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Items: 1 to 50 of 87

1.

Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty.

Chatzou M, Floden EW, Di Tommaso P, Gascuel O, Notredame C.

Syst Biol. 2018 Mar 29. doi: 10.1093/sysbio/syx096. [Epub ahead of print]

PMID:
30295908
2.

Renewing Felsenstein's phylogenetic bootstrap in the era of big data.

Lemoine F, Domelevo Entfellner JB, