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Vol. 10, Issue 4, 516-522, April 2000
METHODS
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  P. Gayral, J.-C. Noa-Carrazana, M. Lescot, F. Lheureux, B. E. L. Lockhart, T. Matsumoto, P. Piffanelli, and M.-L. Iskra-Caruana A Single Banana Streak Virus Integration Event in the Banana Genome as the Origin of Infectious Endogenous Pararetrovirus J. Virol., July 1, 2008; 82(13): 6697 - 6710. [Abstract] [Full Text] [PDF]
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 Genome Information Integration Project And H-Invit The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts Nucleic Acids Res., January 11, 2008; 36(suppl_1): D793 - D799. [Abstract] [Full Text] [PDF]
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 Y.-F. Chen, M. Shi, F. Huang, and X.-x. Chen Characterization of two genes of Cotesia vestalis polydnavirus and their expression patterns in the host Plutella xylostella J. Gen. Virol., December 1, 2007; 88(12): 3317 - 3322. [Abstract] [Full Text] [PDF]
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 M. Dixit, E. Ansseau, A. Tassin, S. Winokur, R. Shi, H. Qian, S. Sauvage, C. Matteotti, A. M. van Acker, O. Leo, et al. DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1 PNAS, November 13, 2007; 104(46): 18157 - 18162. [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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 A. Coghlan and R. Durbin Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron exon structure Bioinformatics, June 15, 2007; 23(12): 1468 - 1475. [Abstract] [Full Text] [PDF]
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 S. Sato, Y. Nakamura, E. Asamizu, S. Isobe, and S. Tabata Genome Sequencing and Genome Resources in Model Legumes Plant Physiology, June 1, 2007; 144(2): 588 - 593. [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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W. Zhu and C. R. Buell Improvement of whole-genome annotation of cereals through comparative analyses Genome Res., March 1, 2007; 17(3): 299 - 310. [Abstract] [Full Text] [PDF]
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 Z. Zhao, J. H. Thomas, N. Chen, J. A. Sheps, and D. L. Baillie Comparative Genomics and Adaptive Selection of the ATP-Binding-Cassette Gene Family in Caenorhabditis Species Genetics, March 1, 2007; 175(3): 1407 - 1418. [Abstract] [Full Text] [PDF]
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L. Wang, S. Wang, Y. Li, M. S. R. Paradesi, and S. J. Brown BeetleBase: the model organism database for Tribolium castaneum Nucleic Acids Res., January 12, 2007; 35(suppl_1): D476 - D479. [Abstract] [Full Text] [PDF]
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S. Foret and R. Maleszka Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera) Genome Res., November 1, 2006; 16(11): 1404 - 1413. [Abstract] [Full Text] [PDF]
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C. Rehmeyer, W. Li, M. Kusaba, Y.-S. Kim, D. Brown, C. Staben, R. Dean, and M. Farman Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae Nucleic Acids Res., October 18, 2006; 34(17): 4685 - 4701. [Abstract] [Full Text] [PDF]
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R. Bruggmann, A. K. Bharti, H. Gundlach, J. Lai, S. Young, A. C. Pontaroli, F. Wei, G. Haberer, G. Fuks, C. Du, et al. Uneven chromosome contraction and expansion in the maize genome Genome Res., October 1, 2006; 16(10): 1241 - 1251. [Abstract] [Full Text] [PDF]
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 G. A. Tuskan, S. DiFazio, S. Jansson, J. Bohlmann, I. Grigoriev, U. Hellsten, N. Putnam, S. Ralph, S. Rombauts, A. Salamov, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, September 15, 2006; 313(5793): 1596 - 1604. [Abstract] [Full Text] [PDF]
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C. O. Ortiz, J. F. Etchberger, S. L. Posy, C. Frokjaer-Jensen, S. Lockery, B. Honig, and O. Hobert Searching for Neuronal Left/Right Asymmetry: Genomewide Analysis of Nematode Receptor-Type Guanylyl Cyclases Genetics, May 1, 2006; 173(1): 131 - 149. [Abstract] [Full Text] [PDF]
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Y. Wang, X. Tang, Z. Cheng, L. Mueller, J. Giovannoni, and S. D. Tanksley Euchromatin and Pericentromeric Heterochromatin: Comparative Composition in the Tomato Genome Genetics, April 1, 2006; 172(4): 2529 - 2540. [Abstract] [Full Text] [PDF]
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D. E. Gundersen-Rindal and M. J. Pedroni Characterization and transcriptional analysis of protein tyrosine phosphatase genes and an ankyrin repeat gene of the parasitoid Glyptapanteles indiensis polydnavirus in the parasitized host J. Gen. Virol., February 1, 2006; 87(2): 311 - 322. [Abstract] [Full Text] [PDF]
