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Vol. 11, Issue 5, 803-816, May 2001
LETTER
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  D. Palakodeti, M. Smielewska, Y.-C. Lu, G. W. Yeo, and B. R. Graveley The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians RNA, June 1, 2008; 14(6): 1174 - 1186. [Abstract] [Full Text] [PDF]
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 C. M. Whittington, A. T. Papenfuss, P. Bansal, A. M. Torres, E. S.W. Wong, J. E. Deakin, T. Graves, A. Alsop, K. Schatzkamer, C. Kremitzki, et al. Defensins and the convergent evolution of platypus and reptile venom genes Genome Res., June 1, 2008; 18(6): 986 - 994. [Abstract] [Full Text] [PDF]
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D. DeCaprio, J. P. Vinson, M. D. Pearson, P. Montgomery, M. Doherty, and J. E. Galagan Conrad: Gene prediction using conditional random fields Genome Res., September 1, 2007; 17(9): 1389 - 1398. [Abstract] [Full Text] [PDF]
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K. Belov, C. E. Sanderson, J. E. Deakin, E. S.W. Wong, D. Assange, K. A. McColl, A. Gout, B. de Bono, A. D. Barrow, T. P. Speed, et al. Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system Genome Res., July 1, 2007; 17(7): 982 - 991. [Abstract] [Full Text] [PDF]
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 G. Parra, K. Bradnam, and I. Korf CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes Bioinformatics, May 1, 2007; 23(9): 1061 - 1067. [Abstract] [Full Text] [PDF]
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 K. Knapp and Y.-P. P. Chen An evaluation of contemporary hidden Markov model genefinders with a predicted exon taxonomy Nucleic Acids Res., January 12, 2007; 35(1): 317 - 324. [Abstract] [Full Text] [PDF]
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 S. Vilanova, M. L. Badenes, L. Burgos, J. Martinez-Calvo, G. Llacer, and C. Romero Self-Compatibility of Two Apricot Selections Is Associated with Two Pollen-Part Mutations of Different Nature Plant Physiology, October 1, 2006; 142(2): 629 - 641. [Abstract] [Full Text] [PDF]
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A. Yao, R. Charlab, and P. Li Systematic identification of pseudogenes through whole genome expression evidence profiling Nucleic Acids Res., September 11, 2006; 34(16): 4477 - 4485. [Abstract] [Full Text] [PDF]
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 Q. Zhang, X. Su, S. Gong, Q. Zeng, B. Zhu, Z. Wu, T. Peng, C. Zhang, and R. Zhou Comparative genomic analysis of two strains of human adenovirus type 3 isolated from children with acute respiratory infection in southern China J. Gen. Virol., June 1, 2006; 87(6): 1531 - 1541. [Abstract] [Full Text] [PDF]
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 P. A. Antinozzi, A. Garcia-Diaz, C. Hu, and J. E. Rothman Functional mapping of disease susceptibility loci using cell biology. PNAS, March 7, 2006; 103(10): 3698 - 3703. [Abstract] [Full Text] [PDF]
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 Y. Xiao, Y. Cai, Y. R. Bommineni, S. C. Fernando, O. Prakash, S. E. Gilliland, and G. Zhang Identification and Functional Characterization of Three Chicken Cathelicidins with Potent Antimicrobial Activity J. Biol. Chem., February 3, 2006; 281(5): 2858 - 2867. [Abstract] [Full Text] [PDF]
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M. R. Brent Genome annotation past, present, and future: How to define an ORF at each locus Genome Res., December 1, 2005; 15(12): 1777 - 1786. [Abstract] [Full Text] [PDF]
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 A. A. Patil, Y. Cai, Y. Sang, F. Blecha, and G. Zhang Cross-species analysis of the mammalian {beta}-defensin gene family: presence of syntenic gene clusters and preferential expression in the male reproductive tract Physiol Genomics, September 21, 2005; 23(1): 5 - 17. [Abstract] [Full Text] [PDF]
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 A. Purkayastha, J. Su, J. McGraw, S. E. Ditty, T. L. Hadfield, J. Seto, K. L. Russell, C. Tibbetts, and D. Seto Genomic and Bioinformatics Analyses of HAdV-4vac and HAdV-7vac, Two Human Adenovirus (HAdV) Strains That Constituted Original Prophylaxis against HAdV-Related Acute Respiratory Disease, a Reemerging Epidemic Disease J. Clin. Microbiol., July 1, 2005; 43(7): 3083 - 3094. [Abstract] [Full Text] [PDF]
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D. Conklin, B. Haldeman, and Z. Gao Gene finding for the helical cytokines Bioinformatics, May 1, 2005; 21(9): 1776 - 1781. [Abstract] [Full Text] [PDF]
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M. S. Katari, V. Balija, R. K. Wilson, R. A. Martienssen, and W. R. McCombie Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana Genome Res., April 1, 2005; 15(4): 496 - 504. [Abstract] [Full Text] [PDF]
