BioPerl publications/2004

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  1. Error fetching PMID 15632092: [adai2004]
  2. Error fetching PMID 15005798: [naderi2004]
  3. Error fetching PMID 14734326: [estpage]
  4. Error fetching PMID 14734305: [juretic2004]
  5. Error fetching PMID 15626672: [bai2004]
  6. Error fetching PMID 14693811: [medblast]
  7. Error fetching PMID 14672977: [conreal]
  8. Error fetching PMID 14681443: [cadre]
  9. Error fetching PMID 12949126: [moilanen]
  10. Error fetching PMID 14681471: [hgvbase]
  11. Error fetching PMID 14681444: [phenoblast]
  12. Error fetching PMID 14681387: [trsdb]
  13. Error fetching PMID 14770300: [bellgard2004]
  14. Error fetching PMID 14993208: [matsuzaki2004]
  15. Error fetching PMID 14966544: [lovePLOS2004]
  16. Error fetching PMID 15601538: [burren2004]
  17. Error fetching PMID 14667813: [adelson2004]
  18. Error fetching PMID 14757250: [diener2004]
  19. Error fetching PMID 14751988: [sun2004]
  20. Error fetching PMID 14743482: [ravichandran2004]
  21. Error fetching PMID 14990746: [klee2004]
  22. Error fetching PMID 14751975: [smoot2004]
  23. Error fetching PMID 14704362: [thiel2004]
  24. Error fetching PMID 14871861: [dehoon2004]
  25. Error fetching PMID 14704339: [zakour2004]
  26. Error fetching PMID 14973191: [calin2004]
  27. Error fetching PMID 14988103: [sight2004]
  28. Error fetching PMID 14988115: [partigene]
  29. Error fetching PMID 15123588: [ensembllib]
  30. Hong P, Zhong S, Wong W Towards Ubiquitous Bio-Information Computing: Data Protocols, Middleware, and Web Services for Heterogeneous Biological Information Integration and Retrieval. 2004 Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE’04). [hong2004]
  31. Schmidt B, Feng L, Laud A, Santoso Y. Development of distributed bioinformatics applications with GMP. Concurrency and Computation: Practice and Experience: High Performance Computational Biology 945-959. [schmidt2004]
  32. Error fetching PMID 15105541: [narechania2004]
  33. Error fetching PMID 15099834: [MMTSB]
  34. Error fetching PMID 15095334: [larose2004]
  35. Error fetching PMID 15128450: [elxr]
  36. Stajich JE. Bioperl: Open-Source Bioinformatics Tools 2004 Science Careers 3220. [stajich2004]
  37. Error fetching PMID 15186489: [budd2004]
  38. Error fetching PMID 15171794: [cannon2004]
  39. Error fetching PMID 15132760: [negre2004]
  40. Error fetching PMID 15144565: [SNAP]
  41. Error fetching PMID 15231757: [guryev2004]
  42. Error fetching PMID 15287975: [gutierrez2004]
  43. Error fetching PMID 15208197: [umar2004]
  44. Error fetching PMID 15218019: [petyuk2004]
  45. Qi W, Lacher DW, Bumbaugh AC, Hyma KE, Ouellette LM, Large TM, Tarr CL, Whittam TS. cMLST: An Online Database for Multi Locus Sequence Typing of Pathogenic Escherichia coli Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (CSB'04). [qi2004]
  46. Error fetching PMID 15215379: [mscan]
  47. Error fetching PMID 15215372: [pda]
  48. Error fetching PMID 15215363: [trod]
  49. Error fetching PMID 15231752: [regulog]
  50. Error fetching PMID 15238535: [hahnFIV]
  51. Error fetching PMID 15219390: [blastdigester]
All Medline abstracts: PubMed | HubMed
  1. Jolley KA, Chan MS, and Maiden MC. mlstdbNet - distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics. 2004 Jul 1;5:86. DOI:10.1186/1471-2105-5-86 | PubMed ID:15230973 | HubMed [mlstdbNet]
