BioPerl publications/2008

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  1. Pedroso I, Rivera G, Lazo F, Chacón M, Ossandón F, Veloso FA, and Holmes DS. AlterORF: a database of alternate open reading frames. Nucleic Acids Res. 2008 Jan;36(Database issue):D517-8. DOI:10.1093/nar/gkm886 | PubMed ID:18096612 | HubMed [pedroso2008]
  2. Wang X and El Naqa IM. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics. 2008 Feb 1;24(3):325-32. DOI:10.1093/bioinformatics/btm595 | PubMed ID:18048393 | HubMed [wang2008]
  3. Gront D and Kolinski A. Utility library for structural bioinformatics. Bioinformatics. 2008 Feb 15;24(4):584-5. DOI:10.1093/bioinformatics/btm627 | PubMed ID:18227118 | HubMed [gront2008]
  4. Mangone M, Macmenamin P, Zegar C, Piano F, and Gunsalus KC. a platform for 3'UTR biology in C. elegans. Nucleic Acids Res. 2008 Jan;36(Database issue):D57-62. DOI:10.1093/nar/gkm946 | PubMed ID:17986455 | HubMed [mangone2008]
  5. Pettersson E, Zajac P, Ståhl PL, Jacobsson JA, Fredriksson R, Marcus C, Schiöth HB, Lundeberg J, and Ahmadian A. Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads. Hum Mutat. 2008 Feb;29(2):323-9. DOI:10.1002/humu.20655 | PubMed ID:17994569 | HubMed [pettersson2008]
  6. Cutter AD. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol Biol Evol. 2008 Apr;25(4):778-86. DOI:10.1093/molbev/msn024 | PubMed ID:18234705 | HubMed [cutter2008]
  7. Salgado D, Gimenez G, Coulier F, and Marcelle C. COMPARE, a multi-organism system for cross-species data comparison and transfer of information. Bioinformatics. 2008 Feb 1;24(3):447-9. DOI:10.1093/bioinformatics/btm599 | PubMed ID:18056065 | HubMed [salgado2008]
  8. Antezana E, Egaña M, De Baets B, Kuiper M, and Mironov V. ONTO-PERL: an API for supporting the development and analysis of bio-ontologies. Bioinformatics. 2008 Mar 15;24(6):885-7. DOI:10.1093/bioinformatics/btn042 | PubMed ID:18245124 | HubMed [antezana2008]
  9. Paux E, Legeai F, Guilhot N, Adam-Blondon AF, Alaux M, Salse J, Sourdille P, Leroy P, and Feuillet C. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct Integr Genomics. 2008 Feb;8(1):29-32. DOI:10.1007/s10142-007-0068-1 | PubMed ID:18038165 | HubMed [paux2008]
  10. Paux E, Legeai F, Guilhot N, Adam-Blondon AF, Alaux M, Salse J, Sourdille P, Leroy P, and Feuillet C. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis. Funct Integr Genomics. 2008 Feb;8(1):29-32. DOI:10.1007/s10142-007-0068-1 | PubMed ID:18038165 | HubMed [paux2008]
  11. Romano P. Automation of in-silico data analysis processes through workflow management systems. Brief Bioinform. 2008 Jan;9(1):57-68. DOI:10.1093/bib/bbm056 | PubMed ID:18056132 | HubMed [romano2008]
  12. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, and Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008 Jan;18(1):188-96. DOI:10.1101/gr.6743907 | PubMed ID:18025269 | HubMed [cantarel2008]
  13. Lechat P, Hummel L, Rousseau S, and Moszer I. GenoList: an integrated environment for comparative analysis of microbial genomes. Nucleic Acids Res. 2008 Jan;36(Database issue):D469-74. DOI:10.1093/nar/gkm1042 | PubMed ID:18032431 | HubMed [lechat2008]
