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Results: 1 to 20 of 69

1.

Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection.

Ghouila A, Florent I, Guerfali FZ, Terrapon N, Laouini D, Yahia SB, Gascuel O, Bréhélin L.

PLoS One. 2014 Jun 5;9(6):e95275. doi: 10.1371/journal.pone.0095275. eCollection 2014.

PMID:
24901648
[PubMed - in process]
Free PMC Article
2.

Predicting the ancestral character changes in a tree is typically easier than predicting the root state.

Gascuel O, Steel M.

Syst Biol. 2014 May;63(3):421-35. doi: 10.1093/sysbio/syu010. Epub 2014 Feb 21.

PMID:
24562915
[PubMed - indexed for MEDLINE]
3.

Deep conservation of human protein tandem repeats within the eukaryotes.

Schaper E, Gascuel O, Anisimova M.

Mol Biol Evol. 2014 May;31(5):1132-48. doi: 10.1093/molbev/msu062. Epub 2014 Feb 3.

PMID:
24497029
[PubMed - in process]
Free PMC Article
4.

Sexually-transmitted/founder HIV-1 cannot be directly predicted from plasma or PBMC-derived viral quasispecies in the transmitting partner.

Frange P, Meyer L, Jung M, Goujard C, Zucman D, Abel S, Hochedez P, Gousset M, Gascuel O, Rouzioux C, Chaix ML; ANRS PRIMO Cohort Study Group.

PLoS One. 2013 Jul 9;8(7):e69144. doi: 10.1371/journal.pone.0069144. Print 2013.

PMID:
23874894
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The behavior of admixed populations in neighbor-joining inference of population trees.

Kopelman NM, Stone L, Gascuel O, Rosenberg NA.

Pac Symp Biocomput. 2013:273-84.

PMID:
23424132
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Searching for virus phylotypes.

Chevenet F, Jung M, Peeters M, de Oliveira T, Gascuel O.

Bioinformatics. 2013 Mar 1;29(5):561-70. doi: 10.1093/bioinformatics/btt010. Epub 2013 Jan 17.

PMID:
23329414
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Computational discovery of regulatory elements in a continuous expression space.

Lajoie M, Gascuel O, Lefort V, Bréhélin L.

Genome Biol. 2012 Nov 27;13(11):R109. doi: 10.1186/gb-2012-13-11-r109.

PMID:
23186104
[PubMed - in process]
Free PMC Article
8.

Combinatorics of distance-based tree inference.

Pardi F, Gascuel O.

Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16443-8. doi: 10.1073/pnas.1118368109. Epub 2012 Sep 25.

PMID:
23012403
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum.

Terrapon N, Gascuel O, Maréchal E, Bréhélin L.

BMC Bioinformatics. 2012 May 1;13:67. doi: 10.1186/1471-2105-13-67.

PMID:
22548871
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Modeling protein evolution with several amino acid replacement matrices depending on site rates.

Le SQ, Dang CC, Gascuel O.

Mol Biol Evol. 2012 Oct;29(10):2921-36. Epub 2012 Apr 6.

PMID:
22491036
[PubMed - indexed for MEDLINE]
Free Article
11.

The origin and evolutionary history of HIV-1 subtype C in Senegal.

Jung M, Leye N, Vidal N, Fargette D, Diop H, Toure Kane C, Gascuel O, Peeters M.

PLoS One. 2012;7(3):e33579. doi: 10.1371/journal.pone.0033579. Epub 2012 Mar 28.

PMID:
22470456
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Branch lengths on birth-death trees and the expected loss of phylogenetic diversity.

Mooers A, Gascuel O, Stadler T, Li H, Steel M.

Syst Biol. 2012 Mar;61(2):195-203. doi: 10.1093/sysbio/syr090. Epub 2011 Aug 24.

PMID:
21865336
[PubMed - indexed for MEDLINE]
13.

ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.

Dang CC, Lefort V, Le VS, Le QS, Gascuel O.

Bioinformatics. 2011 Oct 1;27(19):2758-60. doi: 10.1093/bioinformatics/btr435. Epub 2011 Jul 26.

PMID:
21791535
[PubMed - indexed for MEDLINE]
Free Article
14.

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes.

Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O.

Syst Biol. 2011 Oct;60(5):685-99. doi: 10.1093/sysbio/syr041. Epub 2011 May 3.

PMID:
21540409
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes.

Blanquart S, Gascuel O.

BMC Evol Biol. 2011 Mar 15;11:70. doi: 10.1186/1471-2148-11-70.

PMID:
21406081
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Bamako 2009 conference on the bioinformatics of infectious diseases.

Corpas M, Doumbia S, Gascuel O, Mulder N.

Infect Genet Evol. 2011 Jun;11(4):695-7. doi: 10.1016/j.meegid.2011.02.012. Epub 2011 Feb 23. No abstract available.

PMID:
21352953
[PubMed - indexed for MEDLINE]
17.

Bioinformatic strategies to provide functional clues to the unknown genes in Plasmodium falciparum genome.

Florent I, Maréchal E, Gascuel O, Bréhélin L.

Parasite. 2010 Dec;17(4):273-83. Review.

PMID:
21275233
[PubMed - indexed for MEDLINE]
18.

EuPathDomains: the divergent domain database for eukaryotic pathogens.

Ghouila A, Terrapon N, Gascuel O, Guerfali FZ, Laouini D, Maréchal E, Bréhélin L.

Infect Genet Evol. 2011 Jun;11(4):698-707. doi: 10.1016/j.meegid.2010.09.008. Epub 2010 Nov 4.

PMID:
20920608
[PubMed - indexed for MEDLINE]
19.

Inferring ancestral sequences in taxon-rich phylogenies.

Gascuel O, Steel M.

Math Biosci. 2010 Oct;227(2):125-35. doi: 10.1016/j.mbs.2010.07.002. Epub 2010 Jul 11.

PMID:
20627110
[PubMed - indexed for MEDLINE]
20.

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O.

Syst Biol. 2010 May;59(3):307-21. doi: 10.1093/sysbio/syq010. Epub 2010 Mar 29.

PMID:
20525638
[PubMed - indexed for MEDLINE]

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