BioPerl publications/2007

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  1. Dixon RJ, Eperon IC, and Samani NJ. Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression. Bioinformatics. 2007 Jan 15;23(2):150-5. DOI:10.1093/bioinformatics/btl575 | PubMed ID:17105720 | HubMed [dixon2007]
  2. Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, and Dubchak I. RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 2007 Jan;35(Database issue):D407-12. DOI:10.1093/nar/gkl865 | PubMed ID:17142223 | HubMed [kazakov2007]
  3. Walker NS, Stiffler N, and Barkan A. POGs/PlantRBP: a resource for comparative genomics in plants. Nucleic Acids Res. 2007 Jan;35(Database issue):D852-6. DOI:10.1093/nar/gkl795 | PubMed ID:17142226 | HubMed [walker2007]
  4. Chang WJ, Addis VM, Li AJ, Axelsson E, Ardell DH, and Landweber LF. Intron Evolution and Information processing in the DNA polymerase alpha gene in spirotrichous ciliates: a hypothesis for interconversion between DNA and RNA deletion. Biol Direct. 2007 Feb 1;2:6. DOI:10.1186/1745-6150-2-6 | PubMed ID:17270054 | HubMed [chang2007]
  5. Elsik CG, Mackey AJ, Reese JT, Milshina NV, Roos DS, and Weinstock GM. Creating a honey bee consensus gene set. Genome Biol. 2007;8(1):R13. DOI:10.1186/gb-2007-8-1-r13 | PubMed ID:17241472 | HubMed [elsik2007]
  6. Xu H, Yang L, Xu P, Tao Y, and Ma Z. cTrans: generating polypeptide databases from cDNA sequences. Proteomics. 2007 Jan;7(2):177-9. DOI:10.1002/pmic.200600508 | PubMed ID:17146835 | HubMed [xu2007]
  7. Terol J, Conesa A, Colmenero JM, Cercos M, Tadeo F, Agustí J, Alós E, Andres F, Soler G, Brumos J, Iglesias DJ, Götz S, Legaz F, Argout X, Courtois B, Ollitrault P, Dossat C, Wincker P, Morillon R, and Talon M. Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. BMC Genomics. 2007 Jan 25;8:31. DOI:10.1186/1471-2164-8-31 | PubMed ID:17254327 | HubMed [terol2007]
  8. Antao T, Beja-Pereira A, Fonseca MM, Harris DJ. BACA: a mitochondrial genome retriever, organizer and visualizer Molecular Ecology Notes 2007; 7(2):217-220. doi:10.1111/j.1471-8286.2006.01658.x [antao2007]
  9. Kim KH, Cho Y, La Rota M, Cramer RA, Lawrence CB. Functional analysis of the Alternaria brassicicola non-ribosomal peptide synthetase gene AbNPS2 reveals a role in conidial cell wall construction. Molecular Plant Pathology 2007; 8(1):23–39. doi:10.1111/j.1364-3703.2006.00366.x [kim2007]
  10. Richardt S, Lang D, Reski R, Frank W, and Rensing SA. PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol. 2007 Apr;143(4):1452-66. DOI:10.1104/pp.107.095760 | PubMed ID:17337525 | HubMed [richardt2007]
  11. McGuffee JW. Programming languages and the biological sciences. Journal of Computing Sciences in Colleges 2007; 22(4):178 - 183 . ACM link. [mcguffee207]
  12. Rambaldi D, Felice B, Praz V, Bucher P, Cittaro D, and Guffanti A. Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S17. DOI:10.1186/1471-2105-8-S1-S17 | PubMed ID:17430561 | HubMed [rambaldi2007]
  13. Kane MD and Brewer JL. An information technology emphasis in biomedical informatics education. J Biomed Inform. 2007 Feb;40(1):67-72. DOI:10.1016/j.jbi.2006.02.006 | PubMed ID:16549392 | HubMed [kane2007]
  14. Kane MD, Brewer JL. An information technology emphasis in biomedical informatics education. Journal of Biomedical Informatics. 2007; 40(1):67-72. doi:10.1016/j.jbi.2006.02.006. [kane2007]
