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RESEARCH
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  D. Liu, J. M. Brockman, B. Dass, L. N. Hutchins, P. Singh, J. R. McCarrey, C. C. MacDonald, and J. H. Graber Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis Nucleic Acids Res., January 12, 2007; 35(1): 234 - 246. [Abstract] [Full Text] [PDF]
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J. Y. Lee, I. Yeh, J. Y. Park, and B. Tian PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes Nucleic Acids Res., January 12, 2007; 35(suppl_1): D165 - D168. [Abstract] [Full Text] [PDF]
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 S. H. Nagaraj, R. B. Gasser, and S. Ranganathan A hitchhiker's guide to expressed sequence tag (EST) analysis Brief Bioinform, January 1, 2007; 8(1): 6 - 21. [Abstract] [Full Text] [PDF]
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 F. Lopez, S. Granjeaud, T. Ara, B. Ghattas, and D. Gautheret The disparate nature of "intergenic" polyadenylation sites RNA, October 1, 2006; 12(10): 1794 - 1801. [Abstract] [Full Text] [PDF]
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 L. H. Pratt, C. Liang, M. Shah, F. Sun, H. Wang, St. P. Reid, A. R. Gingle, A. H. Paterson, R. Wing, R. Dean, et al. Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis, and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts Plant Physiology, October 1, 2005; 139(2): 869 - 884. [Abstract] [Full Text] [PDF]
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 J. M. Brockman, P. Singh, D. Liu, S. Quinlan, J. Salisbury, and J. H. Graber PACdb: PolyA Cleavage Site and 3'-UTR Database Bioinformatics, September 15, 2005; 21(18): 3691 - 3693. [Abstract] [Full Text] [PDF]
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M. Nakao, R. A. Barrero, Y. Mukai, C. Motono, M. Suwa, and K. Nakai Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals Nucleic Acids Res., April 28, 2005; 33(8): 2355 - 2363. [Abstract] [Full Text] [PDF]
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 J. Yan and T. G. Marr Computational analysis of 3'-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat Genome Res., March 1, 2005; 15(3): 369 - 375. [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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 K. Beck, K. Hayashi, B. Nishiguchi, O. Le Saux, M. Hayashi, and C. D. Boyd The Distribution of Abcc6 in Normal Mouse Tissues Suggests Multiple Functions for this ABC Transporter J. Histochem. Cytochem., July 1, 2003; 51(7): 887 - 902. [Abstract] [Full Text] [PDF]
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P. Carninci, K. Waki, T. Shiraki, H. Konno, K. Shibata, M. Itoh, K. Aizawa, T. Arakawa, Y. Ishii, D. Sasaki, et al. Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia Genome Res., June 1, 2003; 13(6): 1273 - 1289. [Abstract] [Full Text] [PDF]
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K.-B. Choo, H.-H. Chen, T. Y.-C. Liu, and C.-P. Chang Different modes of regulation of transcription and pre-mRNA processing of the structurally juxtaposed homologs, Rnf33 and Rnf35, in eggs and in pre-implantation embryos Nucleic Acids Res., November 15, 2002; 30(22): 4836 - 4844. [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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C. Iseli, B. J. Stevenson, S. J. de Souza, H. B. Samaia, A. A. Camargo, K. H. Buetow, R. L. Strausberg, A. J.G. Simpson, P. Bucher, and C. V. Jongeneel Long-Range Heterogeneity at the 3' Ends of Human mRNAs Genome Res., July 1, 2002; 12(7): 1068 - 1074. [Abstract] [Full Text] [PDF]
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N. Osato, M. Itoh, H. Konno, S. Kondo, K. Shibata, P. Carninci, T. Shiraki, A. Shinagawa, T. Arakawa, S. Kikuchi, et al. A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs Genome Res., July 1, 2002; 12(7): 1127 - 1134. [Abstract] [Full Text] [PDF]
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 D. K. Nam, S. Lee, G. Zhou, X. Cao, C. Wang, T. Clark, J. Chen, J. D. Rowley, and S. M. Wang Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription PNAS, April 30, 2002; 99(9): 6152 - 6156. [Abstract] [Full Text] [PDF]
