BioPerl publications/2005

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  1. Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, and Martienssen RA. Sorghum genome sequencing by methylation filtration. PLoS Biol. 2005 Jan;3(1):e13. DOI:10.1371/journal.pbio.0030013 | PubMed ID:15660154 | HubMed [bedell2005]
  2. Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LE, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, and Aebersold R. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 2005;6(1):R9. DOI:10.1186/gb-2004-6-1-r9 | PubMed ID:15642101 | HubMed [desiere2005]
  3. Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, and Kasschau KD. ASRP: the Arabidopsis Small RNA Project Database. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D637-40. DOI:10.1093/nar/gki127 | PubMed ID:15608278 | HubMed [asrp]
  4. de Magalhães JP, Costa J, and Toussaint O. HAGR: the Human Ageing Genomic Resources. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D537-43. DOI:10.1093/nar/gki017 | PubMed ID:15608256 | HubMed [hagr]
  5. Turinsky AL, Ah-Seng AC, Gordon PM, Stromer JN, Taschuk ML, Xu EW, and Sensen CW. Bioinformatics visualization and integration with open standards: the Bluejay genomic browser. In Silico Biol. 2005;5(2):187-98. PubMed ID:15972014 | HubMed [turinsky2005]
  6. O'Brien KP, Remm M, and Sonnhammer EL. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D476-80. DOI:10.1093/nar/gki107 | PubMed ID:15608241 | HubMed [inparanoid]
  7. Veeramachaneni V and Makalowski W. DED: Database of Evolutionary Distances. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D442-6. DOI:10.1093/nar/gki094 | PubMed ID:15608234 | HubMed [DEB]
  8. Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, Buzadzija K, Cavero R, D'Abreo C, Donaldson I, Dorairajoo D, Dumontier MJ, Dumontier MR, Earles V, Farrall R, Feldman H, Garderman E, Gong Y, Gonzaga R, Grytsan V, Gryz E, Gu V, Haldorsen E, Halupa A, Haw R, Hrvojic A, Hurrell L, Isserlin R, Jack F, Juma F, Khan A, Kon T, Konopinsky S, Le V, Lee E, Ling S, Magidin M, Moniakis J, Montojo J, Moore S, Muskat B, Ng I, Paraiso JP, Parker B, Pintilie G, Pirone R, Salama JJ, Sgro S, Shan T, Shu Y, Siew J, Skinner D, Snyder K, Stasiuk R, Strumpf D, Tuekam B, Tao S, Wang Z, White M, Willis R, Wolting C, Wong S, Wrong A, Xin C, Yao R, Yates B, Zhang S, Zheng K, Pawson T, Ouellette BF, and Hogue CW. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D418-24. DOI:10.1093/nar/gki051 | PubMed ID:15608229 | HubMed [bind2005]
  9. Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Canaran P, Chan J, Chen CK, Chen WJ, Cunningham F, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Pai S, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, and Stein LD. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D383-9. DOI:10.1093/nar/gki066 | PubMed ID:15608221 | HubMed [wormbase2005]
  10. Zhang H, Hu J, Recce M, and Tian B. PolyA_DB: a database for mammalian mRNA polyadenylation. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D116-20. DOI:10.1093/nar/gki055 | PubMed ID:15608159 | HubMed [polyA_DB]
  11. Barta E, Sebestyén E, Pálfy TB, Tóth G, Ortutay CP, and Patthy L. DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D86-90. DOI:10.1093/nar/gki097 | PubMed ID:15608291 | HubMed [doop]
  12. Thornton K and Long M. Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster. Mol Biol Evol. 2005 Feb;22(2):273-84. DOI:10.1093/molbev/msi015 | PubMed ID:15483321 | HubMed [thornton2005]
  13. Yandell M, Bailey AM, Misra S, Shu S, Wiel C, Evans-Holm M, Celniker SE, and Rubin GM. A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1566-71. DOI:10.1073/pnas.0409421102 | PubMed ID:15668397 | HubMed [yandell2005]