  15. Church SA, Livingstone K, Lai Z, Kozik A, Knapp SJ, Michelmore RW, and Rieseberg LH. Using variable rate models to identify genes under selection in sequence pairs: their validity and limitations for EST sequences. J Mol Evol. 2007 Feb;64(2):171-80. DOI:10.1007/s00239-005-0299-5 | PubMed ID:17200807 | HubMed [church2007]
  16. Erwin TA, Jewell EG, Love CG, Lim GA, Li X, Chapman R, Batley J, Stajich JE, Mongin E, Stupka E, Ross B, Spangenberg G, and Edwards D. BASC: an integrated bioinformatics system for Brassica research. Nucleic Acids Res. 2007 Jan;35(Database issue):D870-3. DOI:10.1093/nar/gkl998 | PubMed ID:17148473 | HubMed [erwin2007]
  17. Barrasa MI, Vaglio P, Cavasino F, Jacotot L, and Walhout AJ. EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. BMC Genomics. 2007 Jan 18;8:21. DOI:10.1186/1471-2164-8-21 | PubMed ID:17233892 | HubMed [barrasa2007]
  18. He J, Dai X, and Zhao X. PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results. BMC Bioinformatics. 2007 Feb 9;8:53. DOI:10.1186/1471-2105-8-53 | PubMed ID:17291345 | HubMed [he2007]
  19. Baumgärtner M, Kärst U, Gerstel B, Loessner M, Wehland J, and Jänsch L. Inactivation of Lgt allows systematic characterization of lipoproteins from Listeria monocytogenes. J Bacteriol. 2007 Jan;189(2):313-24. DOI:10.1128/JB.00976-06 | PubMed ID:17041050 | HubMed [baumgartner2007]
  20. Tolentino HD, Matters MD, Walop W, Law B, Tong W, Liu F, Fontelo P, Kohl K, and Payne DC. A UMLS-based spell checker for natural language processing in vaccine safety. BMC Med Inform Decis Mak. 2007 Feb 12;7:3. DOI:10.1186/1472-6947-7-3 | PubMed ID:17295907 | HubMed [tolentino2007]
  21. Gruber AR, Neuböck R, Hofacker IL, and Washietl S. The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W335-8. DOI:10.1093/nar/gkm222 | PubMed ID:17452347 | HubMed [gruber2007]
  22. Carter RW. Mitochondrial diversity within modern human populations. Nucleic Acids Res. 2007;35(9):3039-45. DOI:10.1093/nar/gkm207 | PubMed ID:17439969 | HubMed [carter2007]
  23. Mitchell RA, Castells-Brooke N, Taubert J, Verrier PJ, Leader DJ, and Rawlings CJ. Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W148-51. DOI:10.1093/nar/gkm220 | PubMed ID:17439966 | HubMed [mitchell2007a]
  24. Almeida LM, Silva IT, Silva WA Jr, Castro JP, Riggs PK, Carareto CM, and Amaral ME. The contribution of transposable elements to Bos taurus gene structure. Gene. 2007 Apr 1;390(1-2):180-9. DOI:10.1016/j.gene.2006.10.012 | PubMed ID:17157447 | HubMed [almedia2007]
  25. Rausch C, Hoof I, Weber T, Wohlleben W, and Huson DH. Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution. BMC Evol Biol. 2007 May 16;7:78. DOI:10.1186/1471-2148-7-78 | PubMed ID:17506888 | HubMed [rausch2007]
  26. Liang C, Wang G, Liu L, Ji G, Liu Y, Chen J, Webb JS, Reese G, and Dean JF. WebTraceMiner: a web service for processing and mining EST sequence trace files. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W137-42. DOI:10.1093/nar/gkm299 | PubMed ID:17488839 | HubMed [liang2007]
  27. Mitchell RA, Dupree P, and Shewry PR. A novel bioinformatics approach identifies candidate genes for the synthesis and feruloylation of arabinoxylan. Plant Physiol. 2007 May;144(1):43-53. DOI:10.1104/pp.106.094995 | PubMed ID:17351055 | HubMed [mitchell2007b]
  28. Baux D, Larrieu L, Blanchet C, Hamel C, Ben Salah S, Vielle A, Gilbert-Dussardier B, Holder M, Calvas P, Philip N, Edery P, Bonneau D, Claustres M, Malcolm S, and Roux AF. Molecular and in silico analyses of the full-length isoform of usherin identify new pathogenic alleles in Usher type II patients. Hum Mutat. 2007 Aug;28(8):781-9. DOI:10.1002/humu.20513 | PubMed ID:17405132 | HubMed [baux2007]
