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Vol. 12, Issue 10, 1599-1610, October 2002
RESOURCES
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  N. O'Toole, M. Hattori, C. Andres, K. Iida, C. Lurin, C. Schmitz-Linneweber, M. Sugita, and I. Small On the Expansion of the Pentatricopeptide Repeat Gene Family in Plants Mol. Biol. Evol., June 1, 2008; 25(6): 1120 - 1128. [Abstract] [Full Text] [PDF]
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 I. Albert, S. Wachi, C. Jiang, and B. F. Pugh GeneTrack--a genomic data processing and visualization framework Bioinformatics, May 15, 2008; 24(10): 1305 - 1306. [Abstract] [Full Text] [PDF]
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 M. B. Noyes, X. Meng, A. Wakabayashi, S. Sinha, M. H. Brodsky, and S. A. Wolfe A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system Nucleic Acids Res., May 1, 2008; 36(8): 2547 - 2560. [Abstract] [Full Text] [PDF]
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J. R. Grant and P. Stothard The CGView Server: a comparative genomics tool for circular genomes Nucleic Acids Res., April 14, 2008; (2008) gkn179v1. [Abstract] [Full Text] [PDF]
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 L. Duret, J. Cohen, C. Jubin, P. Dessen, J.-F. Gout, S. Mousset, J.-M. Aury, O. Jaillon, B. Noel, O. Arnaiz, et al. Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: A somatic view of the germline Genome Res., April 1, 2008; 18(4): 585 - 596. [Abstract] [Full Text] [PDF]
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R. D. Morin, G. Aksay, E. Dolgosheina, H. A. Ebhardt, V. Magrini, E. R. Mardis, S. C. Sahinalp, and P. J. Unrau Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa Genome Res., April 1, 2008; 18(4): 571 - 584. [Abstract] [Full Text] [PDF]
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D. Salgado, G. Gimenez, F. Coulier, and C. Marcelle COMPARE, a multi-organism system for cross-species data comparison and transfer of information Bioinformatics, February 1, 2008; 24(3): 447 - 449. [Abstract] [Full Text] [PDF]
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 J. M. Hancock and A.-M. Mallon Phenobabelomics mouse phenotype data resources Brief Funct Genomic Proteomic, January 11, 2008; (2008) elm033v1. [Abstract] [Full Text] [PDF]
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M. Mangone, P. MacMenamin, C. Zegar, F. Piano, and K. C. Gunsalus UTRome.org: a platform for 3'UTR biology in C. elegans Nucleic Acids Res., January 11, 2008; 36(suppl_1): D57 - D62. [Abstract] [Full Text] [PDF]
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S. M.C. Robb, E. Ross, and A. S. Alvarado SmedGD: the Schmidtea mediterranea genome database Nucleic Acids Res., January 11, 2008; 36(suppl_1): D599 - D606. [Abstract] [Full Text] [PDF]
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I. Scheinin, S. Myllykangas, I. Borze, T. Bohling, S. Knuutila, and J. Saharinen CanGEM: mining gene copy number changes in cancer Nucleic Acids Res., January 11, 2008; 36(suppl_1): D830 - D835. [Abstract] [Full Text] [PDF]
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C. J. Schmidt, M. Romanov, O. Ryder, V. Magrini, M. Hickenbotham, J. Glasscock, S. McGrath, E. Mardis, and L. D. Stein Gallus GBrowse: a unified genomic database for the chicken Nucleic Acids Res., January 11, 2008; 36(suppl_1): D719 - D723. [Abstract] [Full Text] [PDF]
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K. Gendler, T. Paulsen, and C. Napoli ChromDB: The Chromatin Database Nucleic Acids Res., January 11, 2008; 36(suppl_1): D298 - D302. [Abstract] [Full Text] [PDF]