  2. Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR, and Wooster R. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer. 2004 Jul 19;91(2):355-8. DOI:10.1038/sj.bjc.6601894 | PubMed ID:15188009 | HubMed [COSMIC]
  3. Hajarnavis A, Korf I, and Durbin R. A probabilistic model of 3' end formation in Caenorhabditis elegans. Nucleic Acids Res. 2004;32(11):3392-9. DOI:10.1093/nar/gkh656 | PubMed ID:15247332 | HubMed [hajarnavis2004]
  4. O'Brien KP, Westerlund I, and Sonnhammer EL. OrthoDisease: a database of human disease orthologs. Hum Mutat. 2004 Aug;24(2):112-9. DOI:10.1002/humu.20068 | PubMed ID:15241792 | HubMed [orthodisease]
  5. Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, and Church GM. The complete genome and proteome of Mycoplasma mobile. Genome Res. 2004 Aug;14(8):1447-61. DOI:10.1101/gr.2674004 | PubMed ID:15289470 | HubMed [jaffe2004]
  6. Boutros PC, Moffat ID, Franc MA, Tijet N, Tuomisto J, Pohjanvirta R, and Okey AB. Dioxin-responsive AHRE-II gene battery: identification by phylogenetic footprinting. Biochem Biophys Res Commun. 2004 Aug 27;321(3):707-15. DOI:10.1016/j.bbrc.2004.06.177 | PubMed ID:15358164 | HubMed [boutros2004]
  7. Zagulski M, Nowak JK, Le Mouël A, Nowacki M, Migdalski A, Gromadka R, Noël B, Blanc I, Dessen P, Wincker P, Keller AM, Cohen J, Meyer E, and Sperling L. High coding density on the largest Paramecium tetraurelia somatic chromosome. Curr Biol. 2004 Aug 10;14(15):1397-404. DOI:10.1016/j.cub.2004.07.029 | PubMed ID:15296759 | HubMed [zagulski2004]
  8. Zelensky AN and Gready JE. C-type lectin-like domains in Fugu rubripes. BMC Genomics. 2004 Aug 1;5(1):51. DOI:10.1186/1471-2164-5-51 | PubMed ID:15285787 | HubMed [zelensky2004]
  9. de Magalhães JP and Toussaint O. GenAge: a genomic and proteomic network map of human ageing. FEBS Lett. 2004 Jul 30;571(1-3):243-7. DOI:10.1016/j.febslet.2004.07.006 | PubMed ID:15280050 | HubMed [deMagalhaes2004]
  10. Troger A. A language for comprehensively supporting the in vitro experimental process in silico Bioinformatics and Bioengineering, 2004. 47-56. [troger2004]
  11. 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 [lipovich2004]
  12. Gabor EM, Alkema WB, and Janssen DB. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol. 2004 Sep;6(9):879-86. DOI:10.1111/j.1462-2920.2004.00640.x | PubMed ID:15305913 | HubMed [gabor2004]
  13. Hulme JS, Barratt BJ, Twells RC, Cooper JD, Lowe CE, Howson JM, Lam AC, Smink LJ, Savage DA, Undlien DE, Guja C, Ionescu-Tîirgoviste C, Tuomilehto-Wolf E, Tuomilehto J, and Todd JA. Association analysis of the lymphocyte-specific protein tyrosine kinase (LCK) gene in type 1 diabetes. Diabetes. 2004 Sep;53(9):2479-82. PubMed ID:15331563 | HubMed [hulme2004]
  14. Berman JJ. Tumor taxonomy for the developmental lineage classification of neoplasms. BMC Cancer. 2004 Nov 30;4:88. DOI:10.1186/1471-2407-4-88 | PubMed ID:15571625 | HubMed [berman2004]
  15. Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, and Celniker SE. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 2004;5(9):R61. DOI:10.1186/gb-2004-5-9-r61 | PubMed ID:15345045 | HubMed [berman2004]
  16. Aerts JA, Jungerius BJ, and Groenen MA. POSA: perl objects for DNA sequencing data analysis. BMC Genomics. 2004 Aug 27;5(1):60. DOI:10.1186/1471-2164-5-60 | PubMed ID:15333141 | HubMed [posa]
  17. Underwood AP and Green J. MOP-UP: an online tool for finding strain-specific primers or motifs in DNA or protein alignments. Clin Microbiol Infect. 2004 Oct;10(10):948-50. DOI:10.1111/j.1469-0691.2004.00943.x | PubMed ID:15373897 | HubMed [underwood2004]