  14. Wallace IM, O'Sullivan O, and Higgins DG. Evaluation of iterative alignment algorithms for multiple alignment. Bioinformatics. 2005 Apr 15;21(8):1408-14. DOI:10.1093/bioinformatics/bti159 | PubMed ID:15564300 | HubMed [wallace2005]
  15. Cutillas PR, Biber J, Marks J, Jacob R, Stieger B, Cramer R, Waterfield M, Burlingame AL, and Unwin RJ. Proteomic analysis of plasma membrane vesicles isolated from the rat renal cortex. Proteomics. 2005 Jan;5(1):101-12. DOI:10.1002/pmic.200400886 | PubMed ID:15593129 | HubMed [cutillas2005]
  16. Stadler MB, Arnold D, Frieden S, Luginbühl S, and Stadler BM. Single nucleotide polymorphisms as a prerequisite for autoantigens. Eur J Immunol. 2005 Feb;35(2):371-8. DOI:10.1002/eji.200425481 | PubMed ID:15627977 | HubMed [stadler2005]
  17. Colbourne JK, Singan VR, and Gilbert DG. wFleaBase: the Daphnia genome database. BMC Bioinformatics. 2005 Mar 7;6:45. DOI:10.1186/1471-2105-6-45 | PubMed ID:15752432 | HubMed [fleabase]
  18. Ting CY, Yonekura S, Chung P, Hsu SN, Robertson HM, Chiba A, and Lee CH. Drosophila N-cadherin functions in the first stage of the two-stage layer-selection process of R7 photoreceptor afferents. Development. 2005 Mar;132(5):953-63. DOI:10.1242/dev.01661 | PubMed ID:15673571 | HubMed [ting2005]
  19. Gadberry MD, Malcomber ST, Doust AN, and Kellogg EA. Primaclade--a flexible tool to find conserved PCR primers across multiple species. Bioinformatics. 2005 Apr 1;21(7):1263-4. DOI:10.1093/bioinformatics/bti134 | PubMed ID:15539448 | HubMed [primaclade]
  20. Wahl MB, Heinzmann U, and Imai K. LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse. Bioinformatics. 2005 Apr 15;21(8):1393-400. DOI:10.1093/bioinformatics/bti207 | PubMed ID:15591356 | HubMed [wahl2005]
  21. Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, and Cavicchioli R. Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii. J Proteome Res. 2005 Mar-Apr;4(2):464-72. DOI:10.1021/pr049797+ | PubMed ID:15822923 | HubMed [saunders2005]
  22. Rouse RJ, Castagnetto J, and Niedner RH. PatGen--a consolidated resource for searching genetic patent sequences. Bioinformatics. 2005 Apr 15;21(8):1707-8. DOI:10.1093/bioinformatics/bti202 | PubMed ID:15728120 | HubMed [patgen]
  23. Alako BT, Veldhoven A, van Baal S, Jelier R, Verhoeven S, Rullmann T, Polman J, and Jenster G. CoPub Mapper: mining MEDLINE based on search term co-publication. BMC Bioinformatics. 2005 Mar 11;6:51. DOI:10.1186/1471-2105-6-51 | PubMed ID:15760478 | HubMed [alako2005]
  24. Tuckwell DS, Nicholson MJ, McSweeney CS, Theodorou MK, and Brookman JL. The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints. Microbiology. 2005 May;151(Pt 5):1557-67. DOI:10.1099/mic.0.27689-0 | PubMed ID:15870465 | HubMed [tuckwell2005]
  25. Mooney S. Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief Bioinform. 2005 Mar;6(1):44-56. PubMed ID:15826356 | HubMed [mooney2005]
  26. Stenger JE, Xu H, Haynes C, Hauser ER, Pericak-Vance M, Goldschmidt-Clermont PJ, and Vance JM. Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser. BMC Bioinformatics. 2005 Apr 12;6:95. DOI:10.1186/1471-2105-6-95 | PubMed ID:15826305 | HubMed [stenger2005]
  27. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, and Ashburner M. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 2005;6(5):R44. DOI:10.1186/gb-2005-6-5-r44 | PubMed ID:15892872 | HubMed [eilbeck2005]
  28. Mitreva M, McCarter JP, Arasu P, Hawdon J, Martin J, Dante M, Wylie T, Xu J, Stajich JE, Kapulkin W, Clifton SW, Waterston RH, and Wilson RK. Investigating hookworm genomes by comparative analysis of two Ancylostoma species. BMC Genomics. 2005 Apr 26;6:58. DOI:10.1186/1471-2164-6-58 | PubMed ID:15854223 | HubMed [mitreva2005]