  29. Ortutay C, Siermala M, and Vihinen M. ImmTree: database of evolutionary relationships of genes and proteins in the human immune system. Immunome Res. 2007 Mar 21;3:4. DOI:10.1186/1745-7580-3-4 | PubMed ID:17376226 | HubMed [ortutay2007a]
  30. Ortutay C, Siermala M, and Vihinen M. Molecular characterization of the immune system: emergence of proteins, processes, and domains. Immunogenetics. 2007 May;59(5):333-48. DOI:10.1007/s00251-007-0191-0 | PubMed ID:17294181 | HubMed [prtutay2007b]
  31. Lee JY, Yeh I, Park JY, and Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. 2007 Jan;35(Database issue):D165-8. DOI:10.1093/nar/gkl870 | PubMed ID:17202160 | HubMed [lee2007polya]
  32. Poptsova MS and Gogarten JP. BranchClust: a phylogenetic algorithm for selecting gene families. BMC Bioinformatics. 2007 Apr 10;8:120. DOI:10.1186/1471-2105-8-120 | PubMed ID:17425803 | HubMed [poptsova2007]
  33. Ou HY, He X, Harrison EM, Kulasekara BR, Thani AB, Kadioglu A, Lory S, Hinton JC, Barer MR, Deng Z, and Rajakumar K. MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W97-W104. DOI:10.1093/nar/gkm380 | PubMed ID:17537813 | HubMed [ou2007]
  34. Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, and Gerstein MB. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res. 2007 Jun;17(6):732-45. DOI:10.1101/gr.5696007 | PubMed ID:17567993 | HubMed [rozowsky2007]
  35. Roma G, Cobellis G, Claudiani P, Maione F, Cruz P, Tripoli G, Sardiello M, Peluso I, and Stupka E. A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells. Genome Res. 2007 Jul;17(7):1051-60. DOI:10.1101/gr.5720807 | PubMed ID:17540781 | HubMed [roma2007]
  36. Kumar S and Dudley J. Bioinformatics software for biologists in the genomics era. Bioinformatics. 2007 Jul 15;23(14):1713-7. DOI:10.1093/bioinformatics/btm239 | PubMed ID:17485425 | HubMed [kumar2007]
  37. Klenov MS, Lavrov SA, Stolyarenko AD, Ryazansky SS, Aravin AA, Tuschl T, and Gvozdev VA. Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res. 2007;35(16):5430-8. DOI:10.1093/nar/gkm576 | PubMed ID:17702759 | HubMed [klenov2007]
  38. Li J, Halgamuge SK, Kells CI, and Tang SL. Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages. BMC Bioinformatics. 2007 May 22;8 Suppl 4:S6. DOI:10.1186/1471-2105-8-S4-S6 | PubMed ID:17570149 | HubMed [li2007]
  39. Hladish T, Gopalan V, Liang C, Qiu W, Yang P, and Stoltzfus A. Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics. 2007 Jun 8;8:191. DOI:10.1186/1471-2105-8-191 | PubMed ID:17559666 | HubMed [hladish2007]
  40. Lenk SG. Perl with Tk and C Applied to Product Verification. Journal of the Association for Laboratory Automation 2007; 12(1):33-39. doi:10.1016/j.jala.2006.08.008. [lenk2007]
  41. Ferragina P, Giancarlo R, Greco V, Manzini G, and Valiente G. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment. BMC Bioinformatics. 2007 Jul 13;8:252. DOI:10.1186/1471-2105-8-252 | PubMed ID:17629909 | HubMed [ferragina2007]
  42. Grissa I, Vergnaud G, and Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007 May 23;8:172. DOI:10.1186/1471-2105-8-172 | PubMed ID:17521438 | HubMed [grissa2007]
  43. Shah JK, Garner HR, White MA, Shames DS, and Minna JD. sIR: siRNA Information Resource, a web-based tool for siRNA sequence design and analysis and an open access siRNA database. BMC Bioinformatics. 2007 May 31;8:178. DOI:10.1186/1471-2105-8-178 | PubMed ID:17540034 | HubMed [shah2007]
