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Results: 12

1.

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

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

Nucleic Acids Res. 2014 Nov 17. pii: gku1142. [Epub ahead of print]

PMID:
25404137
[PubMed - as supplied by publisher]
Free Article
2.

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.

PMID:
24366737
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
24170398
[PubMed - indexed for MEDLINE]
4.

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.

PMID:
24146760
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22536955
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
22194979
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
22039207
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
21979275
[PubMed - indexed for MEDLINE]
9.

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.

PMID:
21558174
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
20614016
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
18179702
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
16164759
[PubMed - indexed for MEDLINE]
Free PMC Article
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