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    Results: 17

    1.

    A user-friendly web portal for T-Coffee on supercomputers.

    Rius J, Cores F, Solsona F, van Hemert JI, Koetsier J, Notredame C.

    BMC Bioinformatics. 2011 May 12;12:150.

    PMID:
    21569428
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

    Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C.

    Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7. Epub 2011 May 9.

    PMID:
    21558174
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    BlastR--fast and accurate database searches for non-coding RNAs.

    Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C.

    Nucleic Acids Res. 2011 Sep 1;39(16):6886-95. Epub 2011 May 30.

    PMID:
    21624887
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

    Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C.

    Nucleic Acids Res. 2011 Jul;39(Web Server issue):W13-7. Epub 2011 May 9.

    PMID:
    21558174
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite proliferation and viability.

    Yau WL, Blisnick T, Taly JF, Helmer-Citterich M, Schiene-Fischer C, Leclercq O, Li J, Schmidt-Arras D, Morales MA, Notredame C, Romo D, Bastin P, Späth GF.

    PLoS Negl Trop Dis. 2010 Jun 29;4(6):e729.

    PMID:
    20614016
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors.

    Magis C, Stricher F, van der Sloot AM, Serrano L, Notredame C.

    J Mol Biol. 2010 Jul 16;400(3):605-17. Epub 2010 May 13.

    PMID:
    20471393
    [PubMed - indexed for MEDLINE]
    7.

    Computing multiple sequence/structure alignments with the T-coffee package.

    Notredame C.

    Curr Protoc Bioinformatics. 2010 Mar;Chapter 3:Unit 3.8.1-25.

    PMID:
    20205190
    [PubMed - indexed for MEDLINE]
    8.

    Predicting phenotypic traits of prokaryotes from protein domain frequencies.

    Lingner T, Mühlhausen S, Gabaldón T, Notredame C, Meinicke P.

    BMC Bioinformatics. 2010 Sep 24;11:481.

    PMID:
    20868492
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    Long noncoding RNAs with enhancer-like function in human cells.

    Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R.

    Cell. 2010 Oct 1;143(1):46-58.

    PMID:
    20887892
    [PubMed - indexed for MEDLINE]
    10.

    Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud.

    Di Tommaso P, Orobitg M, Guirado F, Cores F, Espinosa T, Notredame C.

    Bioinformatics. 2010 Aug 1;26(15):1903-4. Epub 2010 Jul 6.

    PMID:
    20605929
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

    Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.

    PLoS Biol. 2010 Sep 7;8(9). pii: e1000475.

    PMID:
    20838655
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    12.

    Predicting phenotypic traits of prokaryotes from protein domain frequencies.

    Lingner T, Mühlhausen S, Gabaldón T, Notredame C, Meinicke P.

    BMC Bioinformatics. 2010 Sep 24;11:481.

    PMID:
    20868492
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    Long noncoding RNAs with enhancer-like function in human cells.

    Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R.

    Cell. 2010 Oct 1;143(1):46-58.

    PMID:
    20887892
    [PubMed - indexed for MEDLINE]
    14.

    Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions.

    Varas F, Stadtfeld M, de Andres-Aguayo L, Maherali N, di Tullio A, Pantano L, Notredame C, Hochedlinger K, Graf T.

    Stem Cells. 2009 Feb;27(2):300-6.

    PMID:
    19008347
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Upcoming challenges for multiple sequence alignment methods in the high-throughput era.

    Kemena C, Notredame C.

    Bioinformatics. 2009 Oct 1;25(19):2455-65. Epub 2009 Jul 30. Review.

    PMID:
    19648142
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    16.

    Upcoming challenges for multiple sequence alignment methods in the high-throughput era.

    Kemena C, Notredame C.

    Bioinformatics. 2009 Oct 1;25(19):2455-65. Epub 2009 Jul 30. Review.

    PMID:
    19648142
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    17.

    Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions.

    Varas F, Stadtfeld M, de Andres-Aguayo L, Maherali N, di Tullio A, Pantano L, Notredame C, Hochedlinger K, Graf T.

    Stem Cells. 2009 Feb;27(2):300-6.

    PMID:
    19008347
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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