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. 2001 Aug;2(4):265–272. doi: 10.1002/cfg.58

Current Awareness on Comparative and Functional Genomics

PMCID: PMC2447213

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Selected References

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  1. Abdrakhmanov I., Lodygin D., Geroth P., Arakawa H., Law A., Plachy J., Korn B., Buerstedde J. M. A large database of chicken bursal ESTs as a resource for the analysis of vertebrate gene function. Genome Res. 2000 Dec;10(12):2062–2069. doi: 10.1101/gr.10.12.2062. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Afonso C. L., Tulman E. R., Lu Z., Zsak L., Rock D. L., Kutish G. F. The genome of turkey herpesvirus. J Virol. 2001 Jan;75(2):971–978. doi: 10.1128/JVI.75.2.971-978.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Aguan K., Carvajal J. A., Thompson L. P., Weiner C. P. Application of a functional genomics approach to identify differentially expressed genes in human myometrium during pregnancy and labour. Mol Hum Reprod. 2000 Dec;6(12):1141–1145. doi: 10.1093/molehr/6.12.1141. [DOI] [PubMed] [Google Scholar]
  4. Agüero F., Verdún R. E., Frasch A. C., Sánchez D. O. A random sequencing approach for the analysis of the Trypanosoma cruzi genome: general structure, large gene and repetitive DNA families, and gene discovery. Genome Res. 2000 Dec;10(12):1996–2005. doi: 10.1101/gr.gr-1463r. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Albala J. S., Franke K., McConnell I. R., Pak K. L., Folta P. A., Rubinfeld B., Davies A. H., Lennon G. G., Clark R. From genes to proteins: high-throughput expression and purification of the human proteome. J Cell Biochem. 2000 Oct 20;80(2):187–191. doi: 10.1002/1097-4644(20010201)80:2<187::aid-jcb40>3.0.co;2-v. [DOI] [PubMed] [Google Scholar]
  6. Anderson J. B., Wickens C., Khan M., Cowen L. E., Federspiel N., Jones T., Kohn L. M. Infrequent genetic exchange and recombination in the mitochondrial genome of Candida albicans. J Bacteriol. 2001 Feb;183(3):865–872. doi: 10.1128/JB.183.3.865-872.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Andrews J., Bouffard G. G., Cheadle C., Lü J., Becker K. G., Oliver B. Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Res. 2000 Dec;10(12):2030–2043. doi: 10.1101/gr.10.12.2030. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Apweiler R., Attwood T. K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M. D. InterPro--an integrated documentation resource for protein families, domains and functional sites. Bioinformatics. 2000 Dec;16(12):1145–1150. doi: 10.1093/bioinformatics/16.12.1145. [DOI] [PubMed] [Google Scholar]
  9. Baldi P., Baisnée P. F. Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths. Bioinformatics. 2000 Oct;16(10):865–889. doi: 10.1093/bioinformatics/16.10.865. [DOI] [PubMed] [Google Scholar]
  10. Bedell J. A., Korf I., Gish W. MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics. 2000 Nov;16(11):1040–1041. doi: 10.1093/bioinformatics/16.11.1040. [DOI] [PubMed] [Google Scholar]
  11. Beissbarth T., Fellenberg K., Brors B., Arribas-Prat R., Boer J., Hauser N. C., Scheideler M., Hoheisel J. D., Schütz G., Poustka A. Processing and quality control of DNA array hybridization data. Bioinformatics. 2000 Nov;16(11):1014–1022. doi: 10.1093/bioinformatics/16.11.1014. [DOI] [PubMed] [Google Scholar]
  12. Bell A. C., West A. G., Felsenfeld G. Insulators and boundaries: versatile regulatory elements in the eukaryotic genome. Science. 2001 Jan 19;291(5503):447–450. doi: 10.1126/science.291.5503.447. [DOI] [PubMed] [Google Scholar]
  13. Bertucci F., Houlgatte R., Benziane A., Granjeaud S., Adélaïde J., Tagett R., Loriod B., Jacquemier J., Viens P., Jordan B. Gene expression profiling of primary breast carcinomas using arrays of candidate genes. Hum Mol Genet. 2000 Dec 12;9(20):2981–2991. doi: 10.1093/hmg/9.20.2981. [DOI] [PubMed] [Google Scholar]
  14. Betts J. C., Dodson P., Quan S., Lewis A. P., Thomas P. J., Duncan K., McAdam R. A. Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. Microbiology. 2000 Dec;146(Pt 12):3205–3216. doi: 10.1099/00221287-146-12-3205. [DOI] [PubMed] [Google Scholar]
  15. Biagini P., Gallian P., Attoui H., Touinssi M., Cantaloube J., de Micco P., de Lamballerie X. Genetic analysis of full-length genomes and subgenomic sequences of TT virus-like mini virus human isolates. J Gen Virol. 2001 Feb;82(Pt 2):379–383. doi: 10.1099/0022-1317-82-2-379. [DOI] [PubMed] [Google Scholar]
  16. Bingham J., Plowman G. D., Sudarsanam S. Informatics issues in large-scale sequence analysis: elucidating the protein kinases of C. elegans. J Cell Biochem. 2000 Oct 20;80(2):181–186. doi: 10.1002/1097-4644(20010201)80:2<181::aid-jcb30>3.0.co;2-1. [DOI] [PubMed] [Google Scholar]
  17. Boone M., Upton C. BLAST Search Updater: a notification system for new database matches. Bioinformatics. 2000 Nov;16(11):1054–1055. doi: 10.1093/bioinformatics/16.11.1054. [DOI] [PubMed] [Google Scholar]
  18. Bouton C. M., Pevsner J. DRAGON: Database Referencing of Array Genes Online. Bioinformatics. 2000 Nov;16(11):1038–1039. doi: 10.1093/bioinformatics/16.11.1038. [DOI] [PubMed] [Google Scholar]
  19. Broder S., Venter J. C. Whole genomes: the foundation of new biology and medicine. Curr Opin Biotechnol. 2000 Dec;11(6):581–585. doi: 10.1016/s0958-1669(00)00147-6. [DOI] [PubMed] [Google Scholar]
  20. Brüssow H., Desiere F. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol Microbiol. 2001 Jan;39(2):213–222. doi: 10.1046/j.1365-2958.2001.02228.x. [DOI] [PubMed] [Google Scholar]
  21. Buchholz B. A., Doherty E. A., Albarghouthi M. N., Bogdan F. M., Zahn J. M., Barron A. E. Microchannel DNA sequencing matrices with a thermally controlled "viscosity switch". Anal Chem. 2001 Jan 15;73(2):157–164. doi: 10.1021/ac001023z. [DOI] [PubMed] [Google Scholar]