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N. Nikolaidis, I. Makalowska, D. Chalkia, W. Makalowski, J. Klein, and M. Nei Origin and evolution of the chicken leukocyte receptor complex PNAS, March 15, 2005; 102(11): 4057 - 4062. [Abstract] [Full Text] [PDF]
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 A. Purkayastha, S. E. Ditty, J. Su, J. McGraw, T. L. Hadfield, C. Tibbetts, and D. Seto Genomic and Bioinformatics Analysis of HAdV-4, a Human Adenovirus Causing Acute Respiratory Disease: Implications for Gene Therapy and Vaccine Vector Development J. Virol., February 15, 2005; 79(4): 2559 - 2572. [Abstract] [Full Text] [PDF]
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L. Florea, V. Di Francesco, J. Miller, R. Turner, A. Yao, M. Harris, B. Walenz, C. Mobarry, G. V. Merkulov, R. Charlab, et al. Gene and alternative splicing annotation with AIR Genome Res., January 1, 2005; 15(1): 54 - 66. [Abstract] [Full Text] [PDF]
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A. Patil, A. L. Hughes, and G. Zhang Rapid evolution and diversification of mammalian {alpha}-defensins as revealed by comparative analysis of rodent and primate genes Physiol Genomics, December 15, 2004; 20(1): 1 - 11. [Abstract] [Full Text] [PDF]
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S. Dike, V. S. Balija, L. U. Nascimento, Z. Xuan, J. Ou, T. Zutavern, L. E. Palmer, G. Hannon, M. Q. Zhang, and W. R. McCombie The mouse genome: Experimental examination of gene predictions and transcriptional start sites Genome Res., December 1, 2004; 14(12): 2424 - 2429. [Abstract] [Full Text] [PDF]
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K. P. Lauer, I. Llorente, E. Blair, J. Seto, V. Krasnov, A. Purkayastha, S. E. Ditty, T. L. Hadfield, C. Buck, C. Tibbetts, et al. Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1 J. Gen. Virol., September 1, 2004; 85(9): 2615 - 2625. [Abstract] [Full Text] [PDF]
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B. Issac and G. P. S. Raghava EGPred: Prediction of Eukaryotic Genes Using Ab Initio Methods After Combining With Sequence Similarity Approaches Genome Res., September 1, 2004; 14(9): 1756 - 1766. [Abstract] [Full Text] [PDF]
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E. Birney, M. Clamp, and R. Durbin GeneWise and Genomewise Genome Res., May 1, 2004; 14(5): 988 - 995. [Abstract] [Full Text] [PDF]
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I. M. Meyer and R. Durbin Gene structure conservation aids similarity based gene prediction Nucleic Acids Res., February 4, 2004; 32(2): 776 - 783. [Abstract] [Full Text] [PDF]
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J. E. Allen, M. Pertea, and S. L. Salzberg Computational Gene Prediction Using Multiple Sources of Evidence Genome Res., January 1, 2004; 14(1): 142 - 148. [Abstract] [Full Text] [PDF]
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G. Sengle, B. Kobbe, M. Morgelin, M. Paulsson, and R. Wagener Identification and Characterization of AMACO, a New Member of the von Willebrand Factor A-like Domain Protein Superfamily with a Regulated Expression in the Kidney J. Biol. Chem., December 12, 2003; 278(50): 50240 - 50249. [Abstract] [Full Text] [PDF]
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Z. Zhang, P. M. Harrison, Y. Liu, and M. Gerstein Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome Genome Res., December 1, 2003; 13(12): 2541 - 2558. [Abstract] [Full Text] [PDF]
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E. M. Majerus, X. Zheng, E. A. Tuley, and J. E. Sadler Cleavage of the ADAMTS13 Propeptide Is Not Required for Protease Activity J. Biol. Chem., November 21, 2003; 278(47): 46643 - 46648. [Abstract] [Full Text] [PDF]
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B. J. Haas, A. L. Delcher, S. M. Mount, J. R. Wortman, R. K. Smith Jr, L. I. Hannick, R. Maiti, C. M. Ronning, D. B. Rusch, C. D. Town, et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Nucleic Acids Res., October 1, 2003; 31(19): 5654 - 5666. [Abstract] [Full Text] [PDF]
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L. Zhang, V. Pavlovic, C. R Cantor, and S. Kasif Human-Mouse Gene Identification by Comparative Evidence Integration and Evolutionary Analysis Genome Res., June 1, 2003; 13(6): 1190 - 1202. [Abstract] [Full Text] [PDF]
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W. Zhu, S. D. Schlueter, and V. Brendel Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping Plant Physiology, June 1, 2003; 132(2): 469 - 484. [Abstract] [Full Text] [PDF]
