BioPerl publications/2003

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  1. Ernst P, Glatting KH, and Suhai S. A task framework for the web interface W2H. Bioinformatics. 2003 Jan 22;19(2):278-82. PubMed ID:12538250 | HubMed [w2h]
  2. Pan X, Liu H, Clarke J, Jones J, Bevan M, and Stein L. ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Res. 2003 Feb 15;31(4):1245-51. PubMed ID:12582244 | HubMed [ATIDB]
  3. Kossenkov A, Manion FJ, Korotkov E, Moloshok TD, and Ochs MF. ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database. Bioinformatics. 2003 Mar 22;19(5):675-6. PubMed ID:12651736 | HubMed [ASAP]
  4. Arakawa K, Mori K, Ikeda K, Matsuzaki T, Kobayashi Y, and Tomita M. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics. 2003 Jan 22;19(2):305-6. PubMed ID:12538262 | HubMed [G_language]
  5. Jamison DC. Open bioinformatics. Bioinformatics. 2003 Apr 12;19(6):679-80. PubMed ID:12691978 | HubMed [Jamison2002]
  6. Clarke B, Lambrecht M, and Rhee SY. Arabidopsis genomic information for interpreting wheat EST sequences. Funct Integr Genomics. 2003 Mar;3(1-2):33-8. DOI:10.1007/s10142-002-0075-1 | PubMed ID:12590341 | HubMed [clarke2003]
  7. Eckart JD and Sobral BW. A life scientist's gateway to distributed data management and computing: the PathPort/ToolBus framework. OMICS. 2003 Spring;7(1):79-88. DOI:10.1089/153623103322006661 | PubMed ID:12831562 | HubMed [eckart2003]
  8. Moriyama M, Hoshida Y, Otsuka M, Nishimura S, Kato N, Goto T, Taniguchi H, Shiratori Y, Seki N, and Omata M. Relevance network between chemosensitivity and transcriptome in human hepatoma cells. Mol Cancer Ther. 2003 Feb;2(2):199-205. PubMed ID:12589037 | HubMed [moriyama2003]
  9. Macas J, Neumann P, and Pozárková D. Zaba: a novel miniature transposable element present in genomes of legume plants. Mol Genet Genomics. 2003 Aug;269(5):624-31. DOI:10.1007/s00438-003-0869-4 | PubMed ID:12898216 | HubMed [zaba]
  10. Sandelin A, Höglund A, Lenhard B, and Wasserman WW. Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct Integr Genomics. 2003 Jul;3(3):125-34. DOI:10.1007/s10142-003-0086-6 | PubMed ID:12827523 | HubMed [sandelin2003]
  11. Roberg-Perez K, Carlson CM, and Largaespada DA. MTID: a database of Sleeping Beauty transposon insertions in mice. Nucleic Acids Res. 2003 Jan 1;31(1):78-81. PubMed ID:12519952 | HubMed [mtid]
  12. Sugawara H and Miyazaki S. Biological SOAP servers and web services provided by the public sequence data bank. Nucleic Acids Res. 2003 Jul 1;31(13):3836-9. PubMed ID:12824432 | HubMed [sugawara2003]
  13. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, and Pühler A. GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003 Apr 15;31(8):2187-95. PubMed ID:12682369 | HubMed [meyer2003]
  14. Tuggle CK, Green JA, Fitzsimmons C, Woods R, Prather RS, Malchenko S, Soares BM, Kucaba T, Crouch K, Smith C, Tack D, Robinson N, O'Leary B, Scheetz T, Casavant T, Pomp D, Edeal BJ, Zhang Y, Rothschild MF, Garwood K, and Beavis W. EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mamm Genome. 2003 Aug;14(8):565-79. DOI:10.1007/s00335-002-2263-7 | PubMed ID:12925889 | HubMed [tuggle2003]
  15. Massey SE, Moura G, Beltrão P, Almeida R, Garey JR, Tuite MF, and Santos MA. Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp. Genome Res. 2003 Apr;13(4):544-57. DOI:10.1101/gr.811003 | PubMed ID:12670996 | HubMed [massey2003]
  16. King MW, Nguyen T, Calley J, Harty MW, Muzinich MC, Mescher AL, Chalfant C, N'Cho M, McLeaster K, McEntire J, Stocum D, Smith RC, and Neff AW. Identification of genes expressed during Xenopus laevis limb regeneration by using subtractive hybridization. Dev Dyn. 2003 Feb;226(2):398-409. DOI:10.1002/dvdy.10250 | PubMed ID:12557218 | HubMed [king2003]
