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Vol. 11, Issue 8, 1425-1433, August 2001
RESOURCES
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  Y.-T. Huang, F.-C. Chen, C.-J. Chen, H.-L. Chen, and T.-J. Chuang Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons Genome Res., July 1, 2008; 18(7): 1163 - 1170. [Abstract] [Full Text] [PDF]
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 D. Qiu, J. Xiao, W. Xie, H. Liu, X. Li, L. Xiong, and S. Wang Rice Gene Network Inferred from Expression Profiling of Plants Overexpressing OsWRKY13, a Positive Regulator of Disease Resistance Mol Plant, May 1, 2008; 1(3): 538 - 551. [Abstract] [Full Text] [PDF]
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 G. M. Jones, D. S. Cram, B. Song, M. C. Magli, L. Gianaroli, O. Lacham-Kaplan, J. K. Findlay, G. Jenkin, and A. O. Trounson Gene expression profiling of human oocytes following in vivo or in vitro maturation Hum. Reprod., May 1, 2008; 23(5): 1138 - 1144. [Abstract] [Full Text] [PDF]
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 L. Marselli, J. Thorne, Y.-B. Ahn, A. Omer, D. C. Sgroi, T. Libermann, H. H. Otu, A. Sharma, S. Bonner-Weir, and G. C. Weir Gene Expression of Purified {beta}-Cell Tissue Obtained from Human Pancreas with Laser Capture Microdissection J. Clin. Endocrinol. Metab., March 1, 2008; 93(3): 1046 - 1053. [Abstract] [Full Text] [PDF]
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 D. Masotti, C. Nardini, S. Rossi, E. Bonora, G. Romeo, S. Volinia, and L. Benini TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders Bioinformatics, February 1, 2008; 24(3): 428 - 429. [Abstract] [Full Text] [PDF]
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 E. L. Hong, R. Balakrishnan, Q. Dong, K. R. Christie, J. Park, G. Binkley, M. C. Costanzo, S. S. Dwight, S. R. Engel, D. G. Fisk, et al. Gene Ontology annotations at SGD: new data sources and annotation methods Nucleic Acids Res., January 11, 2008; 36(suppl_1): D577 - D581. [Abstract] [Full Text] [PDF]
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The Gene Ontology Consortium The Gene Ontology project in 2008 Nucleic Acids Res., January 11, 2008; 36(suppl_1): D440 - D444. [Abstract] [Full Text] [PDF]
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 F. E. Lovegrove, S. A. Gharib, S. N. Patel, C. A. Hawkes, K. C. Kain, and W. C. Liles Expression Microarray Analysis Implicates Apoptosis and Interferon-Responsive Mechanisms in Susceptibility to Experimental Cerebral Malaria Am. J. Pathol., December 1, 2007; 171(6): 1894 - 1903. [Abstract] [Full Text] [PDF]
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 I. N. Sarkar Biodiversity informatics: organizing and linking information across the spectrum of life Brief Bioinform, September 1, 2007; 8(5): 347 - 357. [Abstract] [Full Text] [PDF]
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J. R. Pollack A Perspective on DNA Microarrays in Pathology Research and Practice Am. J. Pathol., August 1, 2007; 171(2): 375 - 385. [Abstract] [Full Text] [PDF]
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J. Reimand, M. Kull, H. Peterson, J. Hansen, and J. Vilo g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments Nucleic Acids Res., July 13, 2007; 35(suppl_2): W193 - W200. [Abstract] [Full Text] [PDF]
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W. A. Baumgartner Jr, K. B. Cohen, L. M. Fox, G. Acquaah-Mensah, and L. Hunter Manual curation is not sufficient for annotation of genomic databases Bioinformatics, July 1, 2007; 23(13): i41 - i48. [Abstract] [Full Text] [PDF]
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 F.-C. Chen, S.-M. Chaw, Y.-H. Tzeng, S.-S. Wang, and T.-J. Chuang Opposite Evolutionary Effects between Different Alternative Splicing Patterns Mol. Biol. Evol., July 1, 2007; 24(7): 1443 - 1446. [Abstract] [Full Text] [PDF]
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 B. Palenik, J. Grimwood, A. Aerts, P. Rouze, A. Salamov, N. Putnam, C. Dupont, R. Jorgensen, E. Derelle, S. Rombauts, et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation PNAS, May 1, 2007; 104(18): 7705 - 7710. [Abstract] [Full Text] [PDF]
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 E. P. Murchison, P. Stein, Z. Xuan, H. Pan, M. Q. Zhang, R. M. Schultz, and G. J. Hannon Critical roles for Dicer in the female germline Genes & Dev., March 15, 2007; 21(6): 682 - 693. [Abstract] [Full Text] [PDF]
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 F.-C. Chen, S.-S. Wang, S.-M. Chaw, Y.-T. Huang, and T.-J. Chuang Plant Gene and Alternatively Spliced Variant Annotator. A Plant Genome Annotation Pipeline for Rice Gene and Alternatively Spliced Variant Identification with Cross-Species Expressed Sequence Tag Conservation from Seven Plant Species Plant Physiology, March 1, 2007; 143(3): 1086 - 1095. [Abstract] [Full Text] [PDF]