  22. Buetow K. H., Edmonson M., MacDonald R., Clifford R., Yip P., Kelley J., Little D. P., Strausberg R., Koester H., Cantor C. R. High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc Natl Acad Sci U S A. 2001 Jan 2;98(2):581–584. doi: 10.1073/pnas.021506298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Bulger M., Bender M. A., van Doorninck J. H., Wertman B., Farrell C. M., Felsenfeld G., Groudine M., Hardison R. Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse beta-globin gene clusters. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14560–14565. doi: 10.1073/pnas.97.26.14560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Bumol T. F., Watanabe A. M. Genetic information, genomic technologies, and the future of drug discovery. JAMA. 2001 Feb 7;285(5):551–555. doi: 10.1001/jama.285.5.551. [DOI] [PubMed] [Google Scholar]
  25. Burchiel S. W., Knall C. M., Davis J. W., 2nd, Paules R. S., Boggs S. E., Afshari C. A. Analysis of genetic and epigenetic mechanisms of toxicity: potential roles of toxicogenomics and proteomics in toxicology. Toxicol Sci. 2001 Feb;59(2):193–195. doi: 10.1093/toxsci/59.2.193. [DOI] [PubMed] [Google Scholar]
  26. Burczynski M. E., McMillian M., Ciervo J., Li L., Parker J. B., Dunn R. T., 2nd, Hicken S., Farr S., Johnson M. D. Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells. Toxicol Sci. 2000 Dec;58(2):399–415. doi: 10.1093/toxsci/58.2.399. [DOI] [PubMed] [Google Scholar]
  27. Callow M. J., Dudoit S., Gong E. L., Speed T. P., Rubin E. M. Microarray expression profiling identifies genes with altered expression in HDL-deficient mice. Genome Res. 2000 Dec;10(12):2022–2029. doi: 10.1101/gr.10.12.2022. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Campagne F. Clustalnet: the joining of Clustal and CORBA. Bioinformatics. 2000 Jul;16(7):606–612. doi: 10.1093/bioinformatics/16.7.606. [DOI] [PubMed] [Google Scholar]
  29. Cao Y., Fujiwara M., Nikaido M., Okada N., Hasegawa M. Interordinal relationships and timescale of eutherian evolution as inferred from mitochondrial genome data. Gene. 2000 Dec 23;259(1-2):149–158. doi: 10.1016/s0378-1119(00)00427-3. [DOI] [PubMed] [Google Scholar]
  30. Celniker S. E. The Drosophila genome. Curr Opin Genet Dev. 2000 Dec;10(6):612–616. doi: 10.1016/s0959-437x(00)00140-4. [DOI] [PubMed] [Google Scholar]
  31. Chinen A., Uchiyama I., Kobayashi I. Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms. Gene. 2000 Dec 23;259(1-2):109–121. doi: 10.1016/s0378-1119(00)00459-5. [DOI] [PubMed] [Google Scholar]
  32. Choe W., Ersoy O. K., Bina M. Neural network schemes for detecting rare events in human genomic DNA. Bioinformatics. 2000 Dec;16(12):1062–1072. doi: 10.1093/bioinformatics/16.12.1062. [DOI] [PubMed] [Google Scholar]
  33. Choi J. H., Jung H. Y., Kim H. S., Cho H. G. PhyloDraw: a phylogenetic tree drawing system. Bioinformatics. 2000 Nov;16(11):1056–1058. doi: 10.1093/bioinformatics/16.11.1056. [DOI] [PubMed] [Google Scholar]
  34. Chrast R., Scott H. S., Papasavvas M. P., Rossier C., Antonarakis E. S., Barras C., Davisson M. T., Schmidt C., Estivill X., Dierssen M. The mouse brain transcriptome by SAGE: differences in gene expression between P30 brains of the partial trisomy 16 mouse model of Down syndrome (Ts65Dn) and normals. Genome Res. 2000 Dec;10(12):2006–2021. doi: 10.1101/gr.10.12.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Cockett M., Dracopoli N., Sigal E. Applied genomics: integration of the technology within pharmaceutical research and development. Curr Opin Biotechnol. 2000 Dec;11(6):602–609. doi: 10.1016/s0958-1669(00)00151-8. [DOI] [PubMed] [Google Scholar]
  36. Cogoni C., Macino G. Post-transcriptional gene silencing across kingdoms. Curr Opin Genet Dev. 2000 Dec;10(6):638–643. doi: 10.1016/s0959-437x(00)00134-9. [DOI] [PubMed] [Google Scholar]
  37. Cooper A., Lalueza-Fox C., Anderson S., Rambaut A., Austin J., Ward R. Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature. 2001 Feb 8;409(6821):704–707. doi: 10.1038/35055536. [DOI] [PubMed] [Google Scholar]
  38. Dauter Z., Li M., Wlodawer A. Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics. Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):239–249. doi: 10.1107/s0907444900015249. [DOI] [PubMed] [Google Scholar]
  39. Douglas K. R., Camper S. A. Partial transcriptome of the developing pituitary gland. Genomics. 2000 Dec 15;70(3):335–346. doi: 10.1006/geno.2000.6400. [DOI] [PubMed] [Google Scholar]
  40. Dovichi Norman J., Zhang Jianzhong. How Capillary Electrophoresis Sequenced the Human Genome This Essay is based on a lecture given at the Analytica 2000 conference in Munich (Germany) on the occasion of the Heinrich-Emanuel-Merck Prize presentation. . Angew Chem Int Ed Engl. 2000 Dec 15;39(24):4463–4468. doi: 10.1002/1521-3773(20001215)39:24<4463::aid-anie4463>3.0.co;2-8. [DOI] [PubMed] [Google Scholar]
  41. Dow J. M., Daniels M. J. Xylella genomics and bacterial pathogenicity to plants. Yeast. 2000 Dec;17(4):263–271. doi: 10.1002/1097-0061(200012)17:4<263::AID-YEA44>3.0.CO;2-G. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Drenkard E., Richter B. G., Rozen S., Stutius L. M., Angell N. A., Mindrinos M., Cho R. J., Oefner P. J., Davis R. W., Ausubel F. M. A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol. 2000 Dec;124(4):1483–1492. doi: 10.1104/pp.124.4.1483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Eisen J. A. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genet Dev. 2000 Dec;10(6):606–611. doi: 10.1016/s0959-437x(00)00143-x. [DOI] [PubMed] [Google Scholar]
  44. Erlandsen H., Abola E. E., Stevens R. C. Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites. Curr Opin Struct Biol. 2000 Dec;10(6):719–730. doi: 10.1016/s0959-440x(00)00154-8. [DOI] [PubMed] [Google Scholar]
  45. Farlow D. N., Vansant G., Cameron A. A., Chang J., Khoh-Reiter S., Pham N. L., Wu W., Sagara Y., Nicholls J. G., Carlo D. J. Gene expression monitoring for gene discovery in models of peripheral and central nervous system differentiation, regeneration, and trauma. J Cell Biochem. 2000 Oct 20;80(2):171–180. doi: 10.1002/1097-4644(20010201)80:2<171::aid-jcb20>3.3.co;2-x. [DOI] [PubMed] [Google Scholar]
  46. Funk D. J., Helbling L., Wernegreen J. J., Moran N. A. Intraspecific phylogenetic congruence among multiple symbiont genomes. Proc Biol Sci. 2000 Dec 22;267(1461):2517–2521. doi: 10.1098/rspb.2000.1314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Furey T. S., Cristianini N., Duffy N., Bednarski D. W., Schummer M., Haussler D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics. 2000 Oct;16(10):906–914. doi: 10.1093/bioinformatics/16.10.906. [DOI] [PubMed] [Google Scholar]
