BioPerl publications/2006

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  1. Tijet N, Boutros PC, Moffat ID, Okey AB, Tuomisto J, and Pohjanvirta R. Aryl hydrocarbon receptor regulates distinct dioxin-dependent and dioxin-independent gene batteries. Mol Pharmacol. 2006 Jan;69(1):140-53. DOI:10.1124/mol.105.018705 | PubMed ID:16214954 | HubMed [tijet2005]
  2. Droc G, Ruiz M, Larmande P, Pereira A, Piffanelli P, Morel JB, Dievart A, Courtois B, Guiderdoni E, and Périn C. OryGenesDB: a database for rice reverse genetics. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D736-40. DOI:10.1093/nar/gkj012 | PubMed ID:16381969 | HubMed [OryGenes]
  3. Yang J, Chen L, Yu J, Sun L, and Jin Q. ShiBASE: an integrated database for comparative genomics of Shigella. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D398-401. DOI:10.1093/nar/gkj033 | PubMed ID:16381896 | HubMed [ShiBase]
  4. Hartmann S, Lu D, Phillips J, and Vision TJ. Phytome: a platform for plant comparative genomics. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D724-30. DOI:10.1093/nar/gkj045 | PubMed ID:16381967 | HubMed [phytome]
  5. Dieterich G, Kärst U, Fischer E, Wehland J, and Jänsch L. LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D402-6. DOI:10.1093/nar/gkj071 | PubMed ID:16381897 | HubMed [leger]
  6. Donizelli M, Djite MA, and Le Novère N. LGICdb: a manually curated sequence database after the genomes. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D267-9. DOI:10.1093/nar/gkj104 | PubMed ID:16381861 | HubMed [lgicdb]
  7. Sherman D, Durrens P, Iragne F, Beyne E, Nikolski M, and Souciet JL. Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D432-5. DOI:10.1093/nar/gkj160 | PubMed ID:16381905 | HubMed [genoluvresII]
  8. Barbosa-Morais NL, Carmo-Fonseca M, and Aparício S. Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. Genome Res. 2006 Jan;16(1):66-77. DOI:10.1101/gr.3936206 | PubMed ID:16344558 | HubMed [barbosa-morais06]
  9. Lipovich L and King MC. Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. Genome Res. 2006 Jan;16(1):45-54. DOI:10.1101/gr.3883606 | PubMed ID:16344557 | HubMed [liopvich06]
  10. Dunn CA, van de Lagemaat LN, Baillie GJ, and Mager DL. Endogenous retrovirus long terminal repeats as ready-to-use mobile promoters: the case of primate beta3GAL-T5. Gene. 2005 Dec 30;364:2-12. DOI:10.1016/j.gene.2005.05.045 | PubMed ID:16112824 | HubMed [dunn06]
  11. Dieterich G, Kärst U, Wehland J, and Jänsch L. VIS-O-BAC: exploratory visualization of functional genome studies from bacteria. Bioinformatics. 2006 Mar 1;22(5):630-1. DOI:10.1093/bioinformatics/bti814 | PubMed ID:16339284 | HubMed [dieterich2006]
  12. Navas-Delgado I, Rojano-Muñoz Mdel M, Ramírez S, Pérez AJ, Andrés León E, Aldana-Montes JF, and Trelles O. Intelligent client for integrating bioinformatics services. Bioinformatics. 2006 Jan 1;22(1):106-11. DOI:10.1093/bioinformatics/bti740 | PubMed ID:16257987 | HubMed [navas_delgado2006]
  13. Basu S, Bremer E, Zhou C, and Bogenhagen DF. MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation. Bioinformatics. 2006 Feb 15;22(4):485-92. DOI:10.1093/bioinformatics/btk009 | PubMed ID:16368773 | HubMed [basu2006]
  14. Yang G and Hall TC. HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana. Bioinformatics. 2006 Mar 1;22(5):523-6. DOI:10.1093/bioinformatics/btk003 | PubMed ID:16357035 | HubMed [hidenseek]
  15. Claesson MJ and van Sinderen D. BlastXtract--a new way of exploring translated searches. Bioinformatics. 2005 Sep 15;21(18):3667-8. DOI:10.1093/bioinformatics/bti598 | PubMed ID:16046492 | HubMed [BlastXtract]