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A. P. Chan, G. Pertea, F. Cheung, D. Lee, L. Zheng, C. Whitelaw, A. C. Pontaroli, P. SanMiguel, Y. Yuan, J. Bennetzen, et al. The TIGR Maize Database Nucleic Acids Res., January 1, 2006; 34(suppl_1): D771 - D776. [Abstract] [Full Text] [PDF]
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J. E. Galagan, M. R. Henn, L.-J. Ma, C. A. Cuomo, and B. Birren Genomics of the fungal kingdom: Insights into eukaryotic biology Genome Res., December 1, 2005; 15(12): 1620 - 1631. [Abstract] [Full Text] [PDF]
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G. Haberer, S. Young, A. K. Bharti, H. Gundlach, C. Raymond, G. Fuks, E. Butler, R. A. Wing, S. Rounsley, B. Birren, et al. Structure and Architecture of the Maize Genome Plant Physiology, December 1, 2005; 139(4): 1612 - 1624. [Abstract] [Full Text] [PDF]
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W. F. Odenwald, W. Rasband, A. Kuzin, and T. Brody EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA PNAS, October 11, 2005; 102(41): 14700 - 14705. [Abstract] [Full Text] [PDF]
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N. Juretic, D. R. Hoen, M. L. Huynh, P. M. Harrison, and T. E. Bureau The evolutionary fate of MULE-mediated duplications of host gene fragments in rice Genome Res., September 1, 2005; 15(9): 1292 - 1297. [Abstract] [Full Text] [PDF]
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The Rice Chromosome 3 Sequencing Consortium Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species Genome Res., September 1, 2005; 15(9): 1284 - 1291. [Abstract] [Full Text] [PDF]
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X. Pan, L. Stein, and V. Brendel SynBrowse: a synteny browser for comparative sequence analysis Bioinformatics, September 1, 2005; 21(17): 3461 - 3468. [Abstract] [Full Text] [PDF]
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L. Radvanyi, D. Singh-Sandhu, S. Gallichan, C. Lovitt, A. Pedyczak, G. Mallo, K. Gish, K. Kwok, W. Hanna, J. Zubovits, et al. The gene associated with trichorhinophalangeal syndrome in humans is overexpressed in breast cancer PNAS, August 2, 2005; 102(31): 11005 - 11010. [Abstract] [Full Text] [PDF]
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Q. Yuan, S. Ouyang, A. Wang, W. Zhu, R. Maiti, H. Lin, J. Hamilton, B. Haas, R. Sultana, F. Cheung, et al. The Institute for Genomic Research Osa1 Rice Genome Annotation Database Plant Physiology, May 1, 2005; 138(1): 18 - 26. [Abstract] [Full Text] [PDF]
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S. B. Cannon, J. A. Crow, M. L. Heuer, X. Wang, E. K.S. Cannon, C. Dwan, A.-F. Lamblin, J. Vasdewani, J. Mudge, A. Cook, et al. Databases and Information Integration for the Medicago truncatula Genome and Transcriptome Plant Physiology, May 1, 2005; 138(1): 38 - 46. [Abstract] [Full Text] [PDF]
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N. Kim, S. Shin, and S. Lee ECgene: Genome-based EST clustering and gene modeling for alternative splicing Genome Res., April 1, 2005; 15(4): 566 - 576. [Abstract] [Full Text] [PDF]
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C. Wei, P. Lamesch, M. Arumugam, J. Rosenberg, P. Hu, M. Vidal, and M. R. Brent Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions Genome Res., April 1, 2005; 15(4): 577 - 582. [Abstract] [Full Text] [PDF]
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N. D. Young, S. B. Cannon, S. Sato, D. Kim, D. R. Cook, C. D. Town, B. A. Roe, and S. Tabata Sequencing the Genespaces of Medicago truncatula and Lotus japonicus Plant Physiology, April 1, 2005; 137(4): 1174 - 1181. [Full Text] [PDF]
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M. J. Spiering, C. D. Moon, H. H. Wilkinson, and C. L. Schardl Gene Clusters for Insecticidal Loline Alkaloids in the Grass-Endophytic Fungus Neotyphodium uncinatum Genetics, March 1, 2005; 169(3): 1403 - 1414. [Abstract] [Full Text] [PDF]
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A. N. Doust, K. M. Devos, M. D. Gadberry, M. D. Gale, and E. A. Kellogg The Genetic Basis for Inflorescence Variation Between Foxtail and Green Millet (Poaceae) Genetics, March 1, 2005; 169(3): 1659 - 1672. [Abstract] [Full Text] [PDF]
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 O. Vallon Chlamydomonas Immunophilins and Parvulins: Survey and Critical Assessment of Gene Models Eukaryot. Cell, February 1, 2005; 4(2): 230 - 241. [Full Text] [PDF]
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M. Yandell, A. M. Bailey, S. Misra, S. Shu, C. Wiel, M. Evans-Holm, S. E. Celniker, and G. M. Rubin A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome PNAS, February 1, 2005; 102(5): 1566 - 1571. [Abstract] [Full Text] [PDF]
