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    Results: 1 to 20 of 101

    1.

    A computational approach for identifying pseudogenes in the ENCODE regions.

    Zheng D, Gerstein MB.

    Genome Biol. 2006;7 Suppl 1:S13.1-10. Epub 2006 Aug 7.

    PMID:
    16925835
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    Automatic annotation of eukaryotic genes, pseudogenes and promoters.

    Solovyev V, Kosarev P, Seledsov I, Vorobyev D.

    Genome Biol. 2006;7 Suppl 1:S10.1-12. Epub 2006 Aug 7.

    PMID:
    16925832
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    GENCODE: producing a reference annotation for ENCODE.

    Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.

    Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.

    PMID:
    16925838
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    Systematic identification of pseudogenes through whole genome expression evidence profiling.

    Yao A, Charlab R, Li P.

    Nucleic Acids Res. 2006;34(16):4477-85. Epub 2006 Aug 31.

    PMID:
    16945953
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    PseudoPipe: an automated pseudogene identification pipeline.

    Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M.

    Bioinformatics. 2006 Jun 15;22(12):1437-9. Epub 2006 Mar 30.

    PMID:
    16574694
    [PubMed - indexed for MEDLINE]
    Free Article
    6.

    AceView: a comprehensive cDNA-supported gene and transcripts annotation.

    Thierry-Mieg D, Thierry-Mieg J.

    Genome Biol. 2006;7 Suppl 1:S12.1-14. Epub 2006 Aug 7.

    PMID:
    16925834
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

    Arumugam M, Wei C, Brown RH, Brent MR.

    Genome Biol. 2006;7 Suppl 1:S5.1-10. Epub 2006 Aug 7.

    PMID:
    16925839
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    EGASP: the human ENCODE Genome Annotation Assessment Project.

    Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.

    Genome Biol. 2006;7 Suppl 1:S2.1-31. Epub 2006 Aug 7. Review.

    PMID:
    16925836
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome.

    Zhang Z, Harrison PM, Liu Y, Gerstein M.

    Genome Res. 2003 Dec;13(12):2541-58.

    PMID:
    14656962
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    10.

    Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

    Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB.

    Genome Res. 2007 Jun;17(6):839-51.

    PMID:
    17568002
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Segmental duplications in the human genome reveal details of pseudogene formation.

    Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB.

    Nucleic Acids Res. 2010 Nov;38(20):6997-7007. Epub 2010 Jul 8.

    PMID:
    20615899
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    12.

    Integrated pseudogene annotation for human chromosome 22: evidence for transcription.

    Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M.

    J Mol Biol. 2005 May 27;349(1):27-45. Epub 2005 Apr 2.

    PMID:
    15876366
    [PubMed - indexed for MEDLINE]
    13.

    A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case.

    Yu GX, Snyder EE, Boyle SM, Crasta OR, Czar M, Mane SP, Purkayastha A, Sobral B, Setubal JC.

    Nucleic Acids Res. 2007;35(12):3953-62. Epub 2007 Jun 6.

    PMID:
    17553834
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    A genome-wide survey of human pseudogenes.

    Torrents D, Suyama M, Zdobnov E, Bork P.

    Genome Res. 2003 Dec;13(12):2559-67.

    PMID:
    14656963
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

    Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J.

    Genome Res. 2008 Feb;18(2):242-51. Epub 2007 Dec 20.

    PMID:
    18096747
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    16.

    JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

    Latorre M, Silva H, Saba J, Guziolowski C, Vizoso P, Martinez V, Maldonado J, Morales A, Caroca R, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Retamales J, Meisel LA.

    BMC Bioinformatics. 2006 Nov 23;7:513.

    PMID:
    17123449
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    17.

    Computation and analysis of genomic multi-sequence alignments.

    Blanchette M.

    Annu Rev Genomics Hum Genet. 2007;8:193-213. Review.

    PMID:
    17489682
    [PubMed - indexed for MEDLINE]
    18.

    ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.

    van den Berg BH, Konieczka JH, McCarthy FM, Burgess SC.

    BMC Bioinformatics. 2009 Jan 23;10:30.

    PMID:
    19166590
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    19.

    Genome-wide identification of pseudogenes capable of disease-causing gene conversion.

    Bischof JM, Chiang AP, Scheetz TE, Stone EM, Casavant TL, Sheffield VC, Braun TA.

    Hum Mutat. 2006 Jun;27(6):545-52.

    PMID:
    16671097
    [PubMed - indexed for MEDLINE]
    20.

    Pseudofam: the pseudogene families database.

    Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB.

    Nucleic Acids Res. 2009 Jan;37(Database issue):D738-43. Epub 2008 Oct 28.

    PMID:
    18957444
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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