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Vol. 12, Issue 3, 493-502, March 2002
RESOURCES
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  Y. Arai, M. Hayashi, and M. Nishimura Proteomic Analysis of Highly Purified Peroxisomes from Etiolated Soybean Cotyledons Plant Cell Physiol., April 1, 2008; 49(4): 526 - 539. [Abstract] [Full Text] [PDF]
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 L. J. Jensen, P. Julien, M. Kuhn, C. von Mering, J. Muller, T. Doerks, and P. Bork eggNOG: automated construction and annotation of orthologous groups of genes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D250 - D254. [Abstract] [Full Text] [PDF]
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G. C. Nickel, D. Tefft, and M. D. Adams Human PAML browser: a database of positive selection on human genes using phylogenetic methods Nucleic Acids Res., January 11, 2008; 36(suppl_1): D800 - D808. [Abstract] [Full Text] [PDF]
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 K. Rannikko, C. Ortutay, and M. Vihinen Immunity genes and their orthologs: a multi-species database Int. Immunol., December 1, 2007; 19(12): 1361 - 1370. [Abstract] [Full Text] [PDF]
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 A. Schneider, C. Dessimoz, and G. H. Gonnet OMA Browser Exploring orthologous relations across 352 complete genomes Bioinformatics, August 15, 2007; 23(16): 2180 - 2182. [Abstract] [Full Text] [PDF]
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Y. Zhou and L. F. Landweber BLASTO: a tool for searching orthologous groups Nucleic Acids Res., July 13, 2007; 35(suppl_2): W678 - W682. [Abstract] [Full Text] [PDF]
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 J. Quackenbush Extracting biology from high-dimensional biological data J. Exp. Biol., May 1, 2007; 210(9): 1507 - 1517. [Abstract] [Full Text] [PDF]
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 P. Chavan, K. Joshi, and B. Patwardhan DNA Microarrays in Herbal Drug Research Evid. Based Complement. Altern. Med., December 1, 2006; 3(4): 447 - 457. [Abstract] [Full Text] [PDF]
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 F. Wu, L. A. Mueller, D. Crouzillat, V. Petiard, and S. D. Tanksley Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade Genetics, November 1, 2006; 174(3): 1407 - 1420. [Abstract] [Full Text] [PDF]
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C. Dessimoz, B. Boeckmann, A. C. J. Roth, and G. H. Gonnet Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits Nucleic Acids Res., July 11, 2006; 34(11): 3309 - 3316. [Abstract] [Full Text] [PDF]
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R. Jothi, E. Zotenko, A. Tasneem, and T. M. Przytycka COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations Bioinformatics, April 1, 2006; 22(7): 779 - 788. [Abstract] [Full Text] [PDF]
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 X. W. Zhou, B. F. C. Kafsack, R. N. Cole, P. Beckett, R. F. Shen, and V. B. Carruthers The Opportunistic Pathogen Toxoplasma gondii Deploys a Diverse Legion of Invasion and Survival Proteins J. Biol. Chem., October 7, 2005; 280(40): 34233 - 34244. [Abstract] [Full Text] [PDF]
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 S.-F. Ma, D. N. Grigoryev, A. D. Taylor, S. Nonas, S. Sammani, S. Q. Ye, and J. G. N. Garcia Bioinformatic identification of novel early stress response genes in rodent models of lung injury Am J Physiol Lung Cell Mol Physiol, September 1, 2005; 289(3): L468 - L477. [Abstract] [Full Text] [PDF]
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Y. Zhang miRU: an automated plant miRNA target prediction server Nucleic Acids Res., July 1, 2005; 33(suppl_2): W701 - W704. [Abstract] [Full Text] [PDF]
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X. H. Zheng, F. Lu, Z.-Y. Wang, F. Zhong, J. Hoover, and R. Mural Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs Bioinformatics, March 15, 2005; 21(6): 703 - 710. [Abstract] [Full Text] [PDF]
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Y. Lee, J. Tsai, S. Sunkara, S. Karamycheva, G. Pertea, R. Sultana, V. Antonescu, A. Chan, F. Cheung, and J. Quackenbush The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes Nucleic Acids Res., January 1, 2005; 33(suppl_1): D71 - D74. [Abstract] [Full Text] [PDF]
