My NCBISign In
Design and implementation of microarray gene expression markup language (MAGE-ML)
Paul T Spellman, Michael Miller, Jason Stewart, Charles Troup, Ugis Sarkans, Steve Chervitz, Derek Bernhart, Gavin Sherlock, Catherine Ball, Marc Lepage, Marcin Swiatek, WL Marks, Jason Goncalves, Scott Markel, Daniel Iordan, Mohammadreza Shojatalab, Angel Pizarro, Joe White, Robert Hubley, Eric Deutsch, Martin Senger, Bruce J Aronow, Alan Robinson, Doug Bassett, Christian J Stoeckert, Jr, Alvis Brazma
Genome Biol. 2002; 3(9): research0046.1–research0046.9. Published online 2002 August 23.
PMCID:
PMC126871
Abstract Full Text PDF–95K

Is Cited by the Following 64 Articles in this Archive:

MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer
Akhilesh K. Bajpai, Sravanthi Davuluri, Darshan S. Chandrashekar, Selvarajan Ilakya, Mahalakshmi Dinakaran, Kshitish K. Acharya
PLoS One. 2012; 7(5): e36776. Published online 2012 May 11. doi: 10.1371/journal.pone.0036776
PMCID:
PMC3350469
Abstract Full Text PDF–2.1M
When One and One Gives More than Two: Challenges and Opportunities of Integrative Omics
Hyungwon Choi, Norman Pavelka
Front Genet. 2011; 2: 105. Prepublished online 2011 November 2. Published online 2012 January 6. doi: 10.3389/fgene.2011.00105
PMCID:
PMC3262227
Abstract Full Text PDF–544K
Towards interoperable and reproducible QSAR analyses: Exchange of datasets
Ola Spjuth, Egon L Willighagen, Rajarshi Guha, Martin Eklund, Jarl ES Wikberg
J Cheminform. 2010; 2: 5. Published online 2010 June 30. doi: 10.1186/1758-2946-2-5
PMCID:
PMC2909924
Abstract Full Text PDF–1.9M
Disease Gene Characterization through Large-Scale Co-Expression Analysis
Allen Day, Jun Dong, Vincent A. Funari, Bret Harry, Samuel P. Strom, Dan H. Cohn, Stanley F. Nelson
PLoS One. 2009; 4(12): e8491. Published online 2009 December 31. doi: 10.1371/journal.pone.0008491
PMCID:
PMC2797297
Abstract Full Text PDF–419K Supplementary Material
Data reporting standards: making the things we use better
John Quackenbush
Genome Med. 2009; 1(11): 111. Published online 2009 November 25. doi: 10.1186/gm111
PMCID:
PMC2808746
Abstract Full Text PDF–63K
Trends in modeling Biomedical Complex Systems
Luciano Milanesi, Paolo Romano, Gastone Castellani, Daniel Remondini, Petro Liò
BMC Bioinformatics. 2009; 10(Suppl 12): I1. Published online 2009 October 15. doi: 10.1186/1471-2105-10-S12-I1
PMCID:
PMC2762057
Abstract Full Text PDF–388K
Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets
Peter B. McGarvey, Hongzhan Huang, Raja Mazumder, Jian Zhang, Yongxing Chen, Chengdong Zhang, Stephen Cammer, Rebecca Will, Margie Odle, Bruno Sobral, Margaret Moore, Cathy H. Wu
PLoS One. 2009; 4(9): e7162. Published online 2009 September 25. doi: 10.1371/journal.pone.0007162
PMCID:
PMC2745575
Abstract Full Text PDF–762K Supplementary Material
MIMAS 3.0 is a Multiomics Information Management and Annotation System
Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig
BMC Bioinformatics. 2009; 10: 151. Published online 2009 May 18. doi: 10.1186/1471-2105-10-151
PMCID:
PMC2694794
Abstract Full Text PDF–280K
SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes
Hideya Kawaji, Yoshihide Hayashizaki, Carsten O Daub
BMC Bioinformatics. 2009; 10: 133. Published online 2009 May 7. doi: 10.1186/1471-2105-10-133
PMCID:
PMC2689195
Abstract Full Text PDF–1.6M Supplementary Material
Modeling genomic data with type attributes, balancing stability and maintainability
Norbert Busch, Gero Wedemann
BMC Bioinformatics. 2009; 10: 97. Published online 2009 March 27. doi: 10.1186/1471-2105-10-97
PMCID:
PMC2676260
Abstract Full Text PDF–333K
A national clinical decision support infrastructure to enable the widespread and consistent practice of genomic and personalized medicine
Kensaku Kawamoto, David F Lobach, Huntington F Willard, Geoffrey S Ginsburg
BMC Med Inform Decis Mak. 2009; 9: 17. Published online 2009 March 23. doi: 10.1186/1472-6947-9-17
PMCID:
PMC2666673
Abstract Full Text PDF–351K
ebTrack: an environmental bioinformatics system built upon ArrayTrack™
Minjun Chen, Jackson Martin, Hong Fang, Sastry Isukapalli, Panos G Georgopoulos, William J Welsh, Weida Tong
BMC Proc. 2009; 3(Suppl 2): S5. Published online 2009 March 10.