  17. Gimelli G, Pujana MA, Patricelli MG, Russo S, Giardino D, Larizza L, Cheung J, Armengol L, Schinzel A, Estivill X, and Zuffardi O. Genomic inversions of human chromosome 15q11-q13 in mothers of Angelman syndrome patients with class II (BP2/3) deletions. Hum Mol Genet. 2003 Apr 15;12(8):849-58. PubMed ID:12668608 | HubMed [gimelli2003]
  18. Hoebeke M, Nicolas P, and Bessières P. MuGeN: simultaneous exploration of multiple genomes and computer analysis results. Bioinformatics. 2003 May 1;19(7):859-64. PubMed ID:12724296 | HubMed [MuGeN]
  19. Adams MW, Dailey HA, DeLucas LJ, Luo M, Prestegard JH, Rose JP, and Wang BC. The Southeast Collaboratory for Structural Genomics: a high-throughput gene to structure factory. Acc Chem Res. 2003 Mar;36(3):191-8. DOI:10.1021/ar0101382 | PubMed ID:12641476 | HubMed [adams2003]
  20. Raymond J, Zhaxybayeva O, Gogarten JP, and Blankenship RE. Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach. Philos Trans R Soc Lond B Biol Sci. 2003 Jan 29;358(1429):223-30. DOI:10.1098/rstb.2002.1181 | PubMed ID:12594930 | HubMed [raymond2003]
  21. Yu J, Farjo R, MacNee SP, Baehr W, Stambolian DE, and Swaroop A. Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina. Genome Biol. 2003;4(10):R65. DOI:10.1186/gb-2003-4-10-r65 | PubMed ID:14519200 | HubMed [yu2003]
  22. Gatherer D and McEwan NR. Analysis of sequence periodicity in E. coli proteins: empirical investigation of the "duplication and divergence" theory of protein evolution. J Mol Evol. 2003 Aug;57(2):149-58. DOI:10.1007/s00239-002-2462-1 | PubMed ID:14562959 | HubMed [gatherer2003]
  23. McCallum J and Ganesh S. Text mining of DNA sequence homology searches. Appl Bioinformatics. 2003;2(3 Suppl):S59-63. PubMed ID:15130818 | HubMed [mccallum2003]
  24. Della Vedova G and Dondi R. A library of efficient bioinformatics algorithms. Appl Bioinformatics. 2003;2(2):117-21. PubMed ID:15130828 | HubMed [della_vedova2003]
  25. Lipovich L and King MC. Novel transcriptional units and unconventional gene pairs in the human genome: toward a sequence-level basis for primate-specific phenotypes?. Cold Spring Harb Symp Quant Biol. 2003;68:461-70. PubMed ID:15338649 | HubMed [lipovich2002]
  26. Paquola AC, Machado AA, Reis EM, Da Silva AM, and Verjovski-Almeida S. Zerg: a very fast BLAST parser library. Bioinformatics. 2003 May 22;19(8):1035-6. PubMed ID:12761068 | HubMed [zerg]
  27. Della Vedova G and Dondi R. A library of efficient bioinformatics algorithms. Appl Bioinformatics. 2003;2(2):117-21. PubMed ID:15130828 | HubMed [vedova2003]
  28. Hahn MW, Stajich JE, and Wray GA. The effects of selection against spurious transcription factor binding sites. Mol Biol Evol. 2003 Jun;20(6):901-6. DOI:10.1093/molbev/msg096 | PubMed ID:12716998 | HubMed [Hahn2003]
  29. Navarro JD, Niranjan V, Peri S, Jonnalagadda CK, and Pandey A. From biological databases to platforms for biomedical discovery. Trends Biotechnol. 2003 Jun;21(6):263-8. PubMed ID:12788546 | HubMed [Navarro2003]
  30. Doctor KS, Reed JC, Godzik A, and Bourne PE. The apoptosis database. Cell Death Differ. 2003 Jun;10(6):621-33. DOI:10.1038/sj.cdd.4401230 | PubMed ID:12761571 | HubMed [doctor2003]
  31. Moilanen JS and Majamaa K. Phylogenetic network and physicochemical properties of nonsynonymous mutations in the protein-coding genes of human mitochondrial DNA. Mol Biol Evol. 2003 Aug;20(8):1195-210. DOI:10.1093/molbev/msg121 | PubMed ID:12777521 | HubMed [moilanen2003]
  32. Lenhard B, Wahlestedt C, and Wasserman WW. GeneLynx mouse: integrated portal to the mouse genome. Genome Res. 2003 Jun;13(6B):1501-4. DOI:10.1101/gr.951403 | PubMed ID:12819149 | HubMed [genelynx]
  33. Saunders NF, Thomas T, Curmi PM, Mattick JS, Kuczek E, Slade R, Davis J, Franzmann PD, Boone D, Rusterholtz K, Feldman R, Gates C, Bench S, Sowers K, Kadner K, Aerts A, Dehal P, Detter C, Glavina T, Lucas S, Richardson P, Larimer F, Hauser L, Land M, and Cavicchioli R. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 2003 Jul;13(7):1580-8. DOI:10.1101/gr.1180903 | PubMed ID:12805271 | HubMed [saunders2003]