  44. Chaudhuri RR, Ren CP, Desmond L, Vincent GA, Silman NJ, Brehm JK, Elmore MJ, Hudson MJ, Forsman M, Isherwood KE, Gurycová D, Minton NP, Titball RW, Pallen MJ, and Vipond R. Genome sequencing shows that European isolates of Francisella tularensis subspecies tularensis are almost identical to US laboratory strain Schu S4. PLoS One. 2007 Apr 4;2(4):e352. DOI:10.1371/journal.pone.0000352 | PubMed ID:17406676 | HubMed [chaudhuri2007]
  45. Misra M and Schein CH. Flavitrack: an annotated database of flavivirus sequences. Bioinformatics. 2007 Oct 1;23(19):2645-7. DOI:10.1093/bioinformatics/btm383 | PubMed ID:17660525 | HubMed [misra2007]
  46. Burman C, Maqueira B, Coadwell J, and Evans PD. Eleven new putative aminergic G-protein coupled receptors from Amphioxus (Branchiostoma floridae): identification, sequence analysis and phylogenetic relationship. Invert Neurosci. 2007 Jun;7(2):87-98. DOI:10.1007/s10158-006-0041-z | PubMed ID:17225134 | HubMed [burman2007]
  47. Malhi RS, Sickler B, Lin D, Satkoski J, Tito RY, George D, Kanthaswamy S, and Smith DG. MamuSNP: a resource for Rhesus Macaque (Macaca mulatta) genomics. PLoS One. 2007 May 9;2(5):e438. DOI:10.1371/journal.pone.0000438 | PubMed ID:17487284 | HubMed [malhi2007]
  48. Mungall CJ, Emmert DB, and FlyBase Consortium. A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics. 2007 Jul 1;23(13):i337-46. DOI:10.1093/bioinformatics/btm189 | PubMed ID:17646315 | HubMed [mungall2007]
  49. Pporras-Alfaro A, Herrera J, Natvig DO, Sinsabaugh RL. Effect of long-term nitrogen fertilization on mycorrhizal fungi associated with a dominant grass in a semiarid grassland. Plant and Soil. 2007; 296(1-2): 65-75. doi:10.1007/s11104-007-9290-9. [porras-alfaro2007]
All Medline abstracts: PubMed | HubMed
  1. Roma G, Sardiello M, Cobellis G, Cruz P, Lago G, Sanges R, and Stupka E. The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones. Nucleic Acids Res. 2008 Jan;36(Database issue):D741-6. DOI:10.1093/nar/gkm825 | PubMed ID:17942430 | HubMed [roma2007]
  2. Wu J, Zhao F, Wang S, Deng G, Wang J, Bai J, Lu J, Qu J, and Bao Q. cTFbase: a database for comparative genomics of transcription factors in cyanobacteria. BMC Genomics. 2007 Apr 18;8:104. DOI:10.1186/1471-2164-8-104 | PubMed ID:17439663 | HubMed [wu2007]
  3. Tamaki S, Arakawa K, Kono N, and Tomita M. Restauro-G: a rapid genome re-annotation system for comparative genomics. Genomics Proteomics Bioinformatics. 2007 Feb;5(1):53-8. DOI:10.1016/S1672-0229(07)60014-X | PubMed ID:17572364 | HubMed [tamaki2007]
  4. Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, and Ruzzo WL. A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. PLoS Comput Biol. 2007 Jul;3(7):e126. DOI:10.1371/journal.pcbi.0030126 | PubMed ID:17616982 | HubMed [yao2007]
  5. Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, van den Elst H, Filippov DV, Blaser H, Raz E, Moens CB, Plasterk RH, Hannon GJ, Draper BW, and Ketting RF. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish. Cell. 2007 Apr 6;129(1):69-82. DOI:10.1016/j.cell.2007.03.026 | PubMed ID:17418787 | HubMed [houwing2007]
  6. Arnold AE, Henk DA, Eells RL, Lutzoni F, and Vilgalys R. Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia. 2007 Mar-Apr;99(2):185-206. PubMed ID:17682771 | HubMed [arnold2007]