  48. Galliot B. Conserved and divergent genes in apex and axis development of cnidarians. Curr Opin Genet Dev. 2000 Dec;10(6):629–637. doi: 10.1016/s0959-437x(00)00141-6. [DOI] [PubMed] [Google Scholar]
  49. Galloway A. M., Allalunis-Turner J. cDNA expression array analysis of DNA repair genes in human glioma cells that lack or express DNA-PK. Radiat Res. 2000 Dec;154(6):609–615. doi: 10.1667/0033-7587(2000)154[0609:ceaaod]2.0.co;2. [DOI] [PubMed] [Google Scholar]
  50. Garin J., Diez R., Kieffer S., Dermine J. F., Duclos S., Gagnon E., Sadoul R., Rondeau C., Desjardins M. The phagosome proteome: insight into phagosome functions. J Cell Biol. 2001 Jan 8;152(1):165–180. doi: 10.1083/jcb.152.1.165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Gaucher E. A., Miyamoto M. M., Benner S. A. Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):548–552. doi: 10.1073/pnas.98.2.548. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Gerner C., Frohwein U., Gotzmann J., Bayer E., Gelbmann D., Bursch W., Schulte-Hermann R. The Fas-induced apoptosis analyzed by high throughput proteome analysis. J Biol Chem. 2000 Dec 15;275(50):39018–39026. doi: 10.1074/jbc.M006495200. [DOI] [PubMed] [Google Scholar]
  53. Girke T., Todd J., Ruuska S., White J., Benning C., Ohlrogge J. Microarray analysis of developing Arabidopsis seeds. Plant Physiol. 2000 Dec;124(4):1570–1581. doi: 10.1104/pp.124.4.1570. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Grammer T. C., Liu K. J., Mariani F. V., Harland R. M. Use of large-scale expression cloning screens in the Xenopus laevis tadpole to identify gene function. Dev Biol. 2000 Dec 15;228(2):197–210. doi: 10.1006/dbio.2000.9945. [DOI] [PubMed] [Google Scholar]
  55. Groth C., Petersen R. F., Piskur J. Diversity in organization and the origin of gene orders in the mitochondrial DNA molecules of the genus Saccharomyces. Mol Biol Evol. 2000 Dec;17(12):1833–1841. doi: 10.1093/oxfordjournals.molbev.a026284. [DOI] [PubMed] [Google Scholar]
  56. Gurvitz A., Langer S., Piskacek M., Hamilton B., Ruis H., Hartig A. Predicting the function and subcellular location of Caenorhabditis elegans proteins similar to Saccharomyces cerevisiae beta-oxidation enzymes. Yeast. 2000 Sep 30;17(3):188–200. doi: 10.1002/1097-0061(20000930)17:3<188::AID-YEA27>3.0.CO;2-E. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Han M. J., Yoon S. S., Lee S. Y. Proteome analysis of metabolically engineered Escherichia coli producing Poly(3-hydroxybutyrate). J Bacteriol. 2001 Jan;183(1):301–308. doi: 10.1128/JB.183.1.301-308.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Henrissat B., Davies G. J. Glycoside hydrolases and glycosyltransferases. Families, modules, and implications for genomics. Plant Physiol. 2000 Dec;124(4):1515–1519. doi: 10.1104/pp.124.4.1515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Herwig R., Schmitt A. O., Steinfath M., O'Brien J., Seidel H., Meier-Ewert S., Lehrach H., Radelof U. Information theoretical probe selection for hybridisation experiments. Bioinformatics. 2000 Oct;16(10):890–898. doi: 10.1093/bioinformatics/16.10.890. [DOI] [PubMed] [Google Scholar]
  60. Ho T. B., Robertson B. D., Taylor G. M., Shaw R. J., Young D. B. Comparison of Mycobacterium tuberculosis genomes reveals frequent deletions in a 20 kb variable region in clinical isolates. Yeast. 2000 Dec;17(4):272–282. doi: 10.1002/1097-0061(200012)17:4<272::AID-YEA48>3.0.CO;2-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Horrocks P., Bowman S., Kyes S., Waters A. P., Craig A. Entering the post-genomic era of malaria research. Bull World Health Organ. 2003 Nov 17;78(12):1424–1437. [PMC free article] [PubMed] [Google Scholar]
  62. Huang H., Colella S., Kurrer M., Yonekawa Y., Kleihues P., Ohgaki H. Gene expression profiling of low-grade diffuse astrocytomas by cDNA arrays. Cancer Res. 2000 Dec 15;60(24):6868–6874. [PubMed] [Google Scholar]
  63. Irving J. A., Whisstock J. C., Lesk A. M. Protein structural alignments and functional genomics. Proteins. 2001 Feb 15;42(3):378–382. doi: 10.1002/1097-0134(20010215)42:3<378::aid-prot70>3.0.co;2-3. [DOI] [PubMed] [Google Scholar]
  64. Itoh J. I., Kitano H., Matsuoka M., Nagato Y. Shoot organization genes regulate shoot apical meristem organization and the pattern of leaf primordium initiation in rice. Plant Cell. 2000 Nov;12(11):2161–2174. doi: 10.1105/tpc.12.11.2161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Jakt L. M., Cao L., Cheah K. S., Smith D. K. Assessing clusters and motifs from gene expression data. Genome Res. 2001 Jan;11(1):112–123. doi: 10.1101/gr.148301. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Jernvall J., Keränen S. V., Thesleff I. Evolutionary modification of development in mammalian teeth: quantifying gene expression patterns and topography. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14444–14448. doi: 10.1073/pnas.97.26.14444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Johnston M. The yeast genome: on the road to the Golden Age. Curr Opin Genet Dev. 2000 Dec;10(6):617–623. doi: 10.1016/s0959-437x(00)00145-3. [DOI] [PubMed] [Google Scholar]
  68. Justice M. J. Capitalizing on large-scale mouse mutagenesis screens. Nat Rev Genet. 2000 Nov;1(2):109–115. doi: 10.1038/35038549. [DOI] [PubMed] [Google Scholar]
  69. Kadota K., Miki R., Bono H., Shimizu K., Okazaki Y., Hayashizaki Y. Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data. Physiol Genomics. 2001 Jan 19;4(3):183–188. doi: 10.1152/physiolgenomics.2001.4.3.183. [DOI] [PubMed] [Google Scholar]
  70. Karlberg O., Canbäck B., Kurland C. G., Andersson S. G. The dual origin of the yeast mitochondrial proteome. Yeast. 2000 Sep 30;17(3):170–187. doi: 10.1002/1097-0061(20000930)17:3<170::AID-YEA25>3.0.CO;2-V. [DOI] [PMC free article] [PubMed] [Google Scholar]
  71. Kawabata T., Arisaka F., Nishikawa K. Structural/functional assignment of unknown bacteriophage T4 proteins by iterative database searches. Gene. 2000 Dec 23;259(1-2):223–233. doi: 10.1016/s0378-1119(00)00442-x. [DOI] [PubMed] [Google Scholar]
