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.

Publications by the BioMart Community

Title Author Read Online
The BioMart community portal: an innovative alternative to large, centralized data repositories Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J. Brookes, Gabriele Bucci, Iwan Buetti, Sarah Burge, Cedric Cabau, Joseph W. Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J. Cutts, Erik Dassi, Alex Di Genova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon Forbes, Robert C. Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M. Garcia-Manteiga, David Goodstein, Kristian Gray, Jose Afonso Guerra-Assuncao, Bernard Haggarty, Dong-Jin Han, Byung Woo Han, Todd Harris, Jayson Harshbarger, Robert K. Hastings, Richard D. Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe Klopp, Lei K ong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Lio, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jerome Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, Francois Moreews, Ibounyamine Nabihoudine, Nelson Ndegwa, Celine Noirot, Cristian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M. Staines, Delphine Steinbach, Kevin Stone, Elia Stupka, Jon W. Teague, Abu Z. Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, Arek Kasprzyk Nucleic Acids Research 2015.
doi: 10.1093/nar/gkv350
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
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
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 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
Shopping in the genome market with EnsMart Gilbert D Brief Bioinform. 2003 Sep;4(3):292-6