  16. Finak G, Godin N, Hallett M, Pepin F, Rajabi Z, Srivastava V, and Tang Z. BIAS: Bioinformatics Integrated Application Software. Bioinformatics. 2005 Apr 15;21(8):1745-6. DOI:10.1093/bioinformatics/bti170 | PubMed ID:15572471 | HubMed [BIAS]
  17. Chen H, Huang N, and Sun Z. SubLoc: a server/client suite for protein subcellular location based on SOAP. Bioinformatics. 2006 Feb 1;22(3):376-7. DOI:10.1093/bioinformatics/bti822 | PubMed ID:16339283 | HubMed [sublocsoap]
  18. Wilson GM, Flibotte S, Missirlis PI, Marra MA, Jones S, Thornton K, Clark AG, and Holt RA. Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res. 2006 Feb;16(2):173-81. DOI:10.1101/gr.4456006 | PubMed ID:16365383 | HubMed [wilson2006]
  19. Collins L, Penny D, and SMBE Tri-National Young Investigators. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes. Mol Biol Evol. 2006 May;23(5):901-10. DOI:10.1093/molbev/msj084 | PubMed ID:16371412 | HubMed [collins2006]
  20. Collins L, Penny D, and SMBE Tri-National Young Investigators. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Investigating the intron recognition mechanism in eukaryotes. Mol Biol Evol. 2006 May;23(5):901-10. DOI:10.1093/molbev/msj084 | PubMed ID:16371412 | HubMed [collins2006]
  21. Zhao B, Maruo S, Cooper A, R Chase M, Johannsen E, Kieff E, and Cahir-McFarland E. RNAs induced by Epstein-Barr virus nuclear antigen 2 in lymphoblastoid cell lines. Proc Natl Acad Sci U S A. 2006 Feb 7;103(6):1900-5. DOI:10.1073/pnas.0510612103 | PubMed ID:16446431 | HubMed [zhao2006]
  22. Ou HY, Chen LL, Lonnen J, Chaudhuri RR, Thani AB, Smith R, Garton NJ, Hinton J, Pallen M, Barer MR, and Rajakumar K. A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Res. 2006 Jan 9;34(1):e3. DOI:10.1093/nar/gnj005 | PubMed ID:16414954 | HubMed [ou2006]
  23. Croce O, Lamarre M, and Christen R. Querying the public databases for sequences using complex keywords contained in the feature lines. BMC Bioinformatics. 2006 Jan 27;7:45. DOI:10.1186/1471-2105-7-45 | PubMed ID:16441875 | HubMed [croce2006]
  24. Ardell DH and Andersson SG. TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase. Nucleic Acids Res. 2006;34(3):893-904. DOI:10.1093/nar/gkj449 | PubMed ID:16473847 | HubMed [ardell2006]
  25. Gront D and Kolinski A. BioShell--a package of tools for structural biology computations. Bioinformatics. 2006 Mar 1;22(5):621-2. DOI:10.1093/bioinformatics/btk037 | PubMed ID:16407320 | HubMed [gront2006]
  26. Fredman D, Sawyer SL, Strömqvist L, Mottagui-Tabar S, Kidd KK, Wahlestedt C, Chanock SJ, and Brookes AJ. Nonsynonymous SNPs: validation characteristics, derived allele frequency patterns, and suggestive evidence for natural selection. Hum Mutat. 2006 Feb;27(2):173-86. DOI:10.1002/humu.20289 | PubMed ID:16429399 | HubMed [fredman2006]
  27. Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB, Sickler BA, Wilkins TA, Guo JY, Chen XY, Scheffler J, Taliercio E, Turley R, McFadden H, Payton P, Klueva N, Allen R, Zhang D, Haigler C, Wilkerson C, Suo J, Schulze SR, Pierce ML, Essenberg M, Kim H, Llewellyn DJ, Dennis ES, Kudrna D, Wing R, Paterson AH, Soderlund C, and Wendel JF. A global assembly of cotton ESTs. Genome Res. 2006 Mar;16(3):441-50. DOI:10.1101/gr.4602906 | PubMed ID:16478941 | HubMed [udall2006]
  28. Zhan S, Horrocks J, and Lukens LN. Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains. Plant J. 2006 Feb;45(3):347-57. DOI:10.1111/j.1365-313X.2005.02619.x | PubMed ID:16412082 | HubMed [lukens2006a]
  29. Lukens LN, Pires JC, Leon E, Vogelzang R, Oslach L, and Osborn T. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol. 2006 Jan;140(1):336-48. DOI:10.1104/pp.105.066308 | PubMed ID:16377753 | HubMed [lukens2006b]
