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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. doi: 10.1016/j.cell.2010.09.001.


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. doi: 10.1186/1471-2105-11-481.


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. doi: 10.1371/journal.pbio.1000475.


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. doi: 10.1371/journal.pntd.0000729.


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. doi: 10.1093/bioinformatics/btq304. Epub 2010 Jul 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. doi: 10.1016/j.jmb.2010.05.012. Epub 2010 May 13.


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

Notredame C.

Curr Protoc Bioinformatics. 2010 Mar;Chapter 3:Unit 3.8.1-25. doi: 10.1002/0471250953.bi0308s29.


A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis.

Coll O, Villalba A, Bussotti G, Notredame C, Gebauer F.

Genes Dev. 2010 Jan 15;24(2):129-34. doi: 10.1101/gad.568610.


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

Kemena C, Notredame C.

Bioinformatics. 2009 Oct 1;25(19):2455-65. doi: 10.1093/bioinformatics/btp452. Epub 2009 Jul 30. Review.


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. doi: 10.1634/stemcells.2008-0696.


Segment-based multiple sequence alignment.

Rausch T, Emde AK, Weese D, Döring A, Notredame C, Reinert K.

Bioinformatics. 2008 Aug 15;24(16):i187-92. doi: 10.1093/bioinformatics/btn281.


R-Coffee: a web server for accurately aligning noncoding RNA sequences.

Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W10-3. doi: 10.1093/nar/gkn278. Epub 2008 May 15.


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

Notredame C, Suhre K.

Curr Protoc Bioinformatics. 2004 Feb;Chapter 3:Unit3.8. doi: 10.1002/0471250953.bi0308s04.


R-Coffee: a method for multiple alignment of non-coding RNA.

Wilm A, Higgins DG, Notredame C.

Nucleic Acids Res. 2008 May;36(9):e52. doi: 10.1093/nar/gkn174. Epub 2008 Apr 17.


Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time.

Retelska D, Beaudoing E, Notredame C, Jongeneel CV, Bucher P.

BMC Genomics. 2007 Oct 31;8:398.


Recent evolutions of multiple sequence alignment algorithms.

Notredame C.

PLoS Comput Biol. 2007 Aug;3(8):e123. Review. No abstract available.


The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. Epub 2007 May 25.


APDB: a web server to evaluate the accuracy of sequence alignments using structural information.

Armougom F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C.

Bioinformatics. 2006 Oct 1;22(19):2439-40.


The iRMSD: a local measure of sequence alignment accuracy using structural information.

Armougom F, Moretti S, Keduas V, Notredame C.

Bioinformatics. 2006 Jul 15;22(14):e35-9.


Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.

Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8.

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