  29. Garcia Castro A, Thoraval S, Garcia LJ, and Ragan MA. Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator. BMC Bioinformatics. 2005 Apr 7;6:87. DOI:10.1186/1471-2105-6-87 | PubMed ID:15813976 | HubMed [garcia_castro2005]
  30. Braglia P, Percudani R, and Dieci G. Sequence context effects on oligo(dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. J Biol Chem. 2005 May 20;280(20):19551-62. DOI:10.1074/jbc.M412238200 | PubMed ID:15788403 | HubMed [braglia2005]
  31. Kirov SA, Peng X, Baker E, Schmoyer D, Zhang B, and Snoddy J. GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments. BMC Bioinformatics. 2005 Mar 24;6:72. DOI:10.1186/1471-2105-6-72 | PubMed ID:15790402 | HubMed [kirov2005]
  32. Gerrard DT and Filatov DA. Positive and negative selection on mammalian Y chromosomes. Mol Biol Evol. 2005 Jun;22(6):1423-32. DOI:10.1093/molbev/msi128 | PubMed ID:15758204 | HubMed [gerrard2005]
  33. Kivioja T, Arvas M, Saloheimo M, Penttilä M, and Ukkonen E. Optimization of cDNA-AFLP experiments using genomic sequence data. Bioinformatics. 2005 Jun 1;21(11):2573-9. DOI:10.1093/bioinformatics/bti393 | PubMed ID:15774551 | HubMed [kivioka2005]
  34. Tomso DJ, Inga A, Menendez D, Pittman GS, Campbell MR, Storici F, Bell DA, and Resnick MA. Functionally distinct polymorphic sequences in the human genome that are targets for p53 transactivation. Proc Natl Acad Sci U S A. 2005 May 3;102(18):6431-6. DOI:10.1073/pnas.0501721102 | PubMed ID:15843459 | HubMed [tomso2005]
  35. Liu ZJ, Lin D, Tempel W, Praissman JL, Rose JP, and Wang BC. Parameter-space screening: a powerful tool for high-throughput crystal structure determination. Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):520-7. DOI:10.1107/S0907444905003239 | PubMed ID:15858261 | HubMed [liu2005]
  36. Horan K, Lauricha J, Bailey-Serres J, Raikhel N, and Girke T. Genome cluster database. A sequence family analysis platform for Arabidopsis and rice. Plant Physiol. 2005 May;138(1):47-54. DOI:10.1104/pp.104.059048 | PubMed ID:15888677 | HubMed [horan2005]
  37. Pampanwar V, Engler F, Hatfield J, Blundy S, Gupta G, and Soderlund C. FPC Web tools for rice, maize, and distribution. Plant Physiol. 2005 May;138(1):116-26. DOI:10.1104/pp.104.056291 | PubMed ID:15888684 | HubMed [pampanwar2005]
  38. Liu M and Grigoriev A. Fast parsers for Entrez Gene. Bioinformatics. 2005 Jul 15;21(14):3189-90. DOI:10.1093/bioinformatics/bti488 | PubMed ID:15879451 | HubMed [entrezgene]
  39. Hill P, Burford D, Martin DM, and Flavell AJ. Retrotransposon populations of Vicia species with varying genome size. Mol Genet Genomics. 2005 Jun;273(5):371-81. DOI:10.1007/s00438-005-1141-x | PubMed ID:15891910 | HubMed [hill2005]
  40. Roth MJ, Forbes AJ, Boyne MT 2nd, Kim YB, Robinson DE, and Kelleher NL. Precise and parallel characterization of coding polymorphisms, alternative splicing, and modifications in human proteins by mass spectrometry. Mol Cell Proteomics. 2005 Jul;4(7):1002-8. DOI:10.1074/mcp.M500064-MCP200 | PubMed ID:15863400 | HubMed [roth2005]
  41. Lang D, Eisinger J, Reski R, and Rensing SA. Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism in mosses. Plant Biol (Stuttg). 2005 May;7(3):238-50. DOI:10.1055/s-2005-837578 | PubMed ID:15912443 | HubMed [lang2005]
  42. Pappu KS, Ostrin EJ, Middlebrooks BW, Sili BT, Chen R, Atkins MR, Gibbs R, and Mardon G. Dual regulation and redundant function of two eye-specific enhancers of the Drosophila retinal determination gene dachshund. Development. 2005 Jun;132(12):2895-905. DOI:10.1242/dev.01869 | PubMed ID:15930118 | HubMed [pappu2005]
  43. Hamel L, Zhaxybayeva O, and Gogarten JP. PentaPlot: a software tool for the illustration of genome mosaicism. BMC Bioinformatics. 2005 Jun 6;6:139. DOI:10.1186/1471-2105-6-139 | PubMed ID:15938752 | HubMed [pentaplot]