  34. Yang G and Hall TC. MAK, a computational tool kit for automated MITE analysis. Nucleic Acids Res. 2003 Jul 1;31(13):3659-65. PubMed ID:12824388 | HubMed [yang2003]
  35. Nair R and Rost B. LOC3D: annotate sub-cellular localization for protein structures. Nucleic Acids Res. 2003 Jul 1;31(13):3337-40. PubMed ID:12824321 | HubMed [loc3d]
  36. Goto N, Nakao MC, Kawashima S, Katayama T, Kanehisa M BioRuby: Open-Source Bioinformatics Library 2003 Genome Informatics 14:629-630. [bioruby2003]
  37. Garner HR, Pertsemlidis A Computational biology: biological insight from 1s and 0s 2003 BIOSILIOCO 1(1):27-35. [garner2003]
  38. Lord PW, Stevens RD, Brass A, and Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics. 2003 Jul 1;19(10):1275-83. PubMed ID:12835272 | HubMed [lord2003]
  39. Shah SP, McVicker GP, Mackworth AK, Rogic S, and Ouellette BF. GeneComber: combining outputs of gene prediction programs for improved results. Bioinformatics. 2003 Jul 1;19(10):1296-7. PubMed ID:12835277 | HubMed [genecomber]
  40. Hoon S, Ratnapu KK, Chia JM, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, and Stupka E. Biopipe: a flexible framework for protocol-based bioinformatics analysis. Genome Res. 2003 Aug;13(8):1904-15. DOI:10.1101/gr.1363103 | PubMed ID:12869579 | HubMed [biopipe]
  41. Janssen P, Enright AJ, Audit B, Cases I, Goldovsky L, Harte N, Kunin V, and Ouzounis CA. COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics. 2003 Jul 22;19(11):1451-2. PubMed ID:12874064 | HubMed [janseen2003]
  42. Korf I. Serial BLAST searching. Bioinformatics. 2003 Aug 12;19(12):1492-6. PubMed ID:12912829 | HubMed [serialblast]
  43. Bowen NJ, Jordan IK, Epstein JA, Wood V, and Levin HL. Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res. 2003 Sep;13(9):1984-97. DOI:10.1101/gr.1191603 | PubMed ID:12952871 | HubMed [bowen2003]
  44. Cannon SB and Young ND. OrthoParaMap: distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies. BMC Bioinformatics. 2003 Sep 2;4:35. DOI:10.1186/1471-2105-4-35 | PubMed ID:12952558 | HubMed [orthoparamap]
  45. Carlson CM, Dupuy AJ, Fritz S, Roberg-Perez KJ, Fletcher CF, and Largaespada DA. Transposon mutagenesis of the mouse germline. Genetics. 2003 Sep;165(1):243-56. PubMed ID:14504232 | HubMed [carlson2003]
  46. Pichon C and Felden B. Intergenic sequence inspector: searching and identifying bacterial RNAs. Bioinformatics. 2003 Sep 1;19(13):1707-9. PubMed ID:15593399 | HubMed [pichon2003]
  47. Cannon SB, Kozik A, Chan B, Michelmore R, and Young ND. DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization. Genome Biol. 2003;4(10):R68. DOI:10.1186/gb-2003-4-10-r68 | PubMed ID:14519203 | HubMed [diaghunter]
  48. Allen M, Heinzmann A, Noguchi E, Abecasis G, Broxholme J, Ponting CP, Bhattacharyya S, Tinsley J, Zhang Y, Holt R, Jones EY, Lench N, Carey A, Jones H, Dickens NJ, Dimon C, Nicholls R, Baker C, Xue L, Townsend E, Kabesch M, Weiland SK, Carr D, von Mutius E, Adcock IM, Barnes PJ, Lathrop GM, Edwards M, Moffatt MF, and Cookson WO. Positional cloning of a novel gene influencing asthma from chromosome 2q14. Nat Genet. 2003 Nov;35(3):258-63. DOI:10.1038/ng1256 | PubMed ID:14566338 | HubMed [allen2003]
  49. Iacovoni JS. GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome. Bioinformatics. 2003 Nov 22;19(17):2316-8. PubMed ID:14630663 | HubMed [genehuggers]
  50. Shah NH, King DC, Shah PN, and Fedoroff NV. A tool-kit for cDNA microarray and promoter analysis. Bioinformatics. 2003 Sep 22;19(14):1846-8. PubMed ID:14512358 | HubMed [shah2003]
  51. Redmond S, Vadivelu J, and Field MC. RNAit: an automated web-based tool for the selection of RNAi targets in Trypanosoma brucei. Mol Biochem Parasitol. 2003 Apr 25;128(1):115-8. PubMed ID:12706807 | HubMed [rnait]