  72. Kawai J., Shinagawa A., Shibata K., Yoshino M., Itoh M., Ishii Y., Arakawa T., Hara A., Fukunishi Y., Konno H. Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685–690. doi: 10.1038/35055500. [DOI] [PubMed] [Google Scholar]
  73. Kawashima T., Amano N., Koike H., Makino S., Higuchi S., Kawashima-Ohya Y., Watanabe K., Yamazaki M., Kanehori K., Kawamoto T. Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14257–14262. doi: 10.1073/pnas.97.26.14257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  74. Kenzelmann M., Mühlemann K. Transcriptome analysis of fibroblast cells immediate-early after human cytomegalovirus infection. J Mol Biol. 2000 Dec 15;304(5):741–751. doi: 10.1006/jmbi.2000.4271. [DOI] [PubMed] [Google Scholar]
  75. Kersey P., Hermjakob H., Apweiler R. VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL. Bioinformatics. 2000 Nov;16(11):1048–1049. doi: 10.1093/bioinformatics/16.11.1048. [DOI] [PubMed] [Google Scholar]
  76. Kim S., Zeller K., Dang C. V., Sandgren E. P., Lee L. A. A strategy to identify differentially expressed genes using representational difference analysis and cDNA arrays. Anal Biochem. 2001 Jan 15;288(2):141–148. doi: 10.1006/abio.2000.4900. [DOI] [PubMed] [Google Scholar]
  77. King R. D., Karwath A., Clare A., Dehaspe L. Accurate prediction of protein functional class from sequence in the Mycobacterium tuberculosis and Escherichia coli genomes using data mining. Yeast. 2000 Dec;17(4):283–293. doi: 10.1002/1097-0061(200012)17:4<283::AID-YEA52>3.0.CO;2-F. [DOI] [PMC free article] [PubMed] [Google Scholar]
  78. Koike T., Rzhetsky A. A graphic editor for analyzing signal-transduction pathways. Gene. 2000 Dec 23;259(1-2):235–244. doi: 10.1016/s0378-1119(00)00458-3. [DOI] [PubMed] [Google Scholar]
  79. Korf I., Gish W. MPBLAST : improved BLAST performance with multiplexed queries. Bioinformatics. 2000 Nov;16(11):1052–1053. doi: 10.1093/bioinformatics/16.11.1052. [DOI] [PubMed] [Google Scholar]
  80. Krauthammer M., Rzhetsky A., Morozov P., Friedman C. Using BLAST for identifying gene and protein names in journal articles. Gene. 2000 Dec 23;259(1-2):245–252. doi: 10.1016/s0378-1119(00)00431-5. [DOI] [PubMed] [Google Scholar]
  81. Kuhn K. M., DeRisi J. L., Brown P. O., Sarnow P. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol Cell Biol. 2001 Feb;21(3):916–927. doi: 10.1128/MCB.21.3.916-927.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Le T. H., Blair D., McManus D. P. Mitochondrial genomes of human helminths and their use as markers in population genetics and phylogeny. Acta Trop. 2000 Dec 1;77(3):243–256. doi: 10.1016/s0001-706x(00)00157-1. [DOI] [PubMed] [Google Scholar]
  83. Lewis T. S., Hunt J. B., Aveline L. D., Jonscher K. R., Louie D. F., Yeh J. M., Nahreini T. S., Resing K. A., Ahn N. G. Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry. Mol Cell. 2000 Dec;6(6):1343–1354. doi: 10.1016/s1097-2765(00)00132-5. [DOI] [PubMed] [Google Scholar]
  84. Lewohl J. M., Wang L., Miles M. F., Zhang L., Dodd P. R., Harris R. A. Gene expression in human alcoholism: microarray analysis of frontal cortex. Alcohol Clin Exp Res. 2000 Dec;24(12):1873–1882. [PubMed] [Google Scholar]
  85. Li W., Pio F., Pawłowski K., Godzik A. Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinformatics. 2000 Dec;16(12):1105–1110. doi: 10.1093/bioinformatics/16.12.1105. [DOI] [PubMed] [Google Scholar]
  86. Liao B., Hale W., Epstein C. B., Butow R. A., Garner H. R. MAD: a suite of tools for microarray data management and processing. Bioinformatics. 2000 Oct;16(10):946–947. doi: 10.1093/bioinformatics/16.10.946. [DOI] [PubMed] [Google Scholar]
  87. Liò P., Vannucci M. Finding pathogenicity islands and gene transfer events in genome data. Bioinformatics. 2000 Oct;16(10):932–940. doi: 10.1093/bioinformatics/16.10.932. [DOI] [PubMed] [Google Scholar]
  88. Ljubimova J. Y., Khazenzon N. M., Chen Z., Neyman Y. I., Turner L., Riedinger M. S., Black K. L. Gene expression abnormalities in human glial tumors identified by gene array. Int J Oncol. 2001 Feb;18(2):287–295. doi: 10.3892/ijo.18.2.287. [DOI] [PubMed] [Google Scholar]
  89. Loferer H. Mining bacterial genomes for antimicrobial targets. Mol Med Today. 2000 Dec;6(12):470–474. doi: 10.1016/s1357-4310(00)01815-3. [DOI] [PubMed] [Google Scholar]
  90. Luzi L., Confalonieri S., Di Fiore P. P., Pelicci P. G. Evolution of Shc functions from nematode to human. Curr Opin Genet Dev. 2000 Dec;10(6):668–674. doi: 10.1016/s0959-437x(00)00146-5. [DOI] [PubMed] [Google Scholar]
  91. Mahan M. J., Heithoff D. M., Sinsheimer R. L., Low D. A. Assessment of bacterial pathogenesis by analysis of gene expression in the host. Annu Rev Genet. 2000;34:139–164. doi: 10.1146/annurev.genet.34.1.139. [DOI] [PubMed] [Google Scholar]
  92. Maleck K., Levine A., Eulgem T., Morgan A., Schmid J., Lawton K. A., Dangl J. L., Dietrich R. A. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat Genet. 2000 Dec;26(4):403–410. doi: 10.1038/82521. [DOI] [PubMed] [Google Scholar]
  93. Man M. Z., Wang X., Wang Y. POWER_SAGE: comparing statistical tests for SAGE experiments. Bioinformatics. 2000 Nov;16(11):953–959. doi: 10.1093/bioinformatics/16.11.953. [DOI] [PubMed] [Google Scholar]
  94. Maneu V., Roig P., Gozalbo D. Complementation of Saccharomyces cerevisiae mutations in genes involved in translation and protein folding (EFB1 and SSB1) with Candida albicans cloned genes. Res Microbiol. 2000 Nov;151(9):739–746. doi: 10.1016/s0923-2508(00)01139-6. [DOI] [PubMed] [Google Scholar]
  95. Matte-Tailliez O., Zivanovic Y., Forterre P. Mining archaeal proteomes for eukaryotic proteins with novel functions: the PACE case. Trends Genet. 2000 Dec;16(12):533–536. doi: 10.1016/s0168-9525(00)02137-5. [DOI] [PubMed] [Google Scholar]
  96. Mayor C., Brudno M., Schwartz J. R., Poliakov A., Rubin E. M., Frazer K. A., Pachter L. S., Dubchak I. VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 2000 Nov;16(11):1046–1047. doi: 10.1093/bioinformatics/16.11.1046. [DOI] [PubMed] [Google Scholar]