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 A. Coventry, D. J. Kleitman, and B. Berger MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure PNAS, August 17, 2004; 101(33): 12102 - 12107. [Abstract] [Full Text] [PDF]
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 The Ludwig-FAPESP Transcript Finishing Initiative, M. C. Sogayar, and A. A. Camargo A Transcript Finishing Initiative for Closing Gaps in the Human Transcriptome Genome Res., July 1, 2004; 14(7): 1413 - 1423. [Abstract] [Full Text] [PDF]
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 B. Kutlu, A. K. Cardozo, M. I. Darville, M. Kruhoffer, N. Magnusson, T. Orntoft, and D. L. Eizirik Discovery of Gene Networks Regulating Cytokine-Induced Dysfunction and Apoptosis in Insulin-Producing INS-1 Cells Diabetes, November 1, 2003; 52(11): 2701 - 2719. [Abstract] [Full Text] [PDF]
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 J. M. Stuart, E. Segal, D. Koller, and S. K. Kim A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules Science, October 10, 2003; 302(5643): 249 - 255. [Abstract] [Full Text] [PDF]
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L. Li, C. J. Stoeckert Jr., and D. S. Roos OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes Genome Res., September 1, 2003; 13(9): 2178 - 2189. [Abstract] [Full Text] [PDF]
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 M. J. Sanderson, A. C. Driskell, R. H. Ree, O. Eulenstein, and S. Langley Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases Mol. Biol. Evol., July 1, 2003; 20(7): 1036 - 1042. [Abstract] [Full Text] [PDF]
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 H. Zhu, D.-J. Kim, J.-M. Baek, H.-K. Choi, L. C. Ellis, H. Kuester, W. R. McCombie, H.-M. Peng, and D. R. Cook Syntenic Relationships between Medicago truncatula and Arabidopsis Reveal Extensive Divergence of Genome Organization Plant Physiology, March 1, 2003; 131(3): 1018 - 1026. [Abstract] [Full Text] [PDF]
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Q. Yuan, S. Ouyang, J. Liu, B. Suh, F. Cheung, R. Sultana, D. Lee, J. Quackenbush, and C. R. Buell The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists Nucleic Acids Res., January 1, 2003; 31(1): 229 - 233. [Abstract] [Full Text] [PDF]
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 A. Turchin and I. S. Kohane Gene homology resources on the World Wide Web Physiol Genomics, December 3, 2002; 11(3): 165 - 177. [Abstract] [Full Text] [PDF]
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T. S. Tanaka, T. Kunath, W. L. Kimber, S. A. Jaradat, C. A. Stagg, M. Usuda, T. Yokota, H. Niwa, J. Rossant, and M. S.H. Ko Gene Expression Profiling of Embryo-Derived Stem Cells Reveals Candidate Genes Associated With Pluripotency and Lineage Specificity Genome Res., December 1, 2002; 12(12): 1921 - 1928. [Abstract] [Full Text] [PDF]
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P. Ayoubi, X. Jin, S. Leite, X. Liu, J. Martajaja, A. Abduraham, Q. Wan, W. Yan, E. Misawa, and R. A. Prade PipeOnline 2.0: automated EST processing and functional data sorting Nucleic Acids Res., November 1, 2002; 30(21): 4761 - 4769. [Abstract] [Full Text] [PDF]
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) database to provide a
cross-reference between fully and partially sequenced eukaryotic
transcribed sequences. Starting with the assembled expressed sequence
tag (EST) and gene sequences that comprise the 28 TIGR Gene Indices, we
used high-stringency pair-wise sequence searches and a reflexive,
transitive closure process to associate sequence-specific best hits,
generating 32,652 tentative ortholog groups (TOGs). This has allowed us
to identify putative orthologs and paralogs for known genes, as well as
those that exist only as uncharacterized ESTs and to provide links to
additional information including genome sequence and mapping data. TOGA
provides an important new resource for the analysis of gene function in
eukaryotes. In addition, an analysis of the most widely represented
sequences can begin to provide insight into eukaryotic biological processes.