BioPerl publications/2004

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  1. Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, and Sundaresan V. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res. 2005 Jan;15(1):78-91. DOI:10.1101/gr.2908205 | PubMed ID:15632092 | HubMed [adai2004]
  2. Naderi A, Ahmed AA, Barbosa-Morais NL, Aparicio S, Brenton JD, and Caldas C. Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling. BMC Genomics. 2004 Jan 30;5(1):9. DOI:10.1186/1471-2164-5-9 | PubMed ID:15005798 | HubMed [naderi2004]
  3. Matukumalli LK, Grefenstette JJ, Sonstegard TS, and Van Tassell CP. EST-PAGE--managing and analyzing EST data. Bioinformatics. 2004 Jan 22;20(2):286-8. PubMed ID:14734326 | HubMed [estpage]
  4. Juretic N, Bureau TE, and Bruskiewich RM. Transposable element annotation of the rice genome. Bioinformatics. 2004 Jan 22;20(2):155-60. PubMed ID:14734305 | HubMed [juretic2004]
  5. Bai X, Xu JZ, Li L, Guo Z, Li J, and Zhu YM. [Analysis of codon usage in potato and its application in the modification of t-PA gene]. Yi Chuan. 2004 Jan;26(1):75-83. PubMed ID:15626672 | HubMed [bai2004]
  6. Tu Q, Tang H, and Ding D. MedBlast: searching articles related to a biological sequence. Bioinformatics. 2004 Jan 1;20(1):75-7. PubMed ID:14693811 | HubMed [medblast]
  7. Berezikov E, Guryev V, Plasterk RH, and Cuppen E. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res. 2004 Jan;14(1):170-8. DOI:10.1101/gr.1642804 | PubMed ID:14672977 | HubMed [conreal]
  8. Mabey JE, Anderson MJ, Giles PF, Miller CJ, Attwood TK, Paton NW, Bornberg-Bauer E, Robson GD, Oliver SG, and Denning DW. CADRE: the Central Aspergillus Data REpository. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D401-5. DOI:10.1093/nar/gkh009 | PubMed ID:14681443 | HubMed [cadre]
  9. Moilanen JS, Finnila S, and Majamaa K. Lineage-specific selection in human mtDNA: lack of polymorphisms in a segment of MTND5 gene in haplogroup J. Mol Biol Evol. 2003 Dec;20(12):2132-42. DOI:10.1093/molbev/msg230 | PubMed ID:12949126 | HubMed [moilanen]
  10. Fredman D, Munns G, Rios D, Sjöholm F, Siegfried M, Lenhard B, Lehväslaiho H, and Brookes AJ. HGVbase: a curated resource describing human DNA variation and phenotype relationships. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D516-9. DOI:10.1093/nar/gkh111 | PubMed ID:14681471 | HubMed [hgvbase]
  11. Gunsalus KC, Yueh WC, MacMenamin P, and Piano F. RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D406-10. DOI:10.1093/nar/gkh110 | PubMed ID:14681444 | HubMed [phenoblast]
  12. Hermoso A, Aguilar D, Aviles FX, and Querol E. TrSDB: a proteome database of transcription factors. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D171-3. DOI:10.1093/nar/gkh101 | PubMed ID:14681387 | HubMed [trsdb]
  13. Bellgard M, Ye J, Gojobori T, and Appels R. The bioinformatics challenges in comparative analysis of cereal genomes-an overview. Funct Integr Genomics. 2004 Mar;4(1):1-11. DOI:10.1007/s10142-004-0102-5 | PubMed ID:14770300 | HubMed [bellgard2004]
  14. Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, Di X, Liu WM, Yang G, Liu G, Huang J, Kennedy GC, Ryder TB, Marcus GA, Walsh PS, Shriver MD, Puck JM, Jones KW, and Mei R. Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res. 2004 Mar;14(3):414-25. DOI:10.1101/gr.2014904 | PubMed ID:14993208 | HubMed [matsuzaki2004]
  15. Hubbard T and Love J. A new trade framework for global healthcare R&D. PLoS Biol. 2004 Feb;2(2):E52. DOI:10.1371/journal.pbio.0020052 | PubMed ID:14966544 | HubMed [lovePLOS2004]
  16. Burren OS, Healy BC, Lam AC, Schuilenburg H, Dolman GE, Everett VH, Laneri D, Nutland S, Rance HE, Payne F, Smyth D, Lowe C, Barratt BJ, Twells RC, Rainbow DB, Wicker LS, Todd JA, Walker NM, and Smink LJ. Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. Hum Genomics. 2004 Jan;1(2):98-109. PubMed ID:15601538 | HubMed [burren2004]