  44. Koski LB, Gray MW, Lang BF, and Burger G. AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics. 2005 Jun 16;6:151. DOI:10.1186/1471-2105-6-151 | PubMed ID:15960857 | HubMed [koski2005]
  45. Isken MW, Sugumaran V, Ward TJ, Minds D, and Ferris W. Collection and preparation of sensor network data to support modeling and analysis of outpatient clinics. Health Care Manag Sci. 2005 May;8(2):87-99. PubMed ID:15952606 | HubMed [isken2005]
  46. Cahan P and Kennell JC. Identification and distribution of sequences having similarity to mitochondrial plasmids in mitochondrial genomes of filamentous fungi. Mol Genet Genomics. 2005 Jul;273(6):462-73. DOI:10.1007/s00438-005-1133-x | PubMed ID:15891911 | HubMed [cahan2005]
  47. Neerincx PB and Leunissen JA. Evolution of web services in bioinformatics. Brief Bioinform. 2005 Jun;6(2):178-88. PubMed ID:15975226 | HubMed [neerincx2005]
  48. Hummel J, Keshvari N, Weckwerth W, and Selbig J. Species-specific analysis of protein sequence motifs using mutual information. BMC Bioinformatics. 2005 Jun 29;6:164. DOI:10.1186/1471-2105-6-164 | PubMed ID:15987530 | HubMed [hummel2005]
  49. Missirlis PI, Mead CL, Butland SL, Ouellette BF, Devon RS, Leavitt BR, and Holt RA. Satellog: a database for the identification and prioritization of satellite repeats in disease association studies. BMC Bioinformatics. 2005 Jun 10;6:145. DOI:10.1186/1471-2105-6-145 | PubMed ID:15949044 | HubMed [satellog]
  50. Landsteiner BR, Olson MR, and Rutherford R. Current Comparative Table (CCT) automates customized searches of dynamic biological databases. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W770-3. DOI:10.1093/nar/gki432 | PubMed ID:15980582 | HubMed [CCT]
  51. Arziman Z, Horn T, and Boutros M. E-RNAi: a web application to design optimized RNAi constructs. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W582-8. DOI:10.1093/nar/gki468 | PubMed ID:15980541 | HubMed [ernai]
  52. Klee EW, Shim KJ, Pickart MA, Ekker SC, and Ellis LB. AMOD: a morpholino oligonucleotide selection tool. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W506-11. DOI:10.1093/nar/gki453 | PubMed ID:15980523 | HubMed [AMOD]
All Medline abstracts: PubMed | HubMed
  1. Dantzer J, Moad C, Heiland R, and Mooney S. MutDB services: interactive structural analysis of mutation data. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W311-4. DOI:10.1093/nar/gki404 | PubMed ID:15980479 | HubMed [mutdb]
  2. Li W, Rehmeyer CJ, Staben C, and Farman ML. TruMatch--a BLAST post-processor that identifies bona fide sequence matches to genome assemblies. Bioinformatics. 2005 May 1;21(9):2097-8. DOI:10.1093/bioinformatics/bti257 | PubMed ID:15671115 | HubMed [trumatch]
  3. Kokocinski F, Delhomme N, Wrobel G, Hummerich L, Toedt G, and Lichter P. FACT--a framework for the functional interpretation of high-throughput experiments. BMC Bioinformatics. 2005 Jun 28;6:161. DOI:10.1186/1471-2105-6-161 | PubMed ID:15985174 | HubMed [FACT]
  4. Quest D, Ali HH. A Grammar Based Approach for Mining Bioinformatics Databases (2005) roceedings of the Proceedings of the 38th Annual Hawaii International Conference on System Sciences (HICSS'05) 9:280.2. [quest2005]
  5. Liabres M, Rocha J, Rossello F, Valiente G. On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa [liabres2005]
  6. Hsiao R, Parker RS, Yang H Support for BioIndexing in BLASTgres 2005 Lecture Notes in Computer Science 3615 Data Integration in the Life Sciences: Second International Workshop, DILS 2005, San Diego, CA, USA, July 20-22, 2005. [BLASTgres2005]
  7. Altunay M, Colonnese, Warade C. High Throughput Web Services for Life Sciences Proceedings of the International Conference on Information Technology: Coding and Computing (ITCC'05) - 1(1):329-394. [altunay2005]