  30. Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J, Hartzell G, Lewis S, and Rubin GM. Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput Biol. 2006 Mar;2(3):e15. DOI:10.1371/journal.pcbi.0020015 | PubMed ID:16518452 | HubMed [yandell2006]
  31. Palidwor G, Reynaud EG, and Andrade-Navarro MA. Taxonomic colouring of phylogenetic trees of protein sequences. BMC Bioinformatics. 2006 Feb 17;7:79. DOI:10.1186/1471-2105-7-79 | PubMed ID:16503967 | HubMed [palidowor2006]
  32. Feijão PC, Neiva LS, de Azeredo-Espin AM, and Lessinger AC. AMiGA: the arthropodan mitochondrial genomes accessible database. Bioinformatics. 2006 Apr 1;22(7):902-3. DOI:10.1093/bioinformatics/btl021 | PubMed ID:16446277 | HubMed [amiga2006]
  33. Kuraku S, Ishijima J, Nishida-Umehara C, Agata K, Kuratani S, and Matsuda Y. cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids. Chromosome Res. 2006;14(2):187-202. DOI:10.1007/s10577-006-1035-8 | PubMed ID:16544192 | HubMed [kuraku2006]
  34. Stanley SM, Bailey TL, and Mattick JS. GONOME: measuring correlations between GO terms and genomic positions. BMC Bioinformatics. 2006 Feb 25;7:94. DOI:10.1186/1471-2105-7-94 | PubMed ID:16504139 | HubMed [stanley2006]
  35. Li T, Chamberlin SG, Caraco MD, Liberles DA, Gaucher EA, and Benner SA. Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics. BMC Evol Biol. 2006 Mar 20;6:25. DOI:10.1186/1471-2148-6-25 | PubMed ID:16545144 | HubMed [li2006]
  36. Pastorelli R, Carpi D, Campagna R, Airoldi L, Pohjanvirta R, Viluksela M, Hakansson H, Boutros PC, Moffat ID, Okey AB, and Fanelli R. Differential expression profiling of the hepatic proteome in a rat model of dioxin resistance: correlation with genomic and transcriptomic analyses. Mol Cell Proteomics. 2006 May;5(5):882-94. DOI:10.1074/mcp.M500415-MCP200 | PubMed ID:16497791 | HubMed [pastorelli2006]
  37. Catanho M, Mascarenhas D, Degrave W, and de Miranda AB. BioParser: a tool for processing of sequence similarity analysis reports. Appl Bioinformatics. 2006;5(1):49-53. PubMed ID:16539538 | HubMed [catanho2006]
  38. Catalano D, Licciulli F, Turi A, Grillo G, Saccone C, and D'Elia D. MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. BMC Bioinformatics. 2006 Jan 24;7:36. DOI:10.1186/1471-2105-7-36 | PubMed ID:16433928 | HubMed [catalano2006]
  39. da Fontoura Costa L, Rodrigues FA, Travieso G Protein domain connectivity and essentiality [fontoura2006]
  40. Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, and Van Tassell CP. Application of machine learning in SNP discovery. BMC Bioinformatics. 2006 Jan 6;7:4. DOI:10.1186/1471-2105-7-4 | PubMed ID:16398931 | HubMed [matukumalli2006]
  41. DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, and Andersen GL. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W394-9. DOI:10.1093/nar/gkl244 | PubMed ID:16845035 | HubMed [desantis2006]
  42. Yusuf D, Lim JS, and Wasserman WW. The Gene Set Builder: collation, curation, and distribution of sets of genes. BMC Bioinformatics. 2005 Dec 21;6:305. DOI:10.1186/1471-2105-6-305 | PubMed ID:16371163 | HubMed [yusuf2006]
  43. XML for Bioinformatics Brief in Bioinf. 2006. [heiland2006]
  44. Semeiks JR, Rizki A, Bissell MJ, and Mian IS. Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features. BMC Bioinformatics. 2006 Mar 16;7:147. DOI:10.1186/1471-2105-7-147 | PubMed ID:16542449 | HubMed [semeiks2006]
  45. Beller M, Riedel D, Jänsch L, Dieterich G, Wehland J, Jäckle H, and Kühnlein RP. Characterization of the Drosophila lipid droplet subproteome. Mol Cell Proteomics. 2006 Jun;5(6):1082-94. DOI:10.1074/mcp.M600011-MCP200 | PubMed ID:16543254 | HubMed [beller2006]