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Z. Kan, E. C. Rouchka, W. R. Gish, and D. J. States Gene Structure Prediction and Alternative Splicing Analysis Using Genomically Aligned ESTs Genome Res., May 1, 2001; 11(5): 889 - 900. [Abstract] [Full Text]
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T. A. Vickers, J. R. Wyatt, T. Burckin, C. F. Bennett, and S. M. Freier Fully modified 2' MOE oligonucleotides redirect polyadenylation Nucleic Acids Res., March 15, 2001; 29(6): 1293 - 1299. [Abstract] [Full Text] [PDF]
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J. Muilu, P. Rodriguez-Tomé, and A. Robinson GBuilder---An Application for the Visualization and Integration of EST Cluster Data Genome Res., January 1, 2001; 11(1): 179 - 184. [Abstract] [Full Text]
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S. Kawamoto, J. Yoshii, K. Mizuno, K. Ito, Y. Miyamoto, T. Ohnishi, R. Matoba, N. Hori, Y. Matsumoto, T. Okumura, et al. BodyMap: A Collection of 3' ESTs for Analysis of Human Gene Expression Information Genome Res., November 1, 2000; 10(11): 1817 - 1827. [Abstract] [Full Text]
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E. Beaudoing, S. Freier, J. R. Wyatt, J.-M. Claverie, and D. Gautheret Patterns of Variant Polyadenylation Signal Usage in Human Genes Genome Res., July 1, 2000; 10(7): 1001 - 1010. [Abstract] [Full Text]
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A. A. Mironov, J. W. Fickett, and M. S. Gelfand Frequent Alternative Splicing of Human Genes Genome Res., December 1, 1999; 9(12): 1288 - 1293. [Abstract] [Full Text]
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J. Burke, D. Davison, and W. Hide d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences Genome Res., November 1, 1999; 9(11): 1135 - 1142. [Abstract] [Full Text]
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R. M. Ewing, A. B. Kahla, O. Poirot, F. Lopez, S. Audic, and J.-M. Claverie Large-Scale Statistical Analyses of Rice ESTs Reveal Correlated Patterns of Gene Expression Genome Res., October 1, 1999; 9(10): 950 - 959. [Abstract] [Full Text]
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 J.-M. Claverie Computational methods for theidentification of differential and coordinated gene expression Hum. Mol. Genet., September 1, 1999; 8(10): 1821 - 1832. [Abstract] [Full Text] [PDF]
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J. F. Coy, Z. Sedlacek, D. Bachner, H. Delius, and A. Poustka A complex pattern of evolutionary conservation and alternative polyadenylation within the long 3"-untranslated region of the methyl-CpG-binding protein 2 gene (MeCP2) suggests a regulatory role in gene expression Hum. Mol. Genet., July 1, 1999; 8(7): 1253 - 1262. [Abstract] [Full Text] [PDF]
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D. K. Nam, S. Lee, G. Zhou, X. Cao, C. Wang, T. Clark, J. Chen, J. D. Rowley, and S. M. Wang Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription PNAS, April 30, 2002; 99(9): 6152 - 6156. [Abstract] [Full Text] [PDF]
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H. Konno, Y. Fukunishi, K. Shibata, M. Itoh, P. Carninci, Y. Sugahara, and Y. Hayashizaki Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library Genome Res., February 1, 2001; 11(2): 281 - 289. [Abstract] [Full Text]
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M. D. Clark, S. Hennig, R. Herwig, S. W. Clifton, M. A. Marra, H. Lehrach, S. L. Johnson, and t. W.-G. E. Group An Oligonucleotide Fingerprint Normalized and Expressed Sequence Tag Characterized Zebrafish cDNA Library Genome Res., September 1, 2001; 11(9): 1594 - 1602. [Abstract] [Full Text] [PDF]
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E. Beaudoing and D. Gautheret Identification of Alternate Polyadenylation Sites and Analysis of their Tissue Distribution Using EST Data Genome Res., September 1, 2001; 11(9): 1520 - 1526. [Abstract] [Full Text] [PDF]
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W. A. Hide, V. N. Babenko, P. A. van Heusden, C. Seoighe, and J. F. Kelso The Contribution of Exon-Skipping Events on Chromosome 22 to Protein Coding Diversity Genome Res., November 1, 2001; 11(11): 1848 - 1853. [Abstract] [Full Text] [PDF]
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