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R. Guigo, E. T. Dermitzakis, P. Agarwal, C. P. Ponting, G. Parra, A. Reymond, J. F. Abril, E. Keibler, R. Lyle, C. Ucla, et al. Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes PNAS, February 4, 2003; 100(3): 1140 - 1145. [Abstract] [Full Text] [PDF]
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T.-J. Chuang, W.-C. Lin, H.-C. Lee, C.-W. Wang, K.-L. Hsiao, Z.-H. Wang, D. Shieh, S. C. Lin, and L.-Y. Ch'ang A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences Genome Res., February 1, 2003; 13(2): 313 - 322. [Abstract] [Full Text] [PDF]
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P. Flicek, E. Keibler, P. Hu, I. Korf, and M. R. Brent Leveraging the Mouse Genome for Gene Prediction in Human: From Whole-Genome Shotgun Reads to a Global Synteny Map Genome Res., January 1, 2003; 13(1): 46 - 54. [Abstract] [Full Text] [PDF]
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G. Parra, P. Agarwal, J. F. Abril, T. Wiehe, J. W. Fickett, and R. Guigo Comparative Gene Prediction in Human and Mouse Genome Res., January 1, 2003; 13(1): 108 - 117. [Abstract] [Full Text] [PDF]
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Mammalian Gene Collection Program Team*, R. L. Strausberg, E. A. Feingold, L. H. Grouse, J. G. Derge, R. D. Klausner, F. S. Collins, L. Wagner, C. M. Shenmen, G. D. Schuler, et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences PNAS, December 24, 2002; 99(26): 16899 - 16903. [Abstract] [Full Text] [PDF]
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C. Mathe, M.-F. Sagot, T. Schiex, and P. Rouze Current methods of gene prediction, their strengths and weaknesses Nucleic Acids Res., October 1, 2002; 30(19): 4103 - 4117. [Abstract] [Full Text] [PDF]
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Z. Zhang, P. Harrison, and M. Gerstein Identification and Analysis of Over 2000 Ribosomal Protein Pseudogenes in the Human Genome Genome Res., October 1, 2002; 12(10): 1466 - 1482. [Abstract] [Full Text] [PDF]
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 C. A. Whittaker and R. O. Hynes Distribution and Evolution of von Willebrand/Integrin A Domains: Widely Dispersed Domains with Roles in Cell Adhesion and Elsewhere Mol. Biol. Cell, October 1, 2002; 13(10): 3369 - 3387. [Abstract] [Full Text] [PDF]
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K. L. Howe, T. Chothia, and R. Durbin GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming Genome Res., September 1, 2002; 12(9): 1418 - 1427. [Abstract] [Full Text] [PDF]
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M. Walker, V. Pavlovic, and S. Kasif A comparative genomic method for computational identification of prokaryotic translation initiation sites Nucleic Acids Res., July 15, 2002; 30(14): 3181 - 3191. [Abstract] [Full Text] [PDF]
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N. Echols, P. Harrison, S. Balasubramanian, N. M. Luscombe, P. Bertone, Z. Zhang, and M. Gerstein Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes Nucleic Acids Res., June 1, 2002; 30(11): 2515 - 2523. [Abstract] [Full Text] [PDF]
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T. K. Bera, C. Iavarone, V. Kumar, S. Lee, B. Lee, and I. Pastan MRP9, an unusual truncated member of the ABC transporter superfamily, is highly expressed in breast cancer PNAS, May 14, 2002; 99(10): 6997 - 7002. [Abstract] [Full Text] [PDF]
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 I. Ibanez-Tallon, S. Gorokhova, and N. Heintz Loss of function of axonemal dynein Mdnah5 causes primary ciliary dyskinesia and hydrocephalus Hum. Mol. Genet., March 1, 2002; 11(6): 715 - 721. [Abstract] [Full Text] [PDF]
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P. M. Harrison, A. Kumar, N. Lang, M. Snyder, and M. Gerstein A question of size: the eukaryotic proteome and the problems in defining it Nucleic Acids Res., March 1, 2002; 30(5): 1083 - 1090. [Abstract] [Full Text] [PDF]
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P. M. Harrison, H. Hegyi, S. Balasubramanian, N. M. Luscombe, P. Bertone, N. Echols, T. Johnson, and M. Gerstein Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22 Genome Res., February 1, 2002; 12(2): 272 - 280. [Abstract] [Full Text] [PDF]
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D. Greenbaum, N. M. Luscombe, R. Jansen, J. Qian, and M. Gerstein Interrelating Different Types of Genomic Data, from Proteome to Secretome: 'Oming in on Function Genome Res., September 1, 2001; 11(9): 1463 - 1468. [Abstract] [Full Text] [PDF]
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E. D. Green and A. Chakravarti The Human Genome Sequence Expedition: Views from the "Base Camp" Genome Res., May 1, 2001; 11(5): 645 - 651. [Full Text]
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