  97. McClelland M., Florea L., Sanderson K., Clifton S. W., Parkhill J., Churcher C., Dougan G., Wilson R. K., Miller W. Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Res. 2000 Dec 15;28(24):4974–4986. doi: 10.1093/nar/28.24.4974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  98. McClintick J., Edenberg H. J. BlastReport: a perl script to facilitate the use of sequence databases for mapping and clustering. Biotechniques. 2000 Dec;29(6):1272–1276. doi: 10.2144/00296bc03. [DOI] [PubMed] [Google Scholar]
  99. Mir K. U., Southern E. M. Sequence variation in genes and genomic DNA: methods for large-scale analysis. Annu Rev Genomics Hum Genet. 2000;1:329–360. doi: 10.1146/annurev.genom.1.1.329. [DOI] [PubMed] [Google Scholar]
  100. Misawa K., Tajima F. A simple method for classifying genes and a bootstrap test for classifications. Mol Biol Evol. 2000 Dec;17(12):1879–1884. doi: 10.1093/oxfordjournals.molbev.a026289. [DOI] [PubMed] [Google Scholar]
  101. Moler E. J., Chow M. L., Mian I. S. Analysis of molecular profile data using generative and discriminative methods. Physiol Genomics. 2000 Dec 18;4(2):109–126. doi: 10.1152/physiolgenomics.2000.4.2.109. [DOI] [PubMed] [Google Scholar]
  102. Mollapour M., Piper P. Targeted gene deletion in Zygosaccharomyces bailii. Yeast. 2001 Jan 30;18(2):173–186. doi: 10.1002/1097-0061(20010130)18:2<173::AID-YEA663>3.0.CO;2-F. [DOI] [PubMed] [Google Scholar]
  103. Morgenstern B. A space-efficient algorithm for aligning large genomic sequences. Bioinformatics. 2000 Oct;16(10):948–949. doi: 10.1093/bioinformatics/16.10.948. [DOI] [PubMed] [Google Scholar]
  104. Mouchaty S. K., Catzeflis F., Janke A., Arnason U. Molecular evidence of an African Phiomorpha-South American Caviomorpha clade and support for Hystricognathi based on the complete mitochondrial genome of the cane rat (Thryonomys swinderianus). Mol Phylogenet Evol. 2001 Jan;18(1):127–135. doi: 10.1006/mpev.2000.0870. [DOI] [PubMed] [Google Scholar]
  105. Mugridge N. B., Morrison D. A., Jäkel T., Heckeroth A. R., Tenter A. M., Johnson A. M. Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family sarcocystidae. Mol Biol Evol. 2000 Dec;17(12):1842–1853. doi: 10.1093/oxfordjournals.molbev.a026285. [DOI] [PubMed] [Google Scholar]
  106. Muilu J., Rodriguez-Tomé P., Robinson A. GBuilder--an application for the visualization and integration of EST cluster data. Genome Res. 2001 Jan;11(1):179–184. doi: 10.1101/gr.157501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  107. Murvai J., Vlahovicek K., Pongor S. A simple probabilistic scoring method for protein domain identification. Bioinformatics. 2000 Dec;16(12):1155–1156. doi: 10.1093/bioinformatics/16.12.1155. [DOI] [PubMed] [Google Scholar]
  108. Murén E., Oyen M., Barmark G., Ronne H. Identification of yeast deletion strains that are hypersensitive to brefeldin A or monensin, two drugs that affect intracellular transport. Yeast. 2001 Jan 30;18(2):163–172. doi: 10.1002/1097-0061(20010130)18:2<163::AID-YEA659>3.0.CO;2-#. [DOI] [PubMed] [Google Scholar]
  109. Möller S., Kriventseva E. V., Apweiler R. A collection of well characterised integral membrane proteins. Bioinformatics. 2000 Dec;16(12):1159–1160. doi: 10.1093/bioinformatics/16.12.1159. [DOI] [PubMed] [Google Scholar]
  110. Nadadur S. S., Schladweiler M. C., Kodavanti U. P. A pulmonary rat gene array for screening altered expression profiles in air pollutant-induced lung injury. Inhal Toxicol. 2000 Dec;12(12):1239–1254. doi: 10.1080/08958370050198566. [DOI] [PubMed] [Google Scholar]
  111. Nekrutenko A., Li W. H. Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res. 2000 Dec;10(12):1986–1995. doi: 10.1101/gr.10.12.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Nickrent D. L., Parkinson C. L., Palmer J. D., Duff R. J. Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants. Mol Biol Evol. 2000 Dec;17(12):1885–1895. doi: 10.1093/oxfordjournals.molbev.a026290. [DOI] [PubMed] [Google Scholar]
  113. Nishikawa T., Ota T., Isogai T. Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences. Bioinformatics. 2000 Nov;16(11):960–967. doi: 10.1093/bioinformatics/16.11.960. [DOI] [PubMed] [Google Scholar]
  114. Nobusato A., Uchiyama I., Ohashi S., Kobayashi I. Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene. 2000 Dec 23;259(1-2):99–108. doi: 10.1016/s0378-1119(00)00456-x. [DOI] [PubMed] [Google Scholar]
  115. Ochman H., Jones I. B. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 2000 Dec 15;19(24):6637–6643. doi: 10.1093/emboj/19.24.6637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  116. Ogawa N., DeRisi J., Brown P. O. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell. 2000 Dec;11(12):4309–4321. doi: 10.1091/mbc.11.12.4309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Page R. D. Circles: automating the comparative analysis of RNA secondary structure. Bioinformatics. 2000 Nov;16(11):1042–1043. doi: 10.1093/bioinformatics/16.11.1042. [DOI] [PubMed] [Google Scholar]
  118. Pannuti A., Lucchesi J. C. Recycling to remodel: evolution of dosage-compensation complexes. Curr Opin Genet Dev. 2000 Dec;10(6):644–650. doi: 10.1016/s0959-437x(00)00136-2. [DOI] [PubMed] [Google Scholar]
  119. Pardo-Manuel de Villena F., de la Casa-Esperón E., Sapienza C. Natural selection and the function of genome imprinting: beyond the silenced minority. Trends Genet. 2000 Dec;16(12):573–579. doi: 10.1016/s0168-9525(00)02134-x. [DOI] [PubMed] [Google Scholar]
  120. Park J., Dietmann S., Heger A., Holm L. Estimating the significance of sequence order in protein secondary structure and prediction. Bioinformatics. 2000 Nov;16(11):978–987. doi: 10.1093/bioinformatics/16.11.978. [DOI] [PubMed] [Google Scholar]
  121. Pennacchio L. A., Rubin E. M. Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet. 2001 Feb;2(2):100–109. doi: 10.1038/35052548. [DOI] [PubMed] [Google Scholar]
  122. Perna N. T., Plunkett G., 3rd, Burland V., Mau B., Glasner J. D., Rose D. J., Mayhew G. F., Evans P. S., Gregor J., Kirkpatrick H. A. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 2001 Jan 25;409(6819):529–533. doi: 10.1038/35054089. [DOI] [PubMed] [Google Scholar]