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 H.-S. Hofmann, G. Hansen, G. Richter, C. Taege, A. Simm, R.-E. Silber, and S. Burdach Matrix Metalloproteinase-12 Expression Correlates with Local Recurrence and Metastatic Disease in Non-Small Cell Lung Cancer Patients Clin. Cancer Res., February 1, 2005; 11(3): 1086 - 1092. [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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J. Wang, Q. Xia, X. He, M. Dai, J. Ruan, J. Chen, G. Yu, H. Yuan, Y. Hu, R. Li, et al. SilkDB: a knowledgebase for silkworm biology and genomics Nucleic Acids Res., January 1, 2005; 33(suppl_1): D399 - D402. [Abstract] [Full Text] [PDF]
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J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, P. Meidl, S. M. Searle, J. Stalker, R. Storey, S. Trevanion, et al. The Vertebrate Genome Annotation (Vega) database Nucleic Acids Res., January 1, 2005; 33(suppl_1): D459 - D465. [Abstract] [Full Text] [PDF]
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L. Ding, A. Sabo, N. Berkowicz, R. R. Meyer, Y. Shotland, M. R. Johnson, K. H. Pepin, R. K. Wilson, and J. Spieth EAnnot: A genome annotation tool using experimental evidence Genome Res., December 1, 2004; 14(12): 2503 - 2509. [Abstract] [Full Text] [PDF]
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V. Stolc, Z. Gauhar, C. Mason, G. Halasz, M. F. van Batenburg, S. A. Rifkin, S. Hua, T. Herreman, W. Tongprasit, P. E. Barbano, et al. A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster Science, October 22, 2004; 306(5696): 655 - 660. [Abstract] [Full Text] [PDF]
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A.-M. Mallon, L. Wilming, J. Weekes, J. G.R. Gilbert, J. Ashurst, S. Peyrefitte, L. Matthews, M. Cadman, R. McKeone, C. A. Sellick, et al. Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse Genome Res., October 1, 2004; 14(10a): 1888 - 1901. [Abstract] [Full Text] [PDF]
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N. Kim, S. Shin, and S. Lee ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences Nucleic Acids Res., July 1, 2004; 32(suppl_2): W181 - W186. [Abstract] [Full Text] [PDF]
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A. N. Doust, K. M. Devos, M. D. Gadberry, M. D. Gale, and E. A. Kellogg Genetic control of branching in foxtail millet PNAS, June 15, 2004; 101(24): 9045 - 9050. [Abstract] [Full Text] [PDF]
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S. Cruveiller, K. Jabbari, O. Clay, and G. Bernardi Compositional Gene Landscapes in Vertebrates Genome Res., May 1, 2004; 14(5): 886 - 892. [Abstract] [Full Text] [PDF]
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L.-H. Li, J.-C. Li, Y.-F. Lin, C.-Y. Lin, C.-Y. Chen, and S.-F. Tsai Genomic shotgun array: a procedure linking large-scale DNA sequencing with regional transcript mapping Nucleic Acids Res., February 11, 2004; 32(3): e27 - e27. [Abstract] [Full Text] [PDF]
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N. F. Lobo, L. Q. Ton, C. A. Hill, C. Emore, J. Romero-Severson, G. J. Hunt, and F. H. Collins Genomic Analysis in the sting-2 Quantitative Trait Locus for Defensive Behavior in the Honey Bee, Apis mellifera Genome Res., December 1, 2003; 13(12): 2588 - 2593. [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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 Y. Li, Q. Qian, Y. Zhou, M. Yan, L. Sun, M. Zhang, Z. Fu, Y. Wang, B. Han, X. Pang, et al. BRITTLE CULM1, Which Encodes a COBRA-Like Protein, Affects the Mechanical Properties of Rice Plants PLANT CELL, September 1, 2003; 15(9): 2020 - 2031. [Abstract] [Full Text] [PDF]
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The Rice Chromosome 10 Sequencing Consortium In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10 Science, June 6, 2003; 300(5625): 1566 - 1569. [Abstract] [Full Text] [PDF]
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V. V. Kapitonov and J. Jurka Molecular paleontology of transposable elements in the Drosophila melanogaster genome PNAS, May 27, 2003; 100(11): 6569 - 6574. [Abstract] [Full Text] [PDF]
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G. Mannhaupt, C. Montrone, D. Haase, H. W. Mewes, V. Aign, J. D. Hoheisel, B. Fartmann, G. Nyakatura, F. Kempken, J. Maier, et al. What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence Nucleic Acids Res., April 1, 2003; 31(7): 1944 - 1954. [Abstract] [Full Text] [PDF]
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 E. B. Brunschwig, K. Wilson, D. Mack, D. Dawson, E. Lawrence, J. K.V. Willson, S. Lu, A. Nosrati, R. M. Rerko, S. Swinler, et al. PMEPA1, a Transforming Growth Factor-{beta}-induced Marker of Terminal Colonocyte Differentiation Whose Expression Is Maintained in Primary and Metastatic Colon Cancer Cancer Res., April 1, 2003; 63(7): 1568 - 1575. [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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D. Karolchik, R. Baertsch, M. Diekhans, T. S. Furey, A. Hinrichs, Y. T. Lu, K. M. Roskin, M. Schwartz, C. W. Sugnet, D. J. Thomas, et al. The UCSC Genome Browser Database Nucleic Acids Res., January 1, 2003; 31(1): 51 - 54. [Abstract] [Full Text] [PDF]
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