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B. Squires, C. Macken, A. Garcia-Sastre, S. Godbole, J. Noronha, V. Hunt, R. Chang, C. N. Larsen, E. Klem, K. Biersack, et al. BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence Nucleic Acids Res., January 11, 2008; 36(suppl_1): D497 - D503. [Abstract] [Full Text] [PDF]
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J. B. Bowes, K. A. Snyder, E. Segerdell, R. Gibb, C. Jarabek, E. Noumen, N. Pollet, and P. D. Vize Xenbase: a Xenopus biology and genomics resource Nucleic Acids Res., January 11, 2008; 36(suppl_1): D761 - D767. [Abstract] [Full Text] [PDF]
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B.-J. Breitkreutz, C. Stark, T. Reguly, L. Boucher, A. Breitkreutz, M. Livstone, R. Oughtred, D. H. Lackner, J. Bahler, V. Wood, et al. The BioGRID Interaction Database: 2008 update Nucleic Acids Res., January 11, 2008; 36(suppl_1): D637 - D640. [Abstract] [Full Text] [PDF]
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J. D. Glasner, G. Plunkett III, B. D. Anderson, D. J. Baumler, B. S. Biehl, V. Burland, E. L. Cabot, A. E. Darling, B. Mau, E. C. Neeno-Eckwall, et al. Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria Nucleic Acids Res., January 11, 2008; 36(suppl_1): D519 - D523. [Abstract] [Full Text] [PDF]
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T. W. H. Backman, C. M. Sullivan, J. S. Cumbie, Z. A. Miller, E. J. Chapman, N. Fahlgren, S. A. Givan, J. C. Carrington, and K. D. Kasschau Update of ASRP: the Arabidopsis Small RNA Project database Nucleic Acids Res., January 11, 2008; 36(suppl_1): D982 - D985. [Abstract] [Full Text] [PDF]
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B. Gajria, A. Bahl, J. Brestelli, J. Dommer, S. Fischer, X. Gao, M. Heiges, J. Iodice, J. C. Kissinger, A. J. Mackey, et al. ToxoDB: an integrated Toxoplasma gondii database resource Nucleic Acids Res., January 11, 2008; 36(suppl_1): D553 - D556. [Abstract] [Full Text] [PDF]
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M. S. Halfon, S. M. Gallo, and C. M. Bergman REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila Nucleic Acids Res., January 11, 2008; 36(suppl_1): D594 - D598. [Abstract] [Full Text] [PDF]
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H. W. Mewes, S. Dietmann, D. Frishman, R. Gregory, G. Mannhaupt, K. F. X. Mayer, M. Munsterkotter, A. Ruepp, M. Spannagl, V. Stumpflen, et al. MIPS: analysis and annotation of genome information in 2007 Nucleic Acids Res., January 11, 2008; 36(suppl_1): D196 - D201. [Abstract] [Full Text] [PDF]
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R. J. Wilson, J. L. Goodman, V. B. Strelets, and The FlyBase Consortium FlyBase: integration and improvements to query tools Nucleic Acids Res., January 11, 2008; 36(suppl_1): D588 - D593. [Abstract] [Full Text] [PDF]
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D. Swarbreck, C. Wilks, P. Lamesch, T. Z. Berardini, M. Garcia-Hernandez, H. Foerster, D. Li, T. Meyer, R. Muller, L. Ploetz, et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation Nucleic Acids Res., January 11, 2008; 36(suppl_1): D1009 - D1014. [Abstract] [Full Text] [PDF]
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Rice Annotation Project The Rice Annotation Project Database (RAP-DB): 2008 update Nucleic Acids Res., January 11, 2008; 36(suppl_1): D1028 - D1033. [Abstract] [Full Text] [PDF]
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P. D. Karp, I. M. Keseler, A. Shearer, M. Latendresse, M. Krummenacker, S. M. Paley, I. Paulsen, J. Collado-Vides, S. Gama-Castro, M. Peralta-Gil, et al. Multidimensional annotation of the Escherichia coli K-12 genome Nucleic Acids Res., December 3, 2007; 35(22): 7577 - 7590. [Abstract] [Full Text] [PDF]