  8. Lee W, Hak-Young K. Genetic Algorithm Implementation in Python Proceedings of the Fourth Annual ACIS International Conference on Computer and Information Science (ICIS'05). [lee2005]
  9. Rai AK. Open and Collaborative Research: A New Model for Biomedicine in Hahn, Robert, Eds. Intellectual Property Rights in Frontier Industries: Software and Biotech. AEI-Brookings Press (forthcoming). [Rai2005]
  10. Miles S. Agent-Oriented Data Curation in Bioinformatics (2005) Proceedings of Workshop on Multi-Agent Systems in Medicine, Computational Biology, and Bioinformatics (MAS*BioMed'05). PDF. [miles2005]
  11. Kane MD, Brewer JL. The creation of interdisciplinary biomedical informatics education in an information technology curriculum (2005) Proceedings of the 6th conference on Information technology education 25 - 29. PDF. [kane2005]
  12. Kassam S, Meyer Peter, Corfield A, Mikuz G, Sergi C. Single Nucleotide Polymorphisms (SNPs): History, Biotechnological Outlook and Practical Applications (2005) Current Pharmacology 3(3): 237-245(9). [kassam2005]
  13. Väliaho J, Riikonen P, and Vihinen M. Distribution of immunodeficiency fact files with XML--from Web to WAP. BMC Med Inform Decis Mak. 2005 Jun 26;5:21. DOI:10.1186/1472-6947-5-21 | PubMed ID:15978138 | HubMed [valiaho2005]
  14. Grimplet J, Gaspar JW, Gancel AL, Sauvage FX, and Romieu C. Including mutations from conceptually translated expressed sequence tags into orthologous proteins improves the preliminary assignment of peptide mass fingerprints on non-model genomes. Proteomics. 2005 Jul;5(11):2769-77. DOI:10.1002/pmic.200401177 | PubMed ID:15996012 | HubMed [grimplet2005]
  15. Dieterich G, Kärst U, Wehland J, and Jänsch L. MineBlast: a literature presentation service supporting protein annotation by data mining of BLAST results. Bioinformatics. 2005 Aug 15;21(16):3450-1. DOI:10.1093/bioinformatics/bti528 | PubMed ID:15941742 | HubMed [mineblast]
  16. Pan X, Stein L, and Brendel V. SynBrowse: a synteny browser for comparative sequence analysis. Bioinformatics. 2005 Sep 1;21(17):3461-8. DOI:10.1093/bioinformatics/bti555 | PubMed ID:15994196 | HubMed [synbrowse]
  17. Riaño-Pachón DM, Dreyer I, and Mueller-Roeber B. Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes. Plant J. 2005 Jul;43(2):205-12. DOI:10.1111/j.1365-313X.2005.02438.x | PubMed ID:15998307 | HubMed [Riano-Pachon2005]
  18. Romualdi A, Siddiqui R, Glöckner G, Lehmann R, and Sühnel J. GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness. Bioinformatics. 2005 Sep 15;21(18):3669-71. DOI:10.1093/bioinformatics/bti606 | PubMed ID:16076887 | HubMed [gencolors]
  19. Nilsson RH, Kristiansson E, Ryberg M, and Larsson KH. Approaching the taxonomic affiliation of unidentified sequences in public databases--an example from the mycorrhizal fungi. BMC Bioinformatics. 2005 Jul 18;6:178. DOI:10.1186/1471-2105-6-178 | PubMed ID:16022740 | HubMed [nilsson2005]
  20. Hibbett DS, Nilsson RH, Snyder M, Fonseca M, Costanzo J, and Shonfeld M. Automated phylogenetic taxonomy: an example in the homobasidiomycetes (mushroom-forming fungi). Syst Biol. 2005 Aug;54(4):660-8. DOI:10.1080/10635150590947104 | PubMed ID:16126660 | HubMed [hibbett2005]
  21. O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, and Vilgalys R. Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microbiol. 2005 Sep;71(9):5544-50. DOI:10.1128/AEM.71.9.5544-5550.2005 | PubMed ID:16151147 | HubMed [obrien2005]
  22. Wang C and Lefkowitz EJ. Genomic multiple sequence alignments: refinement using a genetic algorithm. BMC Bioinformatics. 2005 Aug 8;6:200. DOI:10.1186/1471-2105-6-200 | PubMed ID:16086841 | HubMed [wang2005]