  123. Pertsemlidis A., Pande A., Miller B., Schilling P., Wei M. H., Lerman M. I., Minna J. D., Garner H. R., Mittelman D. PANORAMA: an integrated Web-based sequence analysis tool and its role in gene discovery. Genomics. 2000 Dec 15;70(3):300–306. doi: 10.1006/geno.2000.6359. [DOI] [PubMed] [Google Scholar]
  124. Phay J. E., Hussain H. B., Moley J. F. Strategy for identification of novel glucose transporter family members by using internet-based genomic databases. Surgery. 2000 Dec;128(6):946–951. doi: 10.1067/msy.2000.109967. [DOI] [PubMed] [Google Scholar]
  125. Philippe H., Germot A., Moreira D. The new phylogeny of eukaryotes. Curr Opin Genet Dev. 2000 Dec;10(6):596–601. doi: 10.1016/s0959-437x(00)00137-4. [DOI] [PubMed] [Google Scholar]
  126. Pollock D. D., Eisen J. A., Doggett N. A., Cummings M. P. A case for evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol Biol Evol. 2000 Dec;17(12):1776–1788. doi: 10.1093/oxfordjournals.molbev.a026278. [DOI] [PubMed] [Google Scholar]
  127. Prescott D. M., Dizick S. J. A unique pattern of intrastrand anomalies in base composition of the DNA in hypotrichs. Nucleic Acids Res. 2000 Dec 1;28(23):4679–4688. doi: 10.1093/nar/28.23.4679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  128. Prescott D. M. Genome gymnastics: unique modes of DNA evolution and processing in ciliates. Nat Rev Genet. 2000 Dec;1(3):191–198. doi: 10.1038/35042057. [DOI] [PubMed] [Google Scholar]
  129. Primig M., Williams R. M., Winzeler E. A., Tevzadze G. G., Conway A. R., Hwang S. Y., Davis R. W., Esposito R. E. The core meiotic transcriptome in budding yeasts. Nat Genet. 2000 Dec;26(4):415–423. doi: 10.1038/82539. [DOI] [PubMed] [Google Scholar]
  130. Promponas V. J., Enright A. J., Tsoka S., Kreil D. P., Leroy C., Hamodrakas S., Sander C., Ouzounis C. A. CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics. 2000 Oct;16(10):915–922. doi: 10.1093/bioinformatics/16.10.915. [DOI] [PubMed] [Google Scholar]
  131. Rain J. C., Selig L., De Reuse H., Battaglia V., Reverdy C., Simon S., Lenzen G., Petel F., Wojcik J., Schächter V. The protein-protein interaction map of Helicobacter pylori. Nature. 2001 Jan 11;409(6817):211–215. doi: 10.1038/35051615. [DOI] [PubMed] [Google Scholar]
  132. Ramu C., Gemünd C., Gibson T. J. Object-oriented parsing of biological databases with Python. Bioinformatics. 2000 Jul;16(7):628–638. doi: 10.1093/bioinformatics/16.7.628. [DOI] [PubMed] [Google Scholar]
  133. Rast J. P., Amore G., Calestani C., Livi C. B., Ransick A., Davidson E. H. Recovery of developmentally defined gene sets from high-density cDNA macroarrays. Dev Biol. 2000 Dec 15;228(2):270–286. doi: 10.1006/dbio.2000.9941. [DOI] [PubMed] [Google Scholar]
  134. Rhee S. Y. Bioinformatic resources, challenges, and opportunities using Arabidopsis as a model organism in a post-genomic era. Plant Physiol. 2000 Dec;124(4):1460–1464. doi: 10.1104/pp.124.4.1460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  135. Rininger JA, DiPippo VA, Gould-Rothberg BE. Differential gene expression technologies for identifying surrogate markers of drug efficacy and toxicity. Drug Discov Today. 2000 Dec 1;5(12):560–568. doi: 10.1016/s1359-6446(00)01597-x. [DOI] [PubMed] [Google Scholar]
  136. Rivas E., Eddy S. R. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics. 2000 Jul;16(7):583–605. doi: 10.1093/bioinformatics/16.7.583. [DOI] [PubMed] [Google Scholar]
  137. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M. A., Barrell B. Artemis: sequence visualization and annotation. Bioinformatics. 2000 Oct;16(10):944–945. doi: 10.1093/bioinformatics/16.10.944. [DOI] [PubMed] [Google Scholar]
  138. Rzhetsky A., Koike T., Kalachikov S., Gomez S. M., Krauthammer M., Kaplan S. H., Kra P., Russo J. J., Friedman C. A knowledge model for analysis and simulation of regulatory networks. Bioinformatics. 2000 Dec;16(12):1120–1128. doi: 10.1093/bioinformatics/16.12.1120. [DOI] [PubMed] [Google Scholar]
  139. Sakharkar M. K., Kangueane P., Woon T. W., Tan T. W., Kolatkar P. R., Long M., de Souza S. J. IE-Kb: intron exon knowledge base. Bioinformatics. 2000 Dec;16(12):1151–1152. doi: 10.1093/bioinformatics/16.12.1151. [DOI] [PubMed] [Google Scholar]
  140. Salama N., Guillemin K., McDaniel T. K., Sherlock G., Tompkins L., Falkow S. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14668–14673. doi: 10.1073/pnas.97.26.14668. [DOI] [PMC free article] [PubMed] [Google Scholar]
  141. Salamon H., Kato-Maeda M., Small P. M., Drenkow J., Gingeras T. R. Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data. Genome Res. 2000 Dec;10(12):2044–2054. doi: 10.1101/gr.gr-1529r. [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Sallinen S. L., Sallinen P. K., Haapasalo H. K., Helin H. J., Helén P. T., Schraml P., Kallioniemi O. P., Kononen J. Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. Cancer Res. 2000 Dec 1;60(23):6617–6622. [PubMed] [Google Scholar]
  143. Sanderfoot A. A., Assaad F. F., Raikhel N. V. The Arabidopsis genome. An abundance of soluble N-ethylmaleimide-sensitive factor adaptor protein receptors. Plant Physiol. 2000 Dec;124(4):1558–1569. doi: 10.1104/pp.124.4.1558. [DOI] [PMC free article] [PubMed] [Google Scholar]
  144. Schadt E. E., Li C., Su C., Wong W. H. Analyzing high-density oligonucleotide gene expression array data. J Cell Biochem. 2000 Oct 20;80(2):192–202. [PubMed] [Google Scholar]
  145. Schiefelbein J. W. Constructing a plant cell. The genetic control of root hair development. Plant Physiol. 2000 Dec;124(4):1525–1531. doi: 10.1104/pp.124.4.1525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  146. Schubert M., Holland L. Z., Holland N. D., Jacobs D. K. A phylogenetic tree of the Wnt genes based on all available full-length sequences, including five from the cephalochordate amphioxus. Mol Biol Evol. 2000 Dec;17(12):1896–1903. doi: 10.1093/oxfordjournals.molbev.a026291. [DOI] [PubMed] [Google Scholar]
  147. Schulze A., Downward J. Analysis of gene expression by microarrays: cell biologist's gold mine or minefield? J Cell Sci. 2000 Dec;113(Pt 23):4151–4156. doi: 10.1242/jcs.113.23.4151. [DOI] [PubMed] [Google Scholar]
  148. Schwikowski B., Uetz P., Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol. 2000 Dec;18(12):1257–1261. doi: 10.1038/82360. [DOI] [PubMed] [Google Scholar]
