darren Oakley, Christian Perez-Llamas, Michael Primig, Elena Rivkin, S. Rosanoff, Rebecca Shepherd, Reinhard Simon, B. Skarnes, Damian Smedley, Linda Sperling, William Spooner, Peter Stevenson, Kevin Stone, J. Teague, Jun Wang, Jianxin Wang, Brett Whitty, D. T. Wong, Marie Wong-Erasmus, L. Yao, Ken Youens-Clark, Christina Yung, Junjun Zhang, and Arek Kasprzyk | Database Vol. 2011, doi:10.1093/database/bar041 |
| BioMart: A data federation framework for large collaborative projects | Junjun Zhang, Syed Haider, Joachim Baran, Anthony Cros, Jonathan M. Guberman, Jack Hsu, Yong Liang, Long Yao, and Arek Kasprzyk | Database Vol. 2011, doi:10.1093/database/bar049 |
| International Cancer Genome Consortium Data Portal: A One Stop Shop for Cancer Genomics Data | Junjun Zhang, Joachim Baran, A. Cros, Jonathan M. Guberman, Syed Haider, Jack Hsu, Yong Liang, Elena Rivkin, Jianxin Wang, Brett Whitty, Marie Wong-Erasmus, Long Yao, and Arek Kasprzyk | Database Vol. 2011, doi:10.1093/database/bar026 |
| BioMart Central Portal - unified access to biological data | Haider S, Ballester B, Smedley, D, Zhang J, Rice P, Kasprzyk A | Nucliec Acids Res. 2009 July 1; 37(Web Server issue) : W23-7 |
| BioMart - biological queries made easy | Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A | BMC Genomics. 2009 Jan 14;10:22 |
| BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis | Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W | Bioinformatics. 2005 Aug 15;21(16):3439-40 |
| EnsMart: A Generic System for Fast and Flexible Access to Biological Data | Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E | Genome Res. 2004 Jan; 14(1):160-169 |
Publications by the BioMart Community
| Title | Author | Read Online |
|---|---|---|
| RNAbrowse: RNA-Seq De Novo Assembly Results Browser | Jérôme Mariette, Céline Noirot, Ibounyamine Nabihoudine, Philippe Bardou, Claire Hoede, Anis Djari, Cédric Cabau, Christophe Klopp | PLoS ONE 9(5): e96821. doi:10.1371/journal.pone.0096821 |
| Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations | Nelson Ndegwa, Richard G. Côté, David Ovelleiro, Peter D'Eustachio, Henning Hermjakob, Juan A. Vizcaíno and David Croft | Database Vol. 2011, doi:10.1093/database/bar047 |
| Integrative Cancer Genomics (IntOGen) in BioMart | Christian Perez-Llamas, Gunes Gundem and Nuria Lopez-Bigas | Database Vol. 2011, doi:10.1093/database/bar039 |
| The InterPro BioMart: Powerful, federated query and web-service access to the InterPro resource | Philip Jones, David Binns, Conor McMenamin, Craig McAnulla, and Sarah Hunter | Database Vol. 2011, doi:10.1093/database/bar033 |
| The Reactome BioMart | Robin Haw, David Croft, Christina K Yung, Nelson Ndegwa, Peter D'Eustachio, Henning Hermajakob and Lincoln Stein | Database Vol. 2011, doi:10.1093/database/bar031 |
| Ensembl BioMarts: a hub for data retrieval across the taxonomic space | Rhoda J. Kinsella, Andreas Kähäri, Syed Haider, Jorge Zamora, Glenn Proctor, Giulietta Spudich, Jeff Almeida-King, Daniel Staines, Paul Derwent, Arnaud Kerhornou, Paul Kersey, and Paul Flicek | Database Vol. 2011, doi:10.1093/database/bar030 |
| The BioMart interface to the EMAGE gene expression database | Peter Stevenson, Lorna Richardson, Shanmugasundaram Venkataraman, Yiya Yang, Richard Baldock | Database Vol. 2011, doi:10.1093/database/bar029 |
| BioMart as an integration solution for the International Knockout Mouse Consortium | Darren J. Oakley, Vivek Iyer, William C. Skarnes, and Damian Smedley | Database Vol. 2011, doi:10.1093/database/bar028 |
| SigReannot-mart: A query environment for expression microarray probe re-annotations | François Moreews, Gaelle Rauffet, Patrice Dehais, and Christophe Klopp | Database Vol. 2011, doi:10.1093/database/bar025 |
| Using BioMart as a framework to manage and query pancreatic cancer data | Rosalind J. Cutts, Emanuela Gadaleta, Nicholas R. Lemoine, and Claude Chelala | Database Vol. 2011, doi:10.1093/database/bar024 |
| Data mining using the Catalogue of Somatic Mutations in Cancer BioMart | Rebecca Shepherd, Simon A. Forbes, David Beare, S. Bamford, Charlotte G. Cole, Sari Ward, Nidhi Bindal, Prasad Gunasekaran, Mingming Jia, Chai Yin Kok, Kenric Leung, Andrew Menzies, Adam P. Butler, Jon W. Teague, Peter J. Campbell, Michael R. Stratton, and P. Andrew Futreal | Database Vol. 2011, doi:10.1093/database/bar018 |
| BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. | Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, Huber W | Bioinformatics 2005 Aug;21(16):3439-40 |
| Shopping in the genome market with EnsMart | Gilbert D | Brief Bioinform. 2003 Sep;4(3):292-6 |