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 A. K. Mah, K. R. Armstrong, D. S. Chew, J. S. Chu, D. K. Tu, R. C. Johnsen, N. Chen, H. M. Chamberlin, and D. L. Baillie Transcriptional Regulation of AQP-8, a Caenorhabditis elegans Aquaporin Exclusively Expressed in the Excretory System, by the POU Homeobox Transcription Factor CEH-6 J. Biol. Chem., September 21, 2007; 282(38): 28074 - 28086. [Abstract] [Full Text] [PDF]
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 J. U. Pontius and S. J. O'Brien Genome Annotation Resource Fields GARFIELD: A Genome Browser for Felis catus J. Hered., July 25, 2007; (2007) esm055v2. [Abstract] [Full Text] [PDF]
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C. J. Mungall, D. B. Emmert, and The FlyBase Consortium A Chado case study: an ontology-based modular schema for representing genome-associated biological information Bioinformatics, July 1, 2007; 23(13): i337 - i346. [Abstract] [Full Text] [PDF]
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M. Taylor, W. Valdar, A. Kumar, J. Flint, and R. Mott Management, presentation and interpretation of genome scans using GSCANDB Bioinformatics, June 15, 2007; 23(12): 1545 - 1549. [Abstract] [Full Text] [PDF]
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 A. P.M. Weber, K. L. Weber, K. Carr, C. Wilkerson, and J. B. Ohlrogge Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing Plant Physiology, May 1, 2007; 144(1): 32 - 42. [Abstract] [Full Text] [PDF]
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C. Girardot, O. Sklyar, S. Grosz, W. Huber, and E. E. M. Furlong CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data Bioinformatics, March 15, 2007; 23(6): 771 - 773. [Abstract] [Full Text] [PDF]
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J.-P. Gauthier, F. Legeai, A. Zasadzinski, C. Rispe, and D. Tagu AphidBase: a database for aphid genomic resources Bioinformatics, March 15, 2007; 23(6): 783 - 784. [Abstract] [Full Text] [PDF]
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T. Toyoda, Y. Mochizuki, K. Player, N. Heida, Norio Kobayashi, and Y. Sakaki OmicBrowse: a browser of multidimensional omics annotations Bioinformatics, February 15, 2007; 23(4): 524 - 526. [Abstract] [Full Text] [PDF]
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A. Han, W.-Y. Kim, and S.-M. Park SNP2NMD: A database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay Bioinformatics, February 1, 2007; 23(3): 397 - 399. [Abstract] [Full Text] [PDF]
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D. G. Gilbert DroSpeGe: rapid access database for new Drosophila species genomes Nucleic Acids Res., January 12, 2007; 35(suppl_1): D480 - D485. [Abstract] [Full Text] [PDF]
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M. Spannagl, O. Noubibou, D. Haase, L. Yang, H. Gundlach, T. Hindemitt, K. Klee, G. Haberer, H. Schoof, and K. F. X. Mayer MIPSPlantsDB--plant database resource for integrative and comparative plant genome research Nucleic Acids Res., January 12, 2007; 35(suppl_1): D834 - D840. [Abstract] [Full Text] [PDF]
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C. Chaparro, R. Guyot, A. Zuccolo, B. Piegu, and O. Panaud RetrOryza: a database of the rice LTR-retrotransposons Nucleic Acids Res., January 12, 2007; 35(suppl_1): D66 - D70. [Abstract] [Full Text] [PDF]
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C. Dieterich, M. W. Franz, and M. Vingron Developments in CORG: a gene-centric comparative genomics resource Nucleic Acids Res., January 12, 2007; 35(suppl_1): D32 - D35. [Abstract] [Full Text] [PDF]
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C. Dieterich, W. Roeseler, P. Sobetzko, and R. J. Sommer Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus Nucleic Acids Res., January 12, 2007; 35(suppl_1): D498 - D502. [Abstract] [Full Text] [PDF]
