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Items: 12


SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos.

Cicin-Sain D, Pulido AH, Crombach A, Wotton KR, Jiménez-Guri E, Taly JF, Roma G, Jaeger J.

Nucleic Acids Res. 2015 Jan;43(Database issue):D751-5. doi: 10.1093/nar/gku1142. Epub 2014 Nov 17.


Pharmacological assessment defines Leishmania donovani casein kinase 1 as a drug target and reveals important functions in parasite viability and intracellular infection.

Rachidi N, Taly JF, Durieu E, Leclercq O, Aulner N, Prina E, Pescher P, Notredame C, Meijer L, Späth GF.

Antimicrob Agents Chemother. 2014;58(3):1501-15. doi: 10.1128/AAC.02022-13. Epub 2013 Dec 23.


T-Coffee: Tree-based consistency objective function for alignment evaluation.

Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C.

Methods Mol Biol. 2014;1079:117-29. doi: 10.1007/978-1-62703-646-7_7.


Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations.

Chang JM, Taly JF, Erb I, Sung TY, Hsu WL, Tang CY, Notredame C, Su EC.

PLoS One. 2013 Oct 11;8(10):e75542. doi: 10.1371/journal.pone.0075542. eCollection 2013.


Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee.

Chang JM, Di Tommaso P, Taly JF, Notredame C.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S1. doi: 10.1186/1471-2105-13-S4-S1.


Large-scale screening of a targeted Enterococcus faecalis mutant library identifies envelope fitness factors.

Rigottier-Gois L, Alberti A, Houel A, Taly JF, Palcy P, Manson J, Pinto D, Matos RC, Carrilero L, Montero N, Tariq M, Karsens H, Repp C, Kropec A, Budin-Verneuil A, Benachour A, Sauvageot N, Bizzini A, Gilmore MS, Bessières P, Kok J, Huebner J, Lopes F, Gonzalez-Zorn B, Hartke A, Serror P.

PLoS One. 2011;6(12):e29023. doi: 10.1371/journal.pone.0029023. Epub 2011 Dec 15.


STRIKE: evaluation of protein MSAs using a single 3D structure.

Kemena C, Taly JF, Kleinjung J, Notredame C.

Bioinformatics. 2011 Dec 15;27(24):3385-91. doi: 10.1093/bioinformatics/btr587. Epub 2011 Oct 28.


Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.

Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C.

Nat Protoc. 2011 Nov;6(11):1669-82. doi: 10.1038/nprot.2011.393.


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. doi: 10.1093/nar/gkr245. Epub 2011 May 9.


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.


Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

Taly JF, Marin A, Gibrat JF.

BMC Bioinformatics. 2008 Jan 7;9:6. doi: 10.1186/1471-2105-9-6.


Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.

Martin J, Letellier G, Marin A, Taly JF, de Brevern AG, Gibrat JF.

BMC Struct Biol. 2005 Sep 15;5:17.

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