  18. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, and Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80. DOI:10.1186/gb-2004-5-10-r80 | PubMed ID:15461798 | HubMed [bioconductor]
  19. Gräf S, Borisova BE, Nellen W, Steger G, and Hammann C. A database search for double-strand containing RNAs in Dictyostelium discoideum. Biol Chem. 2004 Oct;385(10):961-5. DOI:10.1515/BC.2004.125 | PubMed ID:15551871 | HubMed [graf2004]
  20. Babenko VN and Krylov DM. Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved. Nucleic Acids Res. 2004;32(17):5029-35. DOI:10.1093/nar/gkh833 | PubMed ID:15448184 | HubMed [baneko2004]
  21. Boutros PC and Okey AB. PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design. Bioinformatics. 2004 Oct 12;20(15):2399-400. DOI:10.1093/bioinformatics/bth257 | PubMed ID:15073008 | HubMed [puns]
  22. Cui W, Ning J, Naik UP, and Duncan MK. OptiRNAi, an RNAi design tool. Comput Methods Programs Biomed. 2004 Jul;75(1):67-73. DOI:10.1016/j.cmpb.2003.09.002 | PubMed ID:15158049 | HubMed [cui2004]
  23. D'Addabbo P, Lenzi L, Facchin F, Casadei R, Canaider S, Vitale L, Frabetti F, Carinci P, Zannotti M, and Strippoli P. GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers. Bioinformatics. 2004 Nov 1;20(16):2883-5. DOI:10.1093/bioinformatics/bth321 | PubMed ID:15145799 | HubMed [generecords]
  24. Yang HH and Lee MP. Application of bioinformatics in cancer epigenetics. Ann N Y Acad Sci. 2004 May;1020:67-76. DOI:10.1196/annals.1310.008 | PubMed ID:15208184 | HubMed [yang2004]
  25. Goodchild A, Saunders NF, Ertan H, Raftery M, Guilhaus M, Curmi PM, and Cavicchioli R. A proteomic determination of cold adaptation in the Antarctic archaeon, Methanococcoides burtonii. Mol Microbiol. 2004 Jul;53(1):309-21. DOI:10.1111/j.1365-2958.2004.04130.x | PubMed ID:15225324 | HubMed [goodchild2004]
  26. Girke T, Lauricha J, Tran H, Keegstra K, and Raikhel N. The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol. 2004 Oct;136(2):3003-8; discussion 3001. DOI:10.1104/pp.104.049965 | PubMed ID:15489283 | HubMed [girke2004]
  27. Smalheiser NR and Torvik VI. A population-based statistical approach identifies parameters characteristic of human microRNA-mRNA interactions. BMC Bioinformatics. 2004 Sep 28;5:139. DOI:10.1186/1471-2105-5-139 | PubMed ID:15453917 | HubMed [smalheiser2004]
  28. Villesen P, Aagaard L, Wiuf C, and Pedersen FS. Identification of endogenous retroviral reading frames in the human genome. Retrovirology. 2004 Oct 11;1:32. DOI:10.1186/1742-4690-1-32 | PubMed ID:15476554 | HubMed [villesen2004]
  29. Blakesley RW, Hansen NF, Mullikin JC, Thomas PJ, McDowell JC, Maskeri B, Young AC, Benjamin B, Brooks SY, Coleman BI, Gupta J, Ho SL, Karlins EM, Maduro QL, Stantripop S, Tsurgeon C, Vogt JL, Walker MA, Masiello CA, Guan X, NISC Comparative Sequencing Program, Bouffard GG, and Green ED. An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Res. 2004 Nov;14(11):2235-44. DOI:10.1101/gr.2648404 | PubMed ID:15479945 | HubMed [blakesley2004]
  30. Moriyama M, Hoshida Y, Kato N, Otsuka M, Yoshida H, Kawabe T, and Omata M. Genes associated with human hepatocellular carcinoma cell chemosensitivity to 5-fluorouracil plus interferon-alpha combination chemotherapy. Int J Oncol. 2004 Nov;25(5):1279-87. PubMed ID:15492816 | HubMed [moriyama2004]
  31. Dondeti VR, Sipe CW, and Saha MS. In silico gene selection strategy for custom microarray design. Biotechniques. 2004 Nov;37(5):768-70, 772, 774-6. PubMed ID:15560133 | HubMed [dondeti2004]