  14. Jabado OJ, Liu Y, Conlan S, Quan PL, Hegyi H, Lussier Y, Briese T, Palacios G, and Lipkin WI. Comprehensive viral oligonucleotide probe design using conserved protein regions. Nucleic Acids Res. 2008 Jan;36(1):e3. DOI:10.1093/nar/gkm1106 | PubMed ID:18079152 | HubMed [jabado2008]
  15. 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 [conte2008]
  16. Wall PK, Leebens-Mack J, Müller KF, Field D, Altman NS, and dePamphilis CW. PlantTribes: a gene and gene family resource for comparative genomics in plants. Nucleic Acids Res. 2008 Jan;36(Database issue):D970-6. DOI:10.1093/nar/gkm972 | PubMed ID:18073194 | HubMed [wall2008]
  17. Dávila AM, Mendes PN, Wagner G, Tschoeke DA, Cuadrat RR, Liberman F, Matos L, Satake T, Ocaña KA, Triana O, Cruz SM, Jucá HC, Cury JC, Silva FN, Geronimo GA, Ruiz M, Ruback E, Silva FP Jr, Probst CM, Grisard EC, Krieger MA, Goldenberg S, Cavalcanti MC, Moraes MO, Campos ML, and Mattoso M. ProtozoaDB: dynamic visualization and exploration of protozoan genomes. Nucleic Acids Res. 2008 Jan;36(Database issue):D547-52. DOI:10.1093/nar/gkm820 | PubMed ID:17981844 | HubMed [davila2008]
  18. Wu J, Wang S, Bai J, Shi L, Li D, Xu Z, Niu Y, Lu J, and Bao Q. ArchaeaTF: an integrated database of putative transcription factors in Archaea. Genomics. 2008 Jan;91(1):102-7. DOI:10.1016/j.ygeno.2007.09.007 | PubMed ID:18035520 | HubMed [wu2008]
  19. Sevin EW and Barloy-Hubler F. RASTA-Bacteria: a web-based tool for identifying toxin-antitoxin loci in prokaryotes. Genome Biol. 2007;8(8):R155. DOI:10.1186/gb-2007-8-8-r155 | PubMed ID:17678530 | HubMed [sevin2008]
  20. Christley S, Lobo NF, and Madey G. Multiple organism algorithm for finding ultraconserved elements. BMC Bioinformatics. 2008 Jan 11;9:15. DOI:10.1186/1471-2105-9-15 | PubMed ID:18186941 | HubMed [christley2008]
  21. Döring A, Weese D, Rausch T, and Reinert K. SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics. 2008 Jan 9;9:11. DOI:10.1186/1471-2105-9-11 | PubMed ID:18184432 | HubMed [doring2008]
  22. Andersen MC, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, and Odeberg J. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol. 2008 Jan;4(1):e5. DOI:10.1371/journal.pcbi.0040005 | PubMed ID:18208319 | HubMed [anderson2008]
  23. Cantrell MA, Scott L, Brown CJ, Martinez AR, and Wichman HA. Loss of LINE-1 activity in the megabats. Genetics. 2008 Jan;178(1):393-404. DOI:10.1534/genetics.107.080275 | PubMed ID:18202382 | HubMed [cantrell2008]
  24. Palacios G, Druce J, Du L, Tran T, Birch C, Briese T, Conlan S, Quan PL, Hui J, Marshall J, Simons JF, Egholm M, Paddock CD, Shieh WJ, Goldsmith CS, Zaki SR, Catton M, and Lipkin WI. A new arenavirus in a cluster of fatal transplant-associated diseases. N Engl J Med. 2008 Mar 6;358(10):991-8. DOI:10.1056/NEJMoa073785 | PubMed ID:18256387 | HubMed [palacios2008]
  25. Forment J, Gilabert F, Robles A, Conejero V, Nuez F, and Blanca JM. EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration. BMC Bioinformatics. 2008 Jan 7;9:5. DOI:10.1186/1471-2105-9-5 | PubMed ID:18179701 | HubMed [forment2008]