  46. Cramer RA, La Rota CM, Cho Y, Thon M, Craven KD, Knudson KL, Mitchell TK, and Lawrence CB. Bioinformatic analysis of expressed sequence tags derived from a compatible Alternaria brassicicola–Brassica oleracea interaction Molecular Plant Pathology 2006; 7:113. [cramer2006]
  47. Thompson J and Gopal S. Genetic algorithm learning as a robust approach to RNA editing site prediction. BMC Bioinformatics. 2006 Mar 16;7:145. DOI:10.1186/1471-2105-7-145 | PubMed ID:16542417 | HubMed [thompson2006]
  48. Liang C, Sun F, Wang H, Qu J, Freeman RM Jr, Pratt LH, and Cordonnier-Pratt MM. MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. BMC Bioinformatics. 2006 Mar 7;7:115. DOI:10.1186/1471-2105-7-115 | PubMed ID:16522212 | HubMed [liang2006]
  49. Colinge J, Masselot A, Carbonell P, and Appel RD. InSilicoSpectro: an open-source proteomics library. J Proteome Res. 2006 Mar;5(3):619-24. DOI:10.1021/pr0504236 | PubMed ID:16512677 | HubMed [colinge2006]
  50. Stajich JE and Dietrich FS. Evidence of mRNA-mediated intron loss in the human-pathogenic fungus Cryptococcus neoformans. Eukaryot Cell. 2006 May;5(5):789-93. DOI:10.1128/EC.5.5.789-793.2006 | PubMed ID:16682456 | HubMed [stajich2006]
  51. Tran T, Havlak P, and Miller J. MicroRNA enrichment among short 'ultraconserved' sequences in insects. Nucleic Acids Res. 2006 May 12;34(9):e65. DOI:10.1093/nar/gkl173 | PubMed ID:16698958 | HubMed [tran2006]
  52. Philippi S and Köhler J. Addressing the problems with life-science databases for traditional uses and systems biology. Nat Rev Genet. 2006 Jun;7(6):482-8. DOI:10.1038/nrg1872 | PubMed ID:16682980 | HubMed [philippi2006]
  53. Lopez-Ochoa L, Ramirez-Prado J, and Hanley-Bowdoin L. Peptide aptamers that bind to a geminivirus replication protein interfere with viral replication in plant cells. J Virol. 2006 Jun;80(12):5841-53. DOI:10.1128/JVI.02698-05 | PubMed ID:16731923 | HubMed [lopez-ochoa2006]
  54. Suyama M, Torrents D, and Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12. DOI:10.1093/nar/gkl315 | PubMed ID:16845082 | HubMed [suyama2006]
  55. Prentiss MC, Hardin C, Eastwood MP, Zong CH, Wolynes PG. Protein Structure Prediction: The Next Generation J. Chem. Theory Comput.; 2006; 2(3) 705-716. [prentiss2006]
  56. Rossello F and Valiente G. The transposition distance for phylogenetic trees. ArXiv 2006. [rosello2006]
  57. Abascal F, Posada D, Knight RD, and Zardoya R. Parallel evolution of the genetic code in arthropod mitochondrial genomes. PLoS Biol. 2006 May;4(5):e127. DOI:10.1371/journal.pbio.0040127 | PubMed ID:16620150 | HubMed [abascal2006a]
  58. Lim D. Ruby in the rough: using VHLLs in bioinformatics. Journal of Computing Sciences in Colleges. 2006. 21(6):108-116. [lim2006]
  59. Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, and States DJ. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol. 2006;7(4):R35. DOI:10.1186/gb-2006-7-4-r35 | PubMed ID:16646984 | HubMed [fermin2006]
  60. Hadzidimitriou A, Stamatopoulos K, Belessi C, Lalayianni C, Stavroyianni N, Smilevska T, Hatzi K, Laoutaris N, Anagnostopoulos A, Kollia P, and Fassas A. Immunoglobulin genes in multiple myeloma: expressed and non-expressed repertoires, heavy and light chain pairings and somatic mutation patterns in a series of 101 cases. Haematologica. 2006 Jun;91(6):781-7. PubMed ID:16769580 | HubMed [hadzidimitriou2006]
  61. Haynes PA, Miller S, Radabaugh T, Galligan M, Breci L, Rohrbough J, Hickman F, and Merchant N. The wildcat toolbox: a set of perl script utilities for use in peptide mass spectral database searching and proteomics experiments. J Biomol Tech. 2006 Apr;17(2):97-102. PubMed ID:16741236 | HubMed [haynes2006]