  52. Gardy JL, Spencer C, Wang K, Ester M, Tusnády GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, and Brinkman FS. PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res. 2003 Jul 1;31(13):3613-7. PubMed ID:12824378 | HubMed [psortb]
  53. Coser KR, Chesnes J, Hur J, Ray S, Isselbacher KJ, and Shioda T. Global analysis of ligand sensitivity of estrogen inducible and suppressible genes in MCF7/BUS breast cancer cells by DNA microarray. Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):13994-9. DOI:10.1073/pnas.2235866100 | PubMed ID:14610279 | HubMed [coser2003]
  54. Dawe AL, McMains VC, Panglao M, Kasahara S, Chen B, and Nuss DL. An ordered collection of expressed sequences from Cryphonectria parasitica and evidence of genomic microsynteny with Neurospora crassa and Magnaporthe grisea. Microbiology. 2003 Sep;149(Pt 9):2373-84. DOI:10.1099/mic.0.26371-0 | PubMed ID:12949163 | HubMed [dawe2003]
  55. Thornton K. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics. 2003 Nov 22;19(17):2325-7. PubMed ID:14630667 | HubMed [thornton2003]
  56. Rockman MV, Hahn MW, Soranzo N, Goldstein DB, and Wray GA. Positive selection on a human-specific transcription factor binding site regulating IL4 expression. Curr Biol. 2003 Dec 2;13(23):2118-23. PubMed ID:14654003 | HubMed [rockman2003]
  57. Ardell DH, Lozupone CA, and Landweber LF. Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea). Genetics. 2003 Dec;165(4):1761-77. PubMed ID:14704164 | HubMed [ardell2003]
  58. Somers DJ, Kirkpatrick R, Moniwa M, and Walsh A. Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome. 2003 Jun;46(3):431-7. DOI:10.1139/g03-027 | PubMed ID:12834059 | HubMed [somers2003]
  59. DeSilva U, Franklin IR, Maddox JF, van Hest B, and Adelson DL. Systematic screening of sheep skin cDNA libraries for microsatellite sequences. Cytogenet Genome Res. 2003;102(1-4):79-84. DOI:75729 | PubMed ID:14970683 | HubMed [desilva2003]
  60. Loraine AE, Helt GA, Cline MS, and Siani-Rose MA. Exploring alternative transcript structure in the human genome using blocks and InterPro. J Bioinform Comput Biol. 2003 Jul;1(2):289-306. PubMed ID:15290774 | HubMed [lorraine2003]
  61. Lewis CT, Sharpe AG, Lydiate DJ, Parkin IAP. The Brassica/Arabidopsis comparative genome browser: a novel approach to genome browsing 2003 J Plant Technology. [lewis2003]
  62. Tyrelle GD, King GC A platform for the description, distribution and analysis of genetic polymorphism data Proceedings of the First Asia-Pacific bioinformatics conference on Bioinformatics 2003 - Volume 19. 2003. [tyrelle2003]
  63. Mersch H and Fuellen G. Paper2sequences: retrieval of sequences listed in a publication. Appl Bioinformatics. 2003;2(2):113-6. PubMed ID:15130827 | HubMed [paper2sequences]
  64. Stanton JA, Macgregor AB, and Green DP. Identifying tissue-enriched gene expression in mouse tissues using the NIH UniGene database. Appl Bioinformatics. 2003;2(3 Suppl):S65-73. PubMed ID:15130819 | HubMed [stanton2003]
  65. Ueno Y, Arita M, Kumagai T, and Asai K. Processing sequence annotation data using the Lua programming language. Genome Inform. 2003;14:154-63. PubMed ID:15706530 | HubMed [ueno2003]
  66. Honts JE. Evolving strategies for the incorporation of bioinformatics within the undergraduate cell biology curriculum. Cell Biol Educ. 2003 Winter;2(4):233-47. DOI:10.1187/cbe.03-06-0026 | PubMed ID:14673489 | HubMed [honts2003]
  67. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, and Waterston RH. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 2003 Nov;1(2):E45. DOI:10.1371/journal.pbio.0000045 | PubMed ID:14624247 | HubMed [stein2003]
  68. Wei X, Kuhn DN, and Narasimhan G. Degenerate primer design via clustering. Proc IEEE Comput Soc Bioinform Conf. 2003;2:75-83. PubMed ID:16452781 | HubMed [wei2003]
All Medline abstracts: PubMed | HubMed
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