  26. Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, and Ast G. Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res. 2008 Jan;18(1):88-103. DOI:10.1101/gr.6818908 | PubMed ID:18032728 | HubMed [schwartz2008]
  27. Duret L, Cohen J, Jubin C, Dessen P, Goût JF, Mousset S, Aury JM, Jaillon O, Noël B, Arnaiz O, Bétermier M, Wincker P, Meyer E, and Sperling L. Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline. Genome Res. 2008 Apr;18(4):585-96. DOI:10.1101/gr.074534.107 | PubMed ID:18256234 | HubMed [duret2008]
  28. Sipos B, Somogyi K, Andó I, and Pénzes Z. T2prhd: a tool to study the patterns of repeat evolution. BMC Bioinformatics. 2008 Jan 18;9:27. DOI:10.1186/1471-2105-9-27 | PubMed ID:18205906 | HubMed [sipos2008]
  29. Schmid R and Blaxter ML. annot8r: GO, EC and KEGG annotation of EST datasets. BMC Bioinformatics. 2008 Apr 9;9:180. DOI:10.1186/1471-2105-9-180 | PubMed ID:18400082 | HubMed [schmid2008]
  30. Struckmann S, Araúzo-Bravo MJ, Schöler HR, Reinbold RA, and Fuellen G. ReXSpecies--a tool for the analysis of the evolution of gene regulation across species. BMC Evol Biol. 2008 Apr 14;8:111. DOI:10.1186/1471-2148-8-111 | PubMed ID:18410675 | HubMed [struckmann2008]
  31. Bekaert M and Teeling EC. UniPrime: a workflow-based platform for improved universal primer design. Nucleic Acids Res. 2008 Jun;36(10):e56. DOI:10.1093/nar/gkn191 | PubMed ID:18424794 | HubMed [bekeart2008]
  32. Gruber AR, Lorenz R, Bernhart SH, Neuböck R, and Hofacker IL. The Vienna RNA websuite. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W70-4. DOI:10.1093/nar/gkn188 | PubMed ID:18424795 | HubMed [gruber2008]
  33. Baker LE and Baker EJ. Reuniting families: an online database to aid in the identification of undocumented immigrant remains. J Forensic Sci. 2008 Jan;53(1):50-3. DOI:10.1111/j.1556-4029.2007.00612.x | PubMed ID:18279239 | HubMed [baker2008]
  34. Bekaert M, Ivanov IP, Atkins JF, and Baranov PV. Ornithine decarboxylase antizyme finder (OAF): fast and reliable detection of antizymes with frameshifts in mRNAs. BMC Bioinformatics. 2008 Apr 2;9:178. DOI:10.1186/1471-2105-9-178 | PubMed ID:18384676 | HubMed [bekaert2008]
  35. Timmermans MJ, Roelofs D, Mariën J, and van Straalen NM. Revealing pancrustacean relationships: phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers. BMC Evol Biol. 2008 Mar 12;8:83. DOI:10.1186/1471-2148-8-83 | PubMed ID:18366624 | HubMed [timmermans2008]
  36. Tikole S and Sankararamakrishnan R. Prediction of translation initiation sites in human mRNA sequences with AUG start codon in weak Kozak context: A neural network approach. Biochem Biophys Res Commun. 2008 May 16;369(4):1166-8. DOI:10.1016/j.bbrc.2008.03.008 | PubMed ID:18342624 | HubMed [tikole2008]
  37. Cai JJ. PGEToolbox: A Matlab toolbox for population genetics and evolution. J Hered. 2008 Jul-Aug;99(4):438-40. DOI:10.1093/jhered/esm127 | PubMed ID:18310616 | HubMed [cai2008]
  38. Wang X. miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA. 2008 Jun;14(6):1012-7. DOI:10.1261/rna.965408 | PubMed ID:18426918 | HubMed [wang_mirRDB2008]
  39. Song H, Sandie R, Wang Y, Andrade-Navarro MA, and Niederweis M. Identification of outer membrane proteins of Mycobacterium tuberculosis. Tuberculosis (Edinb). 2008 Nov;88(6):526-44. DOI:10.1016/ | PubMed ID:18439872 | HubMed [song2008]