  62. Pinto FL, Svensson H, and Lindblad P. Generation of non-genomic oligonucleotide tag sequences for RNA template-specific PCR. BMC Biotechnol. 2006 Jul 5;6:31. DOI:10.1186/1472-6750-6-31 | PubMed ID:16820068 | HubMed [pinto2006]
  63. Horsman S, Moorhouse MJ, de Jager VC, van der Spek P, Grosveld F, Strouboulis J, and Katsantoni EZ. TF Target Mapper: a BLAST search tool for the identification of Transcription Factor target genes. BMC Bioinformatics. 2006 Mar 8;7:120. DOI:10.1186/1471-2105-7-120 | PubMed ID:16524462 | HubMed [horsman2006]
  64. Fredslund J. PHY.FI: fast and easy online creation and manipulation of phylogeny color figures. BMC Bioinformatics. 2006 Jun 22;7:315. DOI:10.1186/1471-2105-7-315 | PubMed ID:16792795 | HubMed [fredslund2006]
  65. Belessi CJ, Davi FB, Stamatopoulos KE, Degano M, Andreou TM, Moreno C, Merle-Béral H, Crespo M, Laoutaris NP, Montserrat E, Caligaris-Cappio F, Anagnostopoulos AZ, and Ghia P. IGHV gene insertions and deletions in chronic lymphocytic leukemia: "CLL-biased" deletions in a subset of cases with stereotyped receptors. Eur J Immunol. 2006 Jul;36(7):1963-74. DOI:10.1002/eji.200535751 | PubMed ID:16783849 | HubMed [belessi2006]
  66. Yao F, Zhang R, Zhu Z, Xia K, and Liu C. MutScreener: primer design tool for PCR-direct sequencing. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W660-4. DOI:10.1093/nar/gkl168 | PubMed ID:16845093 | HubMed [yao2006]
  67. Chen L, Wang W, Ling S, Jia C, and Wang F. KemaDom: a web server for domain prediction using kernel machine with local context. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W158-63. DOI:10.1093/nar/gkl331 | PubMed ID:16844982 | HubMed [chen2006]
All Medline abstracts: PubMed | HubMed
  1. Fredslund J. PHY.FI: fast and easy online creation and manipulation of phylogeny color figures. BMC Bioinformatics. 2006 Jun 22;7:315. DOI:10.1186/1471-2105-7-315 | PubMed ID:16792795 | HubMed [fredslund2006]
  2. Chen P, Li X, Sun Y, Liu Z, Cao R, He Q, Wang M, Xiong J, Xie J, Wang X, and Liang S. Proteomic analysis of rat hippocampal plasma membrane: characterization of potential neuronal-specific plasma membrane proteins. J Neurochem. 2006 Aug;98(4):1126-40. DOI:10.1111/j.1471-4159.2006.03934.x | PubMed ID:16895580 | HubMed [chen2006]
  3. Khaja R, MacDonald JR, Zhang J, and Scherer SW. Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes. Methods Mol Biol. 2006;338:9-20. DOI:10.1385/1-59745-097-9:9 | PubMed ID:16888347 | HubMed [khaja2006]
  4. Pavy N, Parsons LS, Paule C, MacKay J, and Bousquet J. Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics. 2006 Jul 6;7:174. DOI:10.1186/1471-2164-7-174 | PubMed ID:16824208 | HubMed [pavy2006]
  5. Moolhuijzen P, Cakir M, Hunter A, Schibeci D, Macgregor A, Smith C, Francki M, Jones MG, Appels R, and Bellgard M. LegumeDB1 bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species. Genome. 2006 Jun;49(6):689-99. DOI:10.1139/g06-009 | PubMed ID:16936848 | HubMed [legumedb]
  6. Zhang Y, Li S, Skogerbø G, Zhang Z, Zhu X, Zhang Z, Sun S, Lu H, Shi B, and Chen R. Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. BMC Bioinformatics. 2006 May 9;7:252. DOI:10.1186/1471-2105-7-252 | PubMed ID:16684350 | HubMed [zhang2006]
  7. Han S and Kim D. AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs. BMC Bioinformatics. 2006 Mar 30;7:179. DOI:10.1186/1471-2105-7-179 | PubMed ID:16571141 | HubMed [han2006]