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J. M. Mazzarelli, J. Brestelli, R. K. Gorski, J. Liu, E. Manduchi, D. F. Pinney, J. Schug, P. White, K. H. Kaestner, and C. J. Stoeckert Jr EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes Nucleic Acids Res., January 12, 2007; 35(suppl_1): D751 - D755. [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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B. I. Arshinoff, G. Suen, E. M. Just, S. M. Merchant, W. A. Kibbe, R. L. Chisholm, and R. D. Welch Xanthusbase: adapting wikipedia principles to a model organism database Nucleic Acids Res., January 12, 2007; 35(suppl_1): D422 - D426. [Abstract] [Full Text] [PDF]
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M. B. Arnaud, M. C. Costanzo, M. S. Skrzypek, P. Shah, G. Binkley, C. Lane, S. R. Miyasato, and G. Sherlock Sequence resources at the Candida Genome Database Nucleic Acids Res., January 12, 2007; 35(suppl_1): D452 - D456. [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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M. A. Crosby, J. L. Goodman, V. B. Strelets, P. Zhang, W. M. Gelbart, and The FlyBase Consortium FlyBase: genomes by the dozen Nucleic Acids Res., January 12, 2007; 35(suppl_1): D486 - D491. [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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A. E. Kazakov, M. J. Cipriano, P. S. Novichkov, S. Minovitsky, D. V. Vinogradov, A. Arkin, A. A. Mironov, M. S. Gelfand, and I. Dubchak RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes Nucleic Acids Res., January 12, 2007; 35(suppl_1): D407 - D412. [Abstract] [Full Text] [PDF]
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R. Nash, S. Weng, B. Hitz, R. Balakrishnan, K. R. Christie, M. C. Costanzo, S. S. Dwight, S. R. Engel, D. G. Fisk, J. E. Hirschman, et al. Expanded protein information at SGD: new pages and proteome browser Nucleic Acids Res., January 12, 2007; 35(suppl_1): D468 - D471. [Abstract] [Full Text] [PDF]
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M. Pachkov, I. Erb, N. Molina, and E. van Nimwegen SwissRegulon: a database of genome-wide annotations of regulatory sites Nucleic Acids Res., January 12, 2007; 35(suppl_1): D127 - D131. [Abstract] [Full Text] [PDF]
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T. Horn, Z. Arziman, J. Berger, and M. Boutros GenomeRNAi: a database for cell-based RNAi phenotypes Nucleic Acids Res., January 12, 2007; 35(suppl_1): D492 - D497. [Abstract] [Full Text] [PDF]
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J. Park, S. Hwang, Y. S. Lee, S.-C. Kim, and D. Lee SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms Nucleic Acids Res., January 12, 2007; 35(suppl_1): D711 - D715. [Abstract] [Full Text] [PDF]
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L. K. McNeil, C. Reich, R. K. Aziz, D. Bartels, M. Cohoon, T. Disz, R. A. Edwards, S. Gerdes, K. Hwang, M. Kubal, et al. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation Nucleic Acids Res., January 12, 2007; 35(suppl_1): D347 - D353. [Abstract] [Full Text] [PDF]
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S. Ouyang, W. Zhu, J. Hamilton, H. Lin, M. Campbell, K. Childs, F. Thibaud-Nissen, R. L. Malek, Y. Lee, L. Zheng, et al. The TIGR Rice Genome Annotation Resource: improvements and new features Nucleic Acids Res., January 12, 2007; 35(suppl_1): D883 - D887. [Abstract] [Full Text] [PDF]
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K. Hervold, A. Martin, R. A. Kirkpatrick, P. F. Mc Kenna, and F. A. Ramirez-Weber Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community Nucleic Acids Res., January 12, 2007; 35(suppl_1): D595 - D598. [Abstract] [Full Text] [PDF]
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