  149. Searls D. B. Bioinformatics tools for whole genomes. Annu Rev Genomics Hum Genet. 2000;1:251–279. doi: 10.1146/annurev.genom.1.1.251. [DOI] [PubMed] [Google Scholar]
  150. Selinger D. W., Cheung K. J., Mei R., Johansson E. M., Richmond C. S., Blattner F. R., Lockhart D. J., Church G. M. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol. 2000 Dec;18(12):1262–1268. doi: 10.1038/82367. [DOI] [PubMed] [Google Scholar]
  151. Seoighe C., Federspiel N., Jones T., Hansen N., Bivolarovic V., Surzycki R., Tamse R., Komp C., Huizar L., Davis R. W. Prevalence of small inversions in yeast gene order evolution. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14433–14437. doi: 10.1073/pnas.240462997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  152. Serra-Hartmann X., Rebordosa X., Piñol J., Querol E., Martí-Renom M. A. ASAP: analysis of peptide composition. Bioinformatics. 2000 Dec;16(12):1153–1154. doi: 10.1093/bioinformatics/16.12.1153. [DOI] [PubMed] [Google Scholar]
  153. Shi N., Boado R. J., Pardridge W. M. Antisense imaging of gene expression in the brain in vivo. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14709–14714. doi: 10.1073/pnas.250332397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  154. Shiffman D., Porter J. G. Gene expression profiling of cardiovascular disease models. Curr Opin Biotechnol. 2000 Dec;11(6):598–601. doi: 10.1016/s0958-1669(00)00150-6. [DOI] [PubMed] [Google Scholar]
  155. Sicheritz-Pontén T., Andersson S. G. A phylogenomic approach to microbial evolution. Nucleic Acids Res. 2001 Jan 15;29(2):545–552. doi: 10.1093/nar/29.2.545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  156. Silverstein K. A., Kilian A., Freeman J. L., Johnson J. E., Awad I. A., Retzel E. F. PANAL: an integrated resource for Protein sequence ANALysis. Bioinformatics. 2000 Dec;16(12):1157–1158. doi: 10.1093/bioinformatics/16.12.1157. [DOI] [PubMed] [Google Scholar]
  157. Snijders A. M., Meijer G. A., Brakenhoff R. H., van den Brule A. J., van Diest P. J. Microarray techniques in pathology: tool or toy? Mol Pathol. 2000 Dec;53(6):289–294. doi: 10.1136/mp.53.6.289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  158. Sorrentino V., Barone V., Rossi D. Intracellular Ca(2+) release channels in evolution. Curr Opin Genet Dev. 2000 Dec;10(6):662–667. doi: 10.1016/s0959-437x(00)00139-8. [DOI] [PubMed] [Google Scholar]
  159. Steffen D. L., Levine A. E., Yarus S., Baasiri R. A., Wheeler D. A. Digital reviews in molecular biology: approaches to structured digital publication. Bioinformatics. 2000 Jul;16(7):639–649. doi: 10.1093/bioinformatics/16.7.639. [DOI] [PubMed] [Google Scholar]
  160. Stekel D. J., Git Y., Falciani F. The comparison of gene expression from multiple cDNA libraries. Genome Res. 2000 Dec;10(12):2055–2061. doi: 10.1101/gr.gr-1325rr. [DOI] [PMC free article] [PubMed] [Google Scholar]
  161. Stern L. E., Erwin C. R., Falcone R. A., Huang F. S., Kemp C. J., Williams J. L., Warner B. W. cDNA microarray analysis of adapting bowel after intestinal resection. J Pediatr Surg. 2001 Jan;36(1):190–195. doi: 10.1053/jpsu.2001.20050. [DOI] [PubMed] [Google Scholar]
  162. Stockwell B. R. Chemical genetics: ligand-based discovery of gene function. Nat Rev Genet. 2000 Nov;1(2):116–125. doi: 10.1038/35038557. [DOI] [PMC free article] [PubMed] [Google Scholar]
  163. Suzuki N., Nakano Y., Yoshida Y., Nakao H., Yamashita Y., Koga T. Genetic analysis of the gene cluster for the synthesis of serotype a-specific polysaccharide antigen in Aactinobacillus actinomycetemcomitans. Biochim Biophys Acta. 2000 Dec 15;1517(1):135–138. doi: 10.1016/s0167-4781(00)00229-3. [DOI] [PubMed] [Google Scholar]
  164. Sánchez-Pulido L., Yuan Y. P., Andrade M. A., Bork P. NAIL-Network Analysis Interface for Linking HMMER results. Bioinformatics. 2000 Jul;16(7):656–657. doi: 10.1093/bioinformatics/16.7.656. [DOI] [PubMed] [Google Scholar]
  165. Sánchez D. O., Zandomeni R. O., Cravero S., Verdún R. E., Pierrou E., Faccio P., Diaz G., Lanzavecchia S., Agüero F., Frasch A. C. Gene discovery through genomic sequencing of Brucella abortus. Infect Immun. 2001 Feb;69(2):865–868. doi: 10.1128/IAI.69.2.865-868.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  166. Tenenbaum S. A., Carson C. C., Lager P. J., Keene J. D. Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14085–14090. doi: 10.1073/pnas.97.26.14085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  167. Thorne J. L. Models of protein sequence evolution and their applications. Curr Opin Genet Dev. 2000 Dec;10(6):602–605. doi: 10.1016/s0959-437x(00)00142-8. [DOI] [PubMed] [Google Scholar]
  168. Thornton J. W., DeSalle R. Gene family evolution and homology: genomics meets phylogenetics. Annu Rev Genomics Hum Genet. 2000;1:41–73. doi: 10.1146/annurev.genom.1.1.41. [DOI] [PubMed] [Google Scholar]
  169. Ton C., Hwang D. M., Dempsey A. A., Tang H. C., Yoon J., Lim M., Mably J. D., Fishman M. C., Liew C. C. Identification, characterization, and mapping of expressed sequence tags from an embryonic zebrafish heart cDNA library. Genome Res. 2000 Dec;10(12):1915–1927. doi: 10.1101/gr.10.12.1915. [DOI] [PMC free article] [PubMed] [Google Scholar]
  170. Torres M. J., Matvienko M., Yoder J. I. Agricultural genomics and subterranean plant-plant communications. J Cell Biochem. 2000 Oct 20;80(2):203–207. doi: 10.1002/1097-4644(20010201)80:2<203::aid-jcb60>3.0.co;2-j. [DOI] [PubMed] [Google Scholar]
  171. Tracy M. R., Hedges S. B. Evolutionary history of the enolase gene family. Gene. 2000 Dec 23;259(1-2):129–138. doi: 10.1016/s0378-1119(00)00439-x. [DOI] [PubMed] [Google Scholar]
  172. Tsukamoto T., Hashiguchi N., Janicki S. M., Tumbar T., Belmont A. S., Spector D. L. Visualization of gene activity in living cells. Nat Cell Biol. 2000 Dec;2(12):871–878. doi: 10.1038/35046510. [DOI] [PubMed] [Google Scholar]
  173. Vasconcelos A. T., Maia M. A., de Almeida D. F. Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidis. Bioinformatics. 2000 Nov;16(11):968–977. doi: 10.1093/bioinformatics/16.11.968. [DOI] [PubMed] [Google Scholar]