  40. Smith TD and Cotton RG. VariVis: a visualisation toolkit for variation databases. BMC Bioinformatics. 2008 Apr 23;9:206. DOI:10.1186/1471-2105-9-206 | PubMed ID:18430251 | HubMed [smith2008]
  41. Siepen JA, Belhajjame K, Selley JN, Embury SM, Paton NW, Goble CA, Oliver SG, Stevens R, Zamboulis L, Martin N, Poulovassillis A, Jones P, Côté R, Hermjakob H, Pentony MM, Jones DT, Orengo CA, and Hubbard SJ. ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W485-90. DOI:10.1093/nar/gkn196 | PubMed ID:18440977 | HubMed [siepen2008]
  42. Hai Y, Cao W, Liu G, Hong SP, Elela SA, Klinck R, Chu J, and Xie J. A G-tract element in apoptotic agents-induced alternative splicing. Nucleic Acids Res. 2008 Jun;36(10):3320-31. DOI:10.1093/nar/gkn207 | PubMed ID:18440980 | HubMed [hai2008]
  43. Garcia-Boronat M, Diez-Rivero CM, Reinherz EL, and Reche PA. PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W35-41. DOI:10.1093/nar/gkn211 | PubMed ID:18442995 | HubMed [garciaboronat2008]
  44. Brandt BW, Heringa J, and Leunissen JA. SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W255-9. DOI:10.1093/nar/gkn237 | PubMed ID:18463137 | HubMed [brandt2008]
  45. Saunders NF and Kobe B. The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W286-90. DOI:10.1093/nar/gkn279 | PubMed ID:18477637 | HubMed [saunders2008]
  46. Cardona G, Llabrés M, Rosselló F, and Valiente G. A distance metric for a class of tree-sibling phylogenetic networks. Bioinformatics. 2008 Jul 1;24(13):1481-8. DOI:10.1093/bioinformatics/btn231 | PubMed ID:18477576 | HubMed [cardona2008]
  47. Menda N, Buels RM, Tecle I, and Mueller LA. A community-based annotation framework for linking solanaceae genomes with phenomes. Plant Physiol. 2008 Aug;147(4):1788-99. DOI:10.1104/pp.108.119560 | PubMed ID:18539779 | HubMed [menda2008]
  48. Turner LM, Chuong EB, and Hoekstra HE. Comparative analysis of testis protein evolution in rodents. Genetics. 2008 Aug;179(4):2075-89. DOI:10.1534/genetics.107.085902 | PubMed ID:18689890 | HubMed [turner2008]
  49. Grosso AR, Gomes AQ, Barbosa-Morais NL, Caldeira S, Thorne NP, Grech G, von Lindern M, and Carmo-Fonseca M. Tissue-specific splicing factor gene expression signatures. Nucleic Acids Res. 2008 Sep;36(15):4823-32. DOI:10.1093/nar/gkn463 | PubMed ID:18653532 | HubMed [grosso2008]
  50. Hraber P, Kuiken C, Waugh M, Geer S, Bruno WJ, and Leitner T. Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index. J Gen Virol. 2008 Sep;89(Pt 9):2098-107. DOI:10.1099/vir.0.83657-0 | PubMed ID:18753218 | HubMed [hraber2008]
  51. Gollapudi R, Revanna KV, Hemmerich C, Schaack S, and Dong Q. BOV--a web-based BLAST output visualization tool. BMC Genomics. 2008 Sep 15;9:414. DOI:10.1186/1471-2164-9-414 | PubMed ID:18793422 | HubMed [gollapudi2008]
  52. Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, and Schreiber MJ. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008 Sep 15;24(18):2096-7. DOI:10.1093/bioinformatics/btn397 | PubMed ID:18689808 | HubMed [holland2008]
  53. Zhang Z, Cheung KH, and Townsend JP. Bringing Web 2.0 to bioinformatics. Brief Bioinform. 2009 Jan;10(1):1-10. DOI:10.1093/bib/bbn041 | PubMed ID:18842678 | HubMed [zhang2008]