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X. Ma, H. Lee, L. Wang, and F. Sun CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data Bioinformatics, January 15, 2007; 23(2): 215 - 221. [Abstract] [Full Text] [PDF]
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F. Kolpakov, V. Poroikov, R. Sharipov, Y. Kondrakhin, A. Zakharov, A. Lagunin, L. Milanesi, and A. Kel CYCLONET--an integrated database on cell cycle regulation and carcinogenesis Nucleic Acids Res., January 12, 2007; 35(suppl_1): D550 - D556. [Abstract] [Full Text] [PDF]
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T. Bieri, D. Blasiar, P. Ozersky, I. Antoshechkin, C. Bastiani, P. Canaran, J. Chan, N. Chen, W. J. Chen, P. Davis, et al. WormBase: new content and better access Nucleic Acids Res., January 12, 2007; 35(suppl_1): D506 - D510. [Abstract] [Full Text] [PDF]
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O. Arnaiz, S. Cain, J. Cohen, and L. Sperling ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data Nucleic Acids Res., January 12, 2007; 35(suppl_1): D439 - D444. [Abstract] [Full Text] [PDF]
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F.-C. Chen, C.-J. Chen, W.-H. Li, and T.-J. Chuang Human-specific insertions and deletions inferred from mammalian genome sequences Genome Res., January 1, 2007; 17(1): 16 - 22. [Abstract] [Full Text] [PDF]
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 M. Gorantla, P. Babu, V. Reddy Lachagari, A. Reddy, R. Wusirika, J. L. Bennetzen, and A. R. Reddy Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings J. Exp. Bot., January 1, 2007; 58(2): 253 - 265. [Abstract] [Full Text] [PDF]
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S. Draghici, S. Sellamuthu, and P. Khatri Babel's tower revisited: a universal resource for cross-referencing across annotation databases Bioinformatics, December 1, 2006; 22(23): 2934 - 2939. [Abstract] [Full Text] [PDF]
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A. V. Evsikov, J. H. Graber, J. M. Brockman, A. Hampl, A. E. Holbrook, P. Singh, J. J. Eppig, D. Solter, and B. B. Knowles Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo Genes & Dev., October 1, 2006; 20(19): 2713 - 2727. [Abstract] [Full Text] [PDF]
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S. Myhre, H. Tveit, T. Mollestad, and A. Laegreid Additional Gene Ontology structure for improved biological reasoning Bioinformatics, August 15, 2006; 22(16): 2020 - 2027. [Abstract] [Full Text] [PDF]
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S. Rossi, D. Masotti, C. Nardini, E. Bonora, G. Romeo, E. Macii, L. Benini, and S. Volinia TOM: a web-based integrated approach for identification of candidate disease genes. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W285 - W292. [Abstract] [Full Text] [PDF]
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J. Rainer, F. Sanchez-Cabo, G. Stocker, A. Sturn, and Z. Trajanoski CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W498 - W503. [Abstract] [Full Text] [PDF]
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P. Khatri, V. Desai, A. L. Tarca, S. Sellamuthu, D. E. Wildman, R. Romero, and S. Draghici New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W626 - W631. [Abstract] [Full Text] [PDF]
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 T. N. Kristensen, P. Sorensen, K. S. Pedersen, M. Kruhoffer, and V. Loeschcke Inbreeding by Environmental Interactions Affect Gene Expression in Drosophila melanogaster Genetics, July 1, 2006; 173(3): 1329 - 1336. [Abstract] [Full Text] [PDF]
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F. J. Troost, R.-J. M. Brummer, G. R. M. M. Haenen, A. Bast, R. I. van Haaften, C. T. Evelo, and W. H. M. Saris Gene expression in human small intestinal mucosa in vivo is mediated by iron-induced oxidative stress Physiol Genomics, April 11, 2006; 25(2): 242 - 249. [Abstract] [Full Text] [PDF]
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F. J. Troost, R.-J. M. Brummer, G. R. M. M. Haenen, A. Bast, R. I. van Haaften, C. T. Evelo, and W. H. M. Saris Gene expression in human small intestinal mucosa in vivo is mediated by iron-induced oxidative stress Physiol Genomics, April 11, 2006; 25(2): 242 - 249. [Abstract] [Full Text] [PDF]
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P. L. Whetzel, H. Parkinson, H. C. Causton, L. Fan, J. Fostel, G. Fragoso, L. Game, M. Heiskanen, N. Morrison, P. Rocca-Serra, et al. The MGED Ontology: a resource for semantics-based description of microarray experiments Bioinformatics, April 1, 2006; 22(7): 866 - 873. [Abstract] [Full Text] [PDF]
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 S. A. Gharib, W. C. Liles, G. Matute-Bello, R. W. Glenny, T. R. Martin, and W. A. Altemeier Computational Identification of Key Biological Modules and Transcription Factors in Acute Lung Injury Am. J. Respir. Crit. Care Med., March 15, 2006; 173(6): 653 - 658. [Abstract] [Full Text] [PDF]