  32. Plouhinec JL, Granier C, Le Mentec C, Lawson KA, Sabéran-Djoneidi D, Aghion J, Shi DL, Collignon J, and Mazan S. Identification of the mammalian Not gene via a phylogenomic approach. Gene Expr Patterns. 2004 Nov;5(1):11-22. DOI:10.1016/j.modgep.2004.06.010 | PubMed ID:15533813 | HubMed [plouhinec2004]
  33. King GJ. Bioinformatics: harvesting information for plant and crop science. Semin Cell Dev Biol. 2004 Dec;15(6):721-31. DOI:10.1016/j.semcdb.2004.09.006 | PubMed ID:15561592 | HubMed [king2004]
  34. Kumar CG, LeDuc R, Gong G, Roinishivili L, Lewin HA, and Liu L. ESTIMA, a tool for EST management in a multi-project environment. BMC Bioinformatics. 2004 Nov 4;5:176. DOI:10.1186/1471-2105-5-176 | PubMed ID:15527510 | HubMed [kumar2004]
  35. Chia JM and Kolatkar PR. Implications for domain fusion protein-protein interactions based on structural information. BMC Bioinformatics. 2004 Oct 26;5:161. DOI:10.1186/1471-2105-5-161 | PubMed ID:15504241 | HubMed [chia2004]
  36. Bina M, Wyss P, Ren W, Szpankowski W, Thomas E, Randhawa R, Reddy S, John PM, Pares-Matos EI, Stein A, Xu H, and Lazarus SA. Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics. 2004 Dec;84(6):929-40. DOI:10.1016/j.ygeno.2004.08.013 | PubMed ID:15533710 | HubMed [bina2004]
  37. Aliosio G, Cafaro M, Flore S, Mirto M. Bioinformatics Data Access Service in the ProGenGrid System Workshop on Grid Computing and Its Application to Data Analysis (GADA). 3292:211. [aliosio2004]
  38. Hussain S. From sequence to structure using PF2: improving methods for protein folding prediction Computer-Based Medical Systems, 2004. CBMS 2004. 323-328. [hussain2004]
  39. Wasmuth JD and Blaxter ML. prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics. 2004 Nov 30;5:187. DOI:10.1186/1471-2105-5-187 | PubMed ID:15571632 | HubMed [prot4est]
  40. Martin DM, Berriman M, and Barton GJ. GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics. 2004 Nov 18;5:178. DOI:10.1186/1471-2105-5-178 | PubMed ID:15550167 | HubMed [gotcha]
  41. Wahlestedt C, Brookes AJ, and Mottagui-Tabar S. Lower rate of genomic variation identified in the trans-membrane domain of monoamine sub-class of Human G-Protein Coupled Receptors: the Human GPCR-DB Database. BMC Genomics. 2004 Dec 4;5:91. DOI:10.1186/1471-2164-5-91 | PubMed ID:15579207 | HubMed [wahlestedt2004]
  42. Paris J, Virtanen C, Lu Z, and Takahashi M. Identification of MEF2-regulated genes during muscle differentiation. Physiol Genomics. 2004 Dec 15;20(1):143-51. DOI:10.1152/physiolgenomics.00149.2004 | PubMed ID:15507520 | HubMed [paris2004]
  43. Love CG, Batley J, Lim G, Robinson AJ, Savage D, Singh D, Spangenberg GC, Edwards D. New computational tools for Brassica genome research Comparative and Functional Genomics 5(3):276-280. [love2004]
  44. Flanagan K, Stevens R, Pocock M, et al. Ontology for genome comparison and genomic rearrangements COMPARATIVE AND FUNCTIONAL GENOMICS 5 (6-7): 537-544 AUG-OCT 2004 [flanagan2004]
  45. Binneck E, Silva JF, Neumaier N, Farias JR, and Nepomuceno AL. VSQual: a visual system to assist DNA sequencing quality control. Genet Mol Res. 2004 Dec 30;3(4):474-82. PubMed ID:15688314 | HubMed [binneck2004]
  46. Herrera-Cuadra M. ProSA: una interfaz de Web basada en Perl para el análisis de secuencias Proceedings of the National Free Software Conference (CONSOL 2004), México City 2004. (In spanish) [herrera-cuadra2004]
All Medline abstracts: PubMed | HubMed
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