  174. Vertegaal A. C., Kuiperij H. B., van Laar T., Scharnhorst V., van der Eb A. J., Zantema A. cDNA micro array identification of a gene differentially expressed in adenovirus type 5- versus type 12-transformed cells. FEBS Lett. 2000 Dec 29;487(2):151–155. doi: 10.1016/s0014-5793(00)02339-5. [DOI] [PubMed] [Google Scholar]
  175. Vlahovicek K., Pongor S. Model.it: building three dimensional DNA models from sequence data. Bioinformatics. 2000 Nov;16(11):1044–1045. doi: 10.1093/bioinformatics/16.11.1044. [DOI] [PubMed] [Google Scholar]
  176. Voit E. O., Radivoyevitch T. Biochemical systems analysis of genome-wide expression data. Bioinformatics. 2000 Nov;16(11):1023–1037. doi: 10.1093/bioinformatics/16.11.1023. [DOI] [PubMed] [Google Scholar]
  177. Volkert M. R., Elliott N. A., Housman D. E. Functional genomics reveals a family of eukaryotic oxidation protection genes. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14530–14535. doi: 10.1073/pnas.260495897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  178. Waddell E., Wang Y., Stryjewski W., McWhorter S., Henry A. C., Evans D., McCarley R. L., Soper S. A. High-resolution near-infrared imaging of DNA microarrays with time-resolved acquisition of fluorescence lifetimes. Anal Chem. 2000 Dec 15;72(24):5907–5917. doi: 10.1021/ac0009705. [DOI] [PubMed] [Google Scholar]
  179. Wallqvist A., Fukunishi Y., Murphy L. R., Fadel A., Levy R. M. Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases. Bioinformatics. 2000 Nov;16(11):988–1002. doi: 10.1093/bioinformatics/16.11.988. [DOI] [PubMed] [Google Scholar]
  180. Watson S. J., Meng F., Thompson R. C., Akil H. The "chip" as a specific genetic tool. Biol Psychiatry. 2000 Dec 15;48(12):1147–1156. doi: 10.1016/s0006-3223(00)01080-5. [DOI] [PubMed] [Google Scholar]
  181. Wei Y., Lee J. M., Richmond C., Blattner F. R., Rafalski J. A., LaRossa R. A. High-density microarray-mediated gene expression profiling of Escherichia coli. J Bacteriol. 2001 Jan;183(2):545–556. doi: 10.1128/JB.183.2.545-556.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  182. Wheelan S. J., Marchler-Bauer A., Bryant S. H. Domain size distributions can predict domain boundaries. Bioinformatics. 2000 Jul;16(7):613–618. doi: 10.1093/bioinformatics/16.7.613. [DOI] [PubMed] [Google Scholar]
  183. Wheeler R., Hughey R. Optimizing reduced-space sequence analysis. Bioinformatics. 2000 Dec;16(12):1082–1090. doi: 10.1093/bioinformatics/16.12.1082. [DOI] [PubMed] [Google Scholar]
  184. White J. A., Todd J., Newman T., Focks N., Girke T., de Ilárduya O. M., Jaworski J. G., Ohlrogge J. B., Benning C. A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil. Plant Physiol. 2000 Dec;124(4):1582–1594. doi: 10.1104/pp.124.4.1582. [DOI] [PMC free article] [PubMed] [Google Scholar]
  185. Wildsmith S. E., Archer G. E., Winkley A. J., Lane P. W., Bugelski P. J. Maximization of signal derived from cDNA microarrays. Biotechniques. 2001 Jan;30(1):202-6, 208. doi: 10.2144/01301dd04. [DOI] [PubMed] [Google Scholar]
  186. Wisman E., Ohlrogge J. Arabidopsis microarray service facilities. Plant Physiol. 2000 Dec;124(4):1468–1471. doi: 10.1104/pp.124.4.1468. [DOI] [PMC free article] [PubMed] [Google Scholar]
  187. Wolf M., El-Rifai W., Tarkkanen M., Kononen J., Serra M., Eriksen E. F., Elomaa I., Kallioniemi A., Kallioniemi O. P., Knuutila S. Novel findings in gene expression detected in human osteosarcoma by cDNA microarray. Cancer Genet Cytogenet. 2000 Dec;123(2):128–132. doi: 10.1016/s0165-4608(00)00319-8. [DOI] [PubMed] [Google Scholar]
  188. Woods I. G., Kelly P. D., Chu F., Ngo-Hazelett P., Yan Y. L., Huang H., Postlethwait J. H., Talbot W. S. A comparative map of the zebrafish genome. Genome Res. 2000 Dec;10(12):1903–1914. doi: 10.1101/gr.10.12.1903. [DOI] [PMC free article] [PubMed] [Google Scholar]
  189. Wu C. C., Taylor R. S., Lane D. R., Ladinsky M. S., Weisz J. A., Howell K. E. GMx33: a novel family of trans-Golgi proteins identified by proteomics. Traffic. 2000 Dec;1(12):963–975. [PubMed] [Google Scholar]
  190. Ye S. Q., Zhang L. Q., Zheng F., Virgil D., Kwiterovich P. O. miniSAGE: gene expression profiling using serial analysis of gene expression from 1 microg total RNA. Anal Biochem. 2000 Dec 1;287(1):144–152. doi: 10.1006/abio.2000.4846. [DOI] [PubMed] [Google Scholar]
  191. Yu A., Zhao C., Fan Y., Jang W., Mungall A. J., Deloukas P., Olsen A., Doggett N. A., Ghebranious N., Broman K. W. Comparison of human genetic and sequence-based physical maps. Nature. 2001 Feb 15;409(6822):951–953. doi: 10.1038/35057185. [DOI] [PubMed] [Google Scholar]
  192. Zhu H., Schein C. H., Braun W. MASIA: recognition of common patterns and properties in multiple aligned protein sequences. Bioinformatics. 2000 Oct;16(10):950–951. doi: 10.1093/bioinformatics/16.10.950. [DOI] [PubMed] [Google Scholar]
  193. Zhu T., Wang X. Large-scale profiling of the Arabidopsis transcriptome. Plant Physiol. 2000 Dec;124(4):1472–1476. doi: 10.1104/pp.124.4.1472. [DOI] [PMC free article] [PubMed] [Google Scholar]
  194. Zivy M., de Vienne D. Proteomics: a link between genomics, genetics and physiology. Plant Mol Biol. 2000 Nov;44(5):575–580. doi: 10.1023/a:1026525406953. [DOI] [PubMed] [Google Scholar]
  195. Zou D., Kaneko J., Narita S., Kamio Y. Prophage, phiPV83-pro, carrying panton-valentine leukocidin genes, on the Staphylococcus aureus P83 chromosome: comparative analysis of the genome structures of phiPV83-pro, phiPVL, phi11, and other phages. Biosci Biotechnol Biochem. 2000 Dec;64(12):2631–2643. doi: 10.1271/bbb.64.2631. [DOI] [PubMed] [Google Scholar]
  196. Zé-Zé L., Tenreiro R., Paveia H. The Oenococcus oeni genome: physical and genetic mapping of strain GM and comparison with the genome of a 'divergent' strain, PSU-1. Microbiology. 2000 Dec;146(Pt 12):3195–3204. doi: 10.1099/00221287-146-12-3195. [DOI] [PubMed] [Google Scholar]
  197. van Kampen A. H., van Schaik B. D., Pauws E., Michiels E. M., Ruijter J. M., Caron H. N., Versteeg R., Heisterkamp S. H., Leunissen J. A., Baas F. USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression. Bioinformatics. 2000 Oct;16(10):899–905. doi: 10.1093/bioinformatics/16.10.899. [DOI] [PubMed] [Google Scholar]

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