  54. Pirooznia M, Perkins EJ, and Deng Y. Batch Blast Extractor: an automated blastx parser application. BMC Genomics. 2008 Sep 16;9 Suppl 2:S10. DOI:10.1186/1471-2164-9-S2-S10 | PubMed ID:18831775 | HubMed [pirooznia2008]
  55. Ponzielli R, Boutros PC, Katz S, Stojanova A, Hanley AP, Khosravi F, Bros C, Jurisica I, and Penn LZ. Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res. 2008 Dec;36(21):e144. DOI:10.1093/nar/gkn735 | PubMed ID:18940864 | HubMed [ponzielli2008]
  56. Belshaw R, de Oliveira T, Markowitz S, and Rambaut A. The RNA virus database. Nucleic Acids Res. 2009 Jan;37(Database issue):D431-5. DOI:10.1093/nar/gkn729 | PubMed ID:18948277 | HubMed [belshaw2008]
  57. Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, and Brookes AJ. HGVbaseG2P: a central genetic association database. Nucleic Acids Res. 2009 Jan;37(Database issue):D797-802. DOI:10.1093/nar/gkn748 | PubMed ID:18948288 | HubMed [thorisson2008]
  58. Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, and Wasserman WW. The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. Nucleic Acids Res. 2009 Jan;37(Database issue):D54-60. DOI:10.1093/nar/gkn783 | PubMed ID:18971253 | HubMed [portalescasamar2008]
  59. Page MJ and Di Cera E. Evolution of peptidase diversity. J Biol Chem. 2008 Oct 31;283(44):30010-4. DOI:10.1074/jbc.M804650200 | PubMed ID:18768474 | HubMed [page2008]
  60. Somogyi K, Sipos B, Pénzes Z, Kurucz E, Zsámboki J, Hultmark D, and Andó I. Evolution of genes and repeats in the Nimrod superfamily. Mol Biol Evol. 2008 Nov;25(11):2337-47. DOI:10.1093/molbev/msn180 | PubMed ID:18703524 | HubMed [somogyi2008]
  61. Soria-Carrasco V and Castresana J. Estimation of phylogenetic inconsistencies in the three domains of life. Mol Biol Evol. 2008 Nov;25(11):2319-29. DOI:10.1093/molbev/msn176 | PubMed ID:18701430 | HubMed [soriacarrasco2008]
  62. Linheiro RS and Bergman CM. Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element. Nucleic Acids Res. 2008 Nov;36(19):6199-208. DOI:10.1093/nar/gkn563 | PubMed ID:18829720 | HubMed [linheiro2008]
  63. Li Y, Zhu Y, Liu Y, Shu Y, Meng F, Lu Y, Bai X, Liu B, and Guo D. Genome-wide identification of osmotic stress response gene in Arabidopsis thaliana. Genomics. 2008 Dec;92(6):488-93. DOI:10.1016/j.ygeno.2008.08.011 | PubMed ID:18804526 | HubMed [li2008]
  64. Ortutay C and Vihinen M. PseudoGeneQuest - service for identification of different pseudogene types in the human genome. BMC Bioinformatics. 2008 Jul 2;9:299. DOI:10.1186/1471-2105-9-299 | PubMed ID:18597685 | HubMed [ortutay2008]
  65. Maselli V, Di Bernardo D, and Banfi S. CoGemiR: a comparative genomics microRNA database. BMC Genomics. 2008 Oct 6;9:457. DOI:10.1186/1471-2164-9-457 | PubMed ID:18837977 | HubMed [maselli2008]
  66. ISBN:1-59593-753-7 [daCruz2008]
  67. Halling-Brown M and Shepherd AJ. Constructing computational pipelines. Methods Mol Biol. 2008;453:451-70. DOI:10.1007/978-1-60327-429-6_24 | PubMed ID:18712319 | HubMed [hallingbrown2008]
All Medline abstracts: PubMed | HubMed
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