  7. Hsiau TH, Diaconu C, Myers CA, Lee J, Cepko CL, and Corbo JC. The cis-regulatory logic of the mammalian photoreceptor transcriptional network. PLoS One. 2007 Jul 25;2(7):e643. DOI:10.1371/journal.pone.0000643 | PubMed ID:17653270 | HubMed [hsiau2007]
  8. Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, and Huttley GA. PyCogent: a toolkit for making sense from sequence. Genome Biol. 2007;8(8):R171. DOI:10.1186/gb-2007-8-8-r171 | PubMed ID:17708774 | HubMed [knight2007]
  9. Singh A, Olowoyeye A, Baenziger PH, Dantzer J, Kann MG, Radivojac P, Heiland R, and Mooney SD. MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res. 2008 Jan;36(Database issue):D815-9. DOI:10.1093/nar/gkm659 | PubMed ID:17827212 | HubMed [singh2007]
  10. Robb SM, Ross E, and Sánchez Alvarado A. SmedGD: the Schmidtea mediterranea genome database. Nucleic Acids Res. 2008 Jan;36(Database issue):D599-606. DOI:10.1093/nar/gkm684 | PubMed ID:17881371 | HubMed [robb2007]
  11. Gerrard DT and Meyer A. Positive selection and gene conversion in SPP120, a fertilization-related gene, during the East African cichlid fish radiation. Mol Biol Evol. 2007 Oct;24(10):2286-97. DOI:10.1093/molbev/msm159 | PubMed ID:17675335 | HubMed [gerrard2007]
  12. Rannikko K, Ortutay C, and Vihinen M. Immunity genes and their orthologs: a multi-species database. Int Immunol. 2007 Dec;19(12):1361-70. DOI:10.1093/intimm/dxm109 | PubMed ID:17965450 | HubMed [rannikko2007]
  13. Stajich JE, Dietrich FS, and Roy SW. Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biol. 2007;8(10):R223. DOI:10.1186/gb-2007-8-10-r223 | PubMed ID:17949488 | HubMed [stajich2007]
  14. Low WY, Ng HL, Morton CJ, Parker MW, Batterham P, and Robin C. Molecular evolution of glutathione S-transferases in the genus Drosophila. Genetics. 2007 Nov;177(3):1363-75. DOI:10.1534/genetics.107.075838 | PubMed ID:18039872 | HubMed [low2007]
  15. Levine MT, Holloway AK, Arshad U, and Begun DJ. Pervasive and largely lineage-specific adaptive protein evolution in the dosage compensation complex of Drosophila melanogaster. Genetics. 2007 Nov;177(3):1959-62. DOI:10.1534/genetics.107.079459 | PubMed ID:18039888 | HubMed [levine2007]
  16. Woolfe A, Goode DK, Cooke J, Callaway H, Smith S, Snell P, McEwen GK, and Elgar G. CONDOR: a database resource of developmentally associated conserved non-coding elements. BMC Dev Biol. 2007 Aug 30;7:100. DOI:10.1186/1471-213X-7-100 | PubMed ID:17760977 | HubMed [wolfe2007]
  17. Kamatani T and Yamamoto T. Comparison of codon usage and tRNAs in mitochondrial genomes of Candida species. Biosystems. 2007 Sep-Oct;90(2):362-70. DOI:10.1016/j.biosystems.2006.09.039 | PubMed ID:17123703 | HubMed [kamatani]
  18. Howes CG and Foster LJ. PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories. Proteome Sci. 2007 Jun 6;5:8. DOI:10.1186/1477-5956-5-8 | PubMed ID:17553161 | HubMed [howes2007]
  19. Tiwari A and Sekhar AK. Workflow based framework for life science informatics. Comput Biol Chem. 2007 Oct;31(5-6):305-19. DOI:10.1016/j.compbiolchem.2007.08.009 | PubMed ID:17931570 | HubMed [tiwari2007]
  20. Marcello L, Menon S, Ward P, Wilkes JM, Jones NG, Carrington M, and Barry JD. VSGdb: a database for trypanosome variant surface glycoproteins, a large and diverse family of coiled coil proteins. BMC Bioinformatics. 2007 May 2;8:143. DOI:10.1186/1471-2105-8-143 | PubMed ID:17474977 | HubMed [marcello2007]