  17. Adelson DL, Cam GR, DeSilva U, and Franklin IR. Gene expression in sheep skin and wool (hair). Genomics. 2004 Jan;83(1):95-105. PubMed ID:14667813 | HubMed [adelson2004]
  18. Diener SE, Dunn-Coleman N, Foreman P, Houfek TD, Teunissen PJ, van Solingen P, Dankmeyer L, Mitchell TK, Ward M, and Dean RA. Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei. FEMS Microbiol Lett. 2004 Jan 30;230(2):275-82. PubMed ID:14757250 | HubMed [diener2004]
  19. Sun H and Davuluri RV. Java-based application framework for visualization of gene regulatory region annotations. Bioinformatics. 2004 Mar 22;20(5):727-34. DOI:10.1093/bioinformatics/btg476 | PubMed ID:14751988 | HubMed [sun2004]
  20. Ravichandran V, Lubell J, Vásquez GB, Lemkin P, Sriram RD, and Gilliland GL. Ongoing development of two-dimensional polyacrylamide gel electrophoresis data standards. Electrophoresis. 2004 Jan;25(2):297-308. DOI:10.1002/elps.200305748 | PubMed ID:14743482 | HubMed [ravichandran2004]
  21. Klee EW, Carlson DF, Fahrenkrug SC, Ekker SC, and Ellis LB. Identifying secretomes in people, pufferfish and pigs. Nucleic Acids Res. 2004;32(4):1414-21. DOI:10.1093/nar/gkh286 | PubMed ID:14990746 | HubMed [klee2004]
  22. Smoot ME, Guerlain SA, and Pearson WR. Visualization of near-optimal sequence alignments. Bioinformatics. 2004 Apr 12;20(6):953-8. DOI:10.1093/bioinformatics/bth013 | PubMed ID:14751975 | HubMed [smoot2004]
  23. Thiel T, Kota R, Grosse I, Stein N, and Graner A. SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res. 2004 Jan 2;32(1):e5. DOI:10.1093/nar/gnh006 | PubMed ID:14704362 | HubMed [thiel2004]
  24. de Hoon MJ, Imoto S, Nolan J, and Miyano S. Open source clustering software. Bioinformatics. 2004 Jun 12;20(9):1453-4. DOI:10.1093/bioinformatics/bth078 | PubMed ID:14871861 | HubMed [dehoon2004]
  25. Ben Zakour N, Gautier M, Andonov R, Lavenier D, Cochet MF, Veber P, Sorokin A, and Le Loir Y. GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification. Nucleic Acids Res. 2004;32(1):17-24. DOI:10.1093/nar/gkg928 | PubMed ID:14704339 | HubMed [zakour2004]
  26. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M, and Croce CM. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2999-3004. DOI:10.1073/pnas.0307323101 | PubMed ID:14973191 | HubMed [calin2004]
  27. Meskauskas A, Lehmann-Horn F, and Jurkat-Rott K. Sight: automating genomic data-mining without programming skills. Bioinformatics. 2004 Jul 22;20(11):1718-20. DOI:10.1093/bioinformatics/bth151 | PubMed ID:14988103 | HubMed [sight2004]
  28. Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, and Blaxter M. PartiGene--constructing partial genomes. Bioinformatics. 2004 Jun 12;20(9):1398-404. DOI:10.1093/bioinformatics/bth101 | PubMed ID:14988115 | HubMed [partigene]
  29. Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, and Birney E. The Ensembl core software libraries. Genome Res. 2004 May;14(5):929-33. DOI:10.1101/gr.1857204 | PubMed ID:15123588 | HubMed [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. Narechania A, Terai M, Chen Z, DeSalle R, and Burk RD. Lack of the canonical pRB-binding domain in the E7 ORF of artiodactyl papillomaviruses is associated with the development of fibropapillomas. J Gen Virol. 2004 May;85(Pt 5):1243-50. DOI:10.1099/vir.0.19765-0 | PubMed ID:15105541 | HubMed [narechania2004]
  33. Feig M, Karanicolas J, and Brooks CL 3rd. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model. 2004 May;22(5):377-95. DOI:10.1016/j.jmgm.2003.12.005 | PubMed ID:15099834 | HubMed [MMTSB]