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S. Stamm, J.-J. Riethoven, V. Le Texier, C. Gopalakrishnan, V. Kumanduri, Y. Tang, N. L. Barbosa-Morais, and T. A. Thanaraj ASD: a bioinformatics resource on alternative splicing Nucleic Acids Res., January 1, 2006; 34(suppl_1): D46 - D55. [Abstract] [Full Text] [PDF]
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T. Grotkjaer, O. Winther, B. Regenberg, J. Nielsen, and L. K. Hansen Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm Bioinformatics, January 1, 2006; 22(1): 58 - 67. [Abstract] [Full Text] [PDF]
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Gene Ontology Consortium The Gene Ontology (GO) project in 2006 Nucleic Acids Res., January 1, 2006; 34(suppl_1): D322 - D326. [Abstract] [Full Text] [PDF]
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E. M. Schwarz, I. Antoshechkin, C. Bastiani, T. Bieri, D. Blasiar, P. Canaran, J. Chan, N. Chen, W. J. Chen, P. Davis, et al. WormBase: better software, richer content Nucleic Acids Res., January 1, 2006; 34(suppl_1): D475 - D478. [Abstract] [Full Text] [PDF]
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R. M. Zayas, A. Hernandez, B. Habermann, Y. Wang, J. M. Stary, and P. A. Newmark The planarian Schmidtea mediterranea as a model for epigenetic germ cell specification: Analysis of ESTs from the hermaphroditic strain PNAS, December 20, 2005; 102(51): 18491 - 18496. [Abstract] [Full Text] [PDF]
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R. M. Zayas, T. D. Bold, and P. A. Newmark Spliced-Leader trans-Splicing in Freshwater Planarians Mol. Biol. Evol., October 1, 2005; 22(10): 2048 - 2054. [Abstract] [Full Text] [PDF]
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Q.-Y. He, J. Cao, X.-H. Liu, M.-X. Li, Y.-S. Liu, J.-Y. Xie, and S.-P. Liang DEPD: a novel database for differentially expressed proteins Bioinformatics, September 15, 2005; 21(18): 3694 - 3696. [Abstract] [Full Text] [PDF]
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T. N. Kristensen, P. Sorensen, M. Kruhoffer, K. S. Pedersen, and V. Loeschcke Genome-Wide Analysis on Inbreeding Effects on Gene Expression in Drosophila melanogaster Genetics, September 1, 2005; 171(1): 157 - 167. [Abstract] [Full Text] [PDF]
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J. McDermott, R. Bumgarner, and R. Samudrala Functional annotation from predicted protein interaction networks Bioinformatics, August 1, 2005; 21(15): 3217 - 3226. [Abstract] [Full Text] [PDF]
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J. D. Thompson, S. R. Holbrook, K. Katoh, P. Koehl, D. Moras, E. Westhof, and O. Poch MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences Nucleic Acids Res., July 25, 2005; 33(13): 4164 - 4171. [Abstract] [Full Text] [PDF]
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A. Hsiao, T. Ideker, J. M. Olefsky, and S. Subramaniam VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data Nucleic Acids Res., July 1, 2005; 33(suppl_2): W627 - W632. [Abstract] [Full Text] [PDF]
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P. Khatri, S. Sellamuthu, P. Malhotra, K. Amin, A. Done, and S. Draghici Recent additions and improvements to the Onto-Tools Nucleic Acids Res., July 1, 2005; 33(suppl_2): W762 - W765. [Abstract] [Full Text] [PDF]
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P. H. Lee and D. Lee Modularized learning of genetic interaction networks from biological annotations and mRNA expression data Bioinformatics, June 1, 2005; 21(11): 2739 - 2747. [Abstract] [Full Text] [PDF]
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H. Wu, Z. Su, F. Mao, V. Olman, and Y. Xu Prediction of functional modules based on comparative genome analysis and Gene Ontology application Nucleic Acids Res., May 18, 2005; 33(9): 2822 - 2837. [Abstract] [Full Text] [PDF]
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C. H. Busold, S. Winter, N. Hauser, A. Bauer, J. Dippon, J. D. Hoheisel, and K. Fellenberg Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data Bioinformatics, May 15, 2005; 21(10): 2424 - 2429. [Abstract] [Full Text] [PDF]
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P. Zhang, H. Foerster, C. P. Tissier, L. Mueller, S. Paley, P. D. Karp, and S. Y. Rhee MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research Plant Physiology, May 1, 2005; 138(1): 27 - 37. [Abstract] [Full Text] [PDF]
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M. Kloster, C. Tang, and N.S. Wingreen Finding regulatory modules through large-scale gene-expression data analysis Bioinformatics, April 1, 2005; 21(7): 1172 - 1179. [Abstract] [Full Text] [PDF]
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