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Publications of Author

1. Richard Tong, John Quackenbush, Mark Snuffin
   Knowledge-Based Access to the Bio-Medical Literature, Ontologically-Grounded Experiments for the TREC 2003 Genomics Track. [Citation Graph (0, 0)][DBLP]
   TREC, 2003, pp:547-551 [Conf]
   
2. Catherine A. Ball, Gavin Sherlock, Helen E. Parkinson, Philippe Rocca-Serra, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank Holstege, Martin Ringwald, Paul T. Spellman, Christian J. Stoeckert Jr., Jason E. Stewart, Ronald Taylor, Alvis Brazma, John Quackenbush
   An open letter to the scientific journals. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2002, v:18, n:11, pp:1409- [Journal]
   
3. Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, John Quackenbush
   MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2005, v:21, n:15, pp:3324-3326 [Journal]
   
4. Adam A. Margolin, Joel Greshock, Tara L. Naylor, Yael Mosse, John M. Maris, Graham Bignell, Alexander I. Saeed, John Quackenbush, Barbara L. Weber
   CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2005, v:21, n:15, pp:3308-3311 [Journal]
   
5. Geo Pertea, Xiaoqiu Huang, Feng Liang, Valentin Antonescu, Razvan Sultana, Svetlana Karamycheva, Yuandan Lee, Joseph White, Foo Cheung, Babak Parvizi, Jennifer Tsai, John Quackenbush
   TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2003, v:19, n:5, pp:651-652 [Journal]
   
6. John Quackenbush, Steven Salzberg
   It is time to end the patenting of software. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2006, v:22, n:12, pp:1416-1417 [Journal]
   
7. Alexander Sturn, John Quackenbush, Zlatko Trajanoski
   Genesis: cluster analysis of microarray data. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2002, v:18, n:1, pp:207-208 [Journal]
   
8. John Quackenbush, Jennifer Cho, Daniel Lee, Feng Liang, Ingeborg Holt, Svetlana Karamycheva, Babak Parvizi, Geo Pertea, Razvan Sultana, Joseph White
   The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. [Citation Graph (0, 0)][DBLP]
   Nucleic Acids Research, 2001, v:29, n:1, pp:159-164 [Journal]
   
9. John Quackenbush, Feng Liang, Ingeborg Holt, Geo Pertea, Jonathan Upton
   The TIGR Gene Indices: reconstruction and representation of expressed gene sequences. [Citation Graph (0, 0)][DBLP]
   Nucleic Acids Research, 2000, v:28, n:1, pp:141-145 [Journal]
   
10. Qiaoping Yuan, Shu Ouyang, Jia Liu, Bernard Suh, Foo Cheung, Razvan Sultana, Daniel Lee, John Quackenbush, C. Robin Buell
    The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2003, v:31, n:1, pp:229-233 [Journal]
    
11. Yuandan Lee, Jennifer Tsai, S. Sunkara, Svetlana Karamycheva, Geo Pertea, Razvan Sultana, Valentin Antonescu, A. Chan, Foo Cheung, John Quackenbush
    The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:71-74 [Journal]
    
12. Agnes P. Chan, Geo Pertea, Foo Cheung, Dan Lee, Li Zheng, Cathy Whitelaw, Ana C. Pontaroli, Phillip SanMiguel, Yinan Yuan, Jeffrey Bennetzen, William Brad Barbazuk, John Quackenbush, Pablo D. Rabinowicz
    The TIGR Maize Database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2006, v:34, n:Database-Issue, pp:771-776 [Journal]
    
13. Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, X. Shirley Liu
    Microarray blob-defect removal improves array analysis. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2007, v:23, n:8, pp:966-971 [Journal]
    
14. 
    Stochasticity and Networks in Genomic Data. [Citation Graph (, )][DBLP]
    
    
15. 
    Session Introduction. [Citation Graph (, )][DBLP]
    
    
16. 
    Editorial. [Citation Graph (, )][DBLP]
    
    
17. 
    Papers on normalization, variable selection, classification or clustering of microarray data. [Citation Graph (, )][DBLP]
    
    
18. 
    Data-driven normalization strategies for high-throughput quantitative RT-PCR. [Citation Graph (, )][DBLP]
    
    
19. 
    A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. [Citation Graph (, )][DBLP]
    
    
20. 
    An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). [Citation Graph (, )][DBLP]