PMCID:
PMC2654488
Abstract Full Text PDF–308K
TRUNCATULIX – a data warehouse for the legume community
Kolja Henckel, Kai J Runte, Thomas Bekel, Michael Dondrup, Tobias Jakobi, Helge Küster, Alexander Goesmann
BMC Plant Biol. 2009; 9: 19. Published online 2009 February 11. doi: 10.1186/1471-2229-9-19
PMCID:
PMC2654896
Abstract Full Text PDF–1.0M
EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data
Michael Dondrup, Stefan P Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann
BMC Bioinformatics. 2009; 10: 50. Published online 2009 February 6. doi: 10.1186/1471-2105-10-50
PMCID:
PMC2645365
Abstract Full Text PDF–2.3M
MiMiR – an integrated platform for microarray data sharing, mining and analysis
Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou, Pat Soutter, Tim Aitman, Laurence Game
BMC Bioinformatics. 2008; 9: 379. Published online 2008 September 18. doi: 10.1186/1471-2105-9-379
PMCID:
PMC2572073
Abstract Full Text PDF–1.1M Supplementary Material
Data capture in bioinformatics: requirements and experiences with Pedro
Daniel Jameson, Kevin Garwood, Chris Garwood, Tim Booth, Pinar Alper, Stephen G Oliver, Norman W Paton
BMC Bioinformatics. 2008; 9: 183. Published online 2008 April 10. doi: 10.1186/1471-2105-9-183
PMCID:
PMC2335277
Abstract Full Text PDF–969K
A software framework for microarray and gene expression object model (MAGE-OM) array design annotation
Matloob Qureshi, Alasdair Ivens
BMC Genomics. 2008; 9: 133. Published online 2008 March 20. doi: 10.1186/1471-2164-9-133
PMCID:
PMC2358904
Abstract Full Text PDF–431K Supplementary Material
The XBabelPhish MAGE-ML and XML Translator
Don Maier, Farrell Wymore, Gavin Sherlock, Catherine A Ball
BMC Bioinformatics. 2008; 9: 28. Published online 2008 January 18. doi: 10.1186/1471-2105-9-28
PMCID:
PMC2233607
Abstract Full Text PDF–922K
CoryneCenter – An online resource for the integrated analysis of corynebacterial genome and transcriptome data
Heiko Neuweger, Jan Baumbach, Stefan Albaum, Thomas Bekel, Michael Dondrup, Andrea T Hüser, Jörn Kalinowski, Sebastian Oehm, Alfred Pühler, Sven Rahmann, Jochen Weile, Alexander Goesmann
BMC Syst Biol. 2007; 1: 55. Published online 2007 November 22. doi: 10.1186/1752-0509-1-55
PMCID:
PMC2212648
Abstract Full Text PDF–1.9M Supplementary Material
DNA Microarrays: a Powerful Genomic Tool for Biomedical and Clinical Research
Victor Trevino, Francesco Falciani, Hugo A Barrera-Saldaña
Mol Med. 2007 Sep-Oct; 13(9-10): 527–541. doi: 10.2119/2006-00107.Trevino
PMCID:
PMC1933257
Abstract Full Text PDF–5.3M
Celsius: a community resource for Affymetrix microarray data
Allen Day, Marc RJ Carlson, Jun Dong, Brian D O'Connor, Stanley F Nelson
Genome Biol. 2007; 8(6): R112. Published online 2007 June 14. doi: 10.1186/gb-2007-8-6-r112
PMCID:
PMC2394754
Abstract Full Text PDF–583K Supplementary Material
Sharing Detailed Research Data Is Associated with Increased Citation Rate
Heather A. Piwowar, Roger S. Day, Douglas B. Fridsma
PLoS ONE. 2007; 2(3): e308. Published online 2007 March 21. doi: 10.1371/journal.pone.0000308