  34. Larose M, St-Amand J, Yoshioka M, Belleau P, Morissette J, Labrie C, Raymond V, and Labrie F. Transcriptome of mouse uterus by serial analysis of gene expression (SAGE): comparison with skeletal muscle. Mol Reprod Dev. 2004 Jun;68(2):142-8. DOI:10.1002/mrd.20065 | PubMed ID:15095334 | HubMed [larose2004]
  35. Schageman JJ, Horton CJ, Niu S, Garner HR, and Pertsemlidis A. ELXR: a resource for rapid exon-directed sequence analysis. Genome Biol. 2004;5(5):R36. DOI:10.1186/gb-2004-5-5-r36 | PubMed ID:15128450 | HubMed [elxr]
  36. Stajich JE. Bioperl: Open-Source Bioinformatics Tools 2004 Science Careers 3220. [stajich2004]
  37. Budd A, Blandin S, Levashina EA, and Gibson TJ. Bacterial alpha2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?. Genome Biol. 2004;5(6):R38. DOI:10.1186/gb-2004-5-6-r38 | PubMed ID:15186489 | HubMed [budd2004]
  38. Cannon SB, Mitra A, Baumgarten A, Young ND, and May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 2004 Jun 1;4:10. DOI:10.1186/1471-2229-4-10 | PubMed ID:15171794 | HubMed [cannon2004]
  39. Negre V and Grunau C. eL-DASionator: an LDAS upload file generator. BMC Bioinformatics. 2004 May 7;5:55. DOI:10.1186/1471-2105-5-55 | PubMed ID:15132760 | HubMed [negre2004]
  40. Korf I. Gene finding in novel genomes. BMC Bioinformatics. 2004 May 14;5:59. DOI:10.1186/1471-2105-5-59 | PubMed ID:15144565 | HubMed [SNAP]
  41. Guryev V, Berezikov E, Malik R, Plasterk RH, and Cuppen E. Single nucleotide polymorphisms associated with rat expressed sequences. Genome Res. 2004 Jul;14(7):1438-43. DOI:10.1101/gr.2154304 | PubMed ID:15231757 | HubMed [guryev2004]
  42. Gutiérrez RA, Green PJ, Keegstra K, and Ohlrogge JB. Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?. Genome Biol. 2004;5(8):R53. DOI:10.1186/gb-2004-5-8-r53 | PubMed ID:15287975 | HubMed [gutierrez2004]
  43. Umar A. Applications of bioinformatics in cancer detection: a lexicon of bioinformatics terms. Ann N Y Acad Sci. 2004 May;1020:263-76. DOI:10.1196/annals.1310.021 | PubMed ID:15208197 | HubMed [umar2004]
  44. Petyuk V, McDermott J, Cook M, and Sauer B. Functional mapping of Cre recombinase by pentapeptide insertional mutagenesis. J Biol Chem. 2004 Aug 27;279(35):37040-8. DOI:10.1074/jbc.M406042200 | PubMed ID:15218019 | HubMed [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. Alkema WB, Johansson O, Lagergren J, and Wasserman WW. MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W195-8. DOI:10.1093/nar/gkh387 | PubMed ID:15215379 | HubMed [mscan]
  47. Casillas S and Barbadilla A. PDA: a pipeline to explore and estimate polymorphism in large DNA databases. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W166-9. DOI:10.1093/nar/gkh428 | PubMed ID:15215372 | HubMed [pda]
  48. Dudek P and Picard D. TROD: T7 RNAi Oligo Designer. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W121-3. DOI:10.1093/nar/gkh360 | PubMed ID:15215363 | HubMed [trod]
  49. Alkema WB, Lenhard B, and Wasserman WW. Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. Genome Res. 2004 Jul;14(7):1362-73. DOI:10.1101/gr.2242604 | PubMed ID:15231752 | HubMed [regulog]
  50. Hahn MW, Rockman MV, Soranzo N, Goldstein DB, and Wray GA. Population genetic and phylogenetic evidence for positive selection on regulatory mutations at the factor VII locus in humans. Genetics. 2004 Jun;167(2):867-77. DOI:10.1534/genetics.103.025726 | PubMed ID:15238535 | HubMed [hahnFIV]
  51. Ilic K, Berleth T, and Provart NJ. BlastDigester--a web-based program for efficient CAPS marker design. Trends Genet. 2004 Jul;20(7):280-3. DOI:10.1016/j.tig.2004.04.012 | PubMed ID:15219390 | HubMed [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]
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All Medline abstracts: PubMed | HubMed
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