  21. Rispe C, Legeai F, Gauthier JP, and Tagu D. Strong heterogeneity in nucleotidic composition and codon bias in the pea aphid (Acyrthosiphon pisum) shown by EST-based coding genome reconstruction. J Mol Evol. 2007 Oct;65(4):413-24. DOI:10.1007/s00239-007-9023-y | PubMed ID:17928936 | HubMed [rispe2007]
  22. Holloway AK and Begun DJ. Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans. PLoS One. 2007 Oct 31;2(10):e1113. DOI:10.1371/journal.pone.0001113 | PubMed ID:17971876 | HubMed [holloway2007]
  23. Yin H and Lin H. An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature. 2007 Nov 8;450(7167):304-8. DOI:10.1038/nature06263 | PubMed ID:17952056 | HubMed [yin2007]
  24. Giancarlo R, Siragusa A, Siragusa E, and Utro F. A basic analysis toolkit for biological sequences. Algorithms Mol Biol. 2007 Sep 18;2:10. DOI:10.1186/1748-7188-2-10 | PubMed ID:17877802 | HubMed [giancarol2007]
  25. Umylny B, Presting G, Efird JT, Klimovitsky BI, and Ward WS. Most human Alu and murine B1 repeats are unique. J Cell Biochem. 2007 Sep 1;102(1):110-21. DOI:10.1002/jcb.21278 | PubMed ID:17407136 | HubMed [umylny2007]
  26. Umylny B, Presting G, and Ward WS. Evidence of Alu and B1 expression in dbEST. Arch Androl. 2007 Jul-Aug;53(4):207-18. DOI:10.1080/01485010701426422 | PubMed ID:17852045 | HubMed [umylny2007]
  27. Yang J, Chen L, Sun L, Yu J, and Jin Q. VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D539-42. DOI:10.1093/nar/gkm951 | PubMed ID:17984080 | HubMed [yang2007]
  28. Huang Y, Lau SK, Woo PC, and Yuen KY. CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes. Nucleic Acids Res. 2008 Jan;36(Database issue):D504-11. DOI:10.1093/nar/gkm754 | PubMed ID:17913743 | HubMed [huang2007]
  29. Sturgill D, Zhang Y, Parisi M, and Oliver B. Demasculinization of X chromosomes in the Drosophila genus. Nature. 2007 Nov 8;450(7167):238-41. DOI:10.1038/nature06330 | PubMed ID:17994090 | HubMed [sturgill2007]
  30. Drieschner N, Kerschling S, Soller JT, Rippe V, Belge G, Bullerdiek J, and Nimzyk R. A domain of the thyroid adenoma associated gene (THADA) conserved in vertebrates becomes destroyed by chromosomal rearrangements observed in thyroid adenomas. Gene. 2007 Nov 15;403(1-2):110-7. DOI:10.1016/j.gene.2007.06.029 | PubMed ID:17889454 | HubMed [drieschner2007]
  31. Conte MG, Gaillard S, Lanau N, Rouard M, and Périn C. GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D991-8. DOI:10.1093/nar/gkm934 | PubMed ID:17986457 | HubMed [conte2007]
  32. Zimmer A, Lang D, Richardt S, Frank W, Reski R, and Rensing SA. Dating the early evolution of plants: detection and molecular clock analyses of orthologs. Mol Genet Genomics. 2007 Oct;278(4):393-402. DOI:10.1007/s00438-007-0257-6 | PubMed ID:17593393 | HubMed [zimmer2007]
  33. Koru G, El Emam K, Neisa A, and Umarji M. A survey of quality assurance practices in biomedical open source software projects. J Med Internet Res. 2007 May 7;9(2):e8. DOI:10.2196/jmir.9.2.e8 | PubMed ID:17513286 | HubMed [koru2007]
  34. Arvas M, Kivioja T, Mitchell A, Saloheimo M, Ussery D, Penttila M, and Oliver S. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. BMC Genomics. 2007 Sep 17;8:325. DOI:10.1186/1471-2164-8-325 | PubMed ID:17868481 | HubMed [arvas2007]
  35. Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, and Langley CH. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 2007 Nov 6;5(11):e310. DOI:10.1371/journal.pbio.0050310 | PubMed ID:17988176 | HubMed [begun2007]
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