  23. Wang TT, Tavera-Mendoza LE, Laperriere D, Libby E, MacLeod NB, Nagai Y, Bourdeau V, Konstorum A, Lallemant B, Zhang R, Mader S, and White JH. Large-scale in silico and microarray-based identification of direct 1,25-dihydroxyvitamin D3 target genes. Mol Endocrinol. 2005 Nov;19(11):2685-95. DOI:10.1210/me.2005-0106 | PubMed ID:16002434 | HubMed [wang2005]
  24. Kohen R, Kirov S, Navaja GP, Happe HK, Hamblin MW, Snoddy JR, Neumaier JF, and Petty F. Gene expression profiling in the hippocampus of learned helpless and nonhelpless rats. Pharmacogenomics J. 2005;5(5):278-91. DOI:10.1038/sj.tpj.6500322 | PubMed ID:16010284 | HubMed [kohen2005]
  25. Van der Auwera GA, Andrup L, and Mahillon J. Conjugative plasmid pAW63 brings new insights into the genesis of the Bacillus anthracis virulence plasmid pXO2 and of the Bacillus thuringiensis plasmid pBT9727. BMC Genomics. 2005 Jul 26;6:103. DOI:10.1186/1471-2164-6-103 | PubMed ID:16042811 | HubMed [van_derAuwera2005]
  26. Mulvenna JP, Foley FM, and Craik DJ. Discovery, structural determination, and putative processing of the precursor protein that produces the cyclic trypsin inhibitor sunflower trypsin inhibitor 1. J Biol Chem. 2005 Sep 16;280(37):32245-53. DOI:10.1074/jbc.M506060200 | PubMed ID:16036912 | HubMed [mulvenna2005]
  27. Hahn MW, De Bie T, Stajich JE, Nguyen C, and Cristianini N. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res. 2005 Aug;15(8):1153-60. DOI:10.1101/gr.3567505 | PubMed ID:16077014 | HubMed [hahn2005]
  28. Benz C, Nilsson D, Andersson B, Clayton C, and Guilbride DL. Messenger RNA processing sites in Trypanosoma brucei. Mol Biochem Parasitol. 2005 Oct;143(2):125-34. DOI:10.1016/j.molbiopara.2005.05.008 | PubMed ID:15993496 | HubMed [benz2005]
  29. Nandi S, Mehra N, Lynn AM, and Bhattacharya A. Comparison of theoretical proteomes: identification of COGs with conserved and variable pI within the multimodal pI distribution. BMC Genomics. 2005 Sep 9;6:116. DOI:10.1186/1471-2164-6-116 | PubMed ID:16150155 | HubMed [nandi2005]
  30. Bekaert M, Richard H, Prum B, and Rousset JP. Identification of programmed translational -1 frameshifting sites in the genome of Saccharomyces cerevisiae. Genome Res. 2005 Oct;15(10):1411-20. DOI:10.1101/gr.4258005 | PubMed ID:16204194 | HubMed [bekaert2005]
  31. Diener SE, Houfek TD, Kalat SE, Windham DE, Burke M, Opperman C, and Dean RA. Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system. BMC Bioinformatics. 2005 Jun 15;6:147. DOI:10.1186/1471-2105-6-147 | PubMed ID:15958161 | HubMed [alkahest2005]
  32. Allander T, Tammi MT, Eriksson M, Bjerkner A, Tiveljung-Lindell A, and Andersson B. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12891-6. DOI:10.1073/pnas.0504666102 | PubMed ID:16118271 | HubMed [allander2005]
  33. Dunn W, Trang P, Zhong Q, Yang E, van Belle C, and Liu F. Human cytomegalovirus expresses novel microRNAs during productive viral infection. Cell Microbiol. 2005 Nov;7(11):1684-95. DOI:10.1111/j.1462-5822.2005.00598.x | PubMed ID:16207254 | HubMed [dunnW2005]
  34. Engelhardt BE, Jordan MI, Muratore KE, and Brenner SE. Protein molecular function prediction by Bayesian phylogenomics. PLoS Comput Biol. 2005 Oct;1(5):e45. DOI:10.1371/journal.pcbi.0010045 | PubMed ID:16217548 | HubMed [englehart2005]
  35. Leman SC, Chen Y, Stajich JE, Noor MA, and Uyenoyama MK. Likelihoods from summary statistics: recent divergence between species. Genetics. 2005 Nov;171(3):1419-36. DOI:10.1534/genetics.104.040402 | PubMed ID:16143628 | HubMed [leman2005]
  36. Krauss U and Eggert T. insilico.mutagenesis: a primer selection tool designed for sequence scanning applications used in directed evolution experiments. Biotechniques. 2005 Nov;39(5):679-82. PubMed ID:16312216 | HubMed [kraus2005]
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