  8. De Hertogh B, Hancy F, Goffeau A, and Baret PV. Emergence of species-specific transporters during evolution of the hemiascomycete phylum. Genetics. 2006 Feb;172(2):771-81. DOI:10.1534/genetics.105.046813 | PubMed ID:16118182 | HubMed [dehertogh2006]
  9. Philippi S and Köhler J. Addressing the problems with life-science databases for traditional uses and systems biology. Nat Rev Genet. 2006 Jun;7(6):482-8. DOI:10.1038/nrg1872 | PubMed ID:16682980 | HubMed [phillipi2006]
  10. Hegedus T, Riordan JR. Search for proteins with similarity to the CFTR R domain using an optimized RDBMS solution, mBioSQL. Central European Journal of Biology. 2006. 1(1):29-42. doi:10.2478/s11535-006-0003-9. [hegedus2006]
  11. Fischer F and Poetsch A. Protein cleavage strategies for an improved analysis of the membrane proteome. Proteome Sci. 2006 Mar 2;4:2. DOI:10.1186/1477-5956-4-2 | PubMed ID:16512920 | HubMed [fischer2006]
  12. Beller M and Oliver B. One hundred years of high-throughput Drosophila research. Chromosome Res. 2006;14(4):349-62. DOI:10.1007/s10577-006-1065-2 | PubMed ID:16821132 | HubMed [beller2006a]
  13. Ruvinsky A and Ward W. A gradient in the distribution of introns in eukaryotic genes. J Mol Evol. 2006 Jul;63(1):136-41. DOI:10.1007/s00239-005-0261-6 | PubMed ID:16736103 | HubMed [ruvinsky2006]
  14. Cavalcanti AR, Stover NA, and Landweber LF. On the paucity of duplicated genes in Caenorhabditis elegans operons. J Mol Evol. 2006 Jun;62(6):765-71. DOI:10.1007/s00239-005-0203-3 | PubMed ID:16752214 | HubMed [cavalcanti2006]
  15. Jolley KA and Maiden MC. AgdbNet - antigen sequence database software for bacterial typing. BMC Bioinformatics. 2006 Jun 21;7:314. DOI:10.1186/1471-2105-7-314 | PubMed ID:16790057 | HubMed [jolly2006]
  16. Udall JA, Swanson JM, Nettleton D, Percifield RJ, and Wendel JF. A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics. 2006 Jul;173(3):1823-7. DOI:10.1534/genetics.106.058271 | PubMed ID:16702424 | HubMed [udall2006b]
  17. Buschbom J and Barker D. Evolutionary history of vegetative reproduction in Porpidia s.L. (Lichen-forming ascomycota). Syst Biol. 2006 Jun;55(3):471-84. DOI:10.1080/10635150600697465 | PubMed ID:16861210 | HubMed [buschbom2006]
  18. Stajich JE and Lapp H. Open source tools and toolkits for bioinformatics: significance, and where are we?. Brief Bioinform. 2006 Sep;7(3):287-96. DOI:10.1093/bib/bbl026 | PubMed ID:16899494 | HubMed [stajich2006b]
  19. Cramer RA Jr, Stajich JE, Yamanaka Y, Dietrich FS, Steinbach WJ, and Perfect JR. Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus. Gene. 2006 Nov 15;383:24-32. DOI:10.1016/j.gene.2006.07.008 | PubMed ID:16962256 | HubMed [cramer2006b]
  20. Giles SS, Stajich JE, Nichols C, Gerrald QD, Alspaugh JA, Dietrich F, and Perfect JR. The Cryptococcus neoformans catalase gene family and its role in antioxidant defense. Eukaryot Cell. 2006 Sep;5(9):1447-59. DOI:10.1128/EC.00098-06 | PubMed ID:16963629 | HubMed [giles2006]
  21. Mulvenna JP, Mylne JS, Bharathi R, Burton RA, Shirley NJ, Fincher GB, Anderson MA, and Craik DJ. Discovery of cyclotide-like protein sequences in graminaceous crop plants: ancestral precursors of circular proteins?. Plant Cell. 2006 Sep;18(9):2134-44. DOI:10.1105/tpc.106.042812 | PubMed ID:16935986 | HubMed [mulvenna2006]
  22. Toth C, Connelly R. A bioinformatics experience course Journal of Computing Sciences in Colleges. 2006. 21(6):100-107. [toth2006]
  23. Abascal F, Zardoya R, and Posada D. GenDecoder: genetic code prediction for metazoan mitochondria. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W389-93. DOI:10.1093/nar/gkl044 | PubMed ID:16845034 | HubMed [abascal2006b]
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