PMCID:
PMC1817752
Abstract Full Text PDF–89K Supplementary Material
The Genopolis Microarray Database
Andrea Splendiani, Marco Brandizi, Gael Even, Ottavio Beretta, Norman Pavelka, Mattia Pelizzola, Manuel Mayhaus, Maria Foti, Giancarlo Mauri, Paola Ricciardi-Castagnoli
BMC Bioinformatics. 2007; 8(Suppl 1): S21. Published online 2007 March 8. doi: 10.1186/1471-2105-8-S1-S21
PMCID:
PMC1885851
Abstract Full Text PDF–1.0M
Bias, Randomization, and Ovarian Proteomic Data: A Reply to “Producers and Consumers”
Keith A. Baggerly, Kevin R. Coombes, Jeffrey S. Morris
Cancer Inform. 2005; 1(1): 9–14. Published online 2007 February 26.
PMCID:
PMC2657654
Abstract Full Text PDF–2.1M
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research
Jomol P Mathew, Barry S Taylor, Gary D Bader, Saiju Pyarajan, Marco Antoniotti, Arul M Chinnaiyan, Chris Sander, Steven J Burakoff, Bud Mishra
PLoS Comput Biol. 2007 February; 3(2): e12. Published online 2007 February 23. doi: 10.1371/journal.pcbi.0030012
PMCID:
PMC1808026
Full Text PDF–452K
The Stanford Microarray Database: implementation of new analysis tools and open source release of software
Janos Demeter, Catherine Beauheim, Jeremy Gollub, Tina Hernandez-Boussard, Heng Jin, Donald Maier, John C. Matese, Michael Nitzberg, Farrell Wymore, Zachariah K. Zachariah, Patrick O. Brown, Gavin Sherlock, Catherine A. Ball
Nucleic Acids Res. 2007 January; 35(Database issue): D766–D770. Published online 2006 December 20. doi: 10.1093/nar/gkl1019
PMCID:
PMC1781111
Abstract Full Text PDF–380K
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it
Kevin Garwood, Christopher Garwood, Cornelia Hedeler, Tony Griffiths, Neil Swainston, Stephen G Oliver, Norman W Paton
BMC Bioinformatics. 2006; 7: 532. Published online 2006 December 14. doi: 10.1186/1471-2105-7-532
PMCID:
PMC1713253
Abstract Full Text PDF–887K
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Tim F Rayner, Philippe Rocca-Serra, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, Junmin Liu, Donald S Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J Stoeckert, Jr, Joseph White, Patricia L Whetzel, Farrell Wymore, Helen Parkinson, Ugis Sarkans, Catherine A Ball, Alvis Brazma
BMC Bioinformatics. 2006; 7: 489. Published online 2006 November 6. doi: 10.1186/1471-2105-7-489
PMCID:
PMC1687205
Abstract Full Text PDF–1.1M
XML schemas for common bioinformatic data types and their application in workflow systems
Philipp N Seibel, Jan Krüger, Sven Hartmeier, Knut Schwarzer, Kai Löwenthal, Henning Mersch, Thomas Dandekar, Robert Giegerich
BMC Bioinformatics. 2006; 7: 490. Published online 2006 November 6. doi: 10.1186/1471-2105-7-490
PMCID:
PMC2001303
Abstract Full Text PDF–495K
A fisheye viewer for microarray-based gene expression data
Min Wu, Cheng Thao, Xiangming Mu, Ethan V Munson
BMC Bioinformatics. 2006; 7: 452. Published online 2006 October 13. doi: 10.1186/1471-2105-7-452
PMCID:
PMC1635570
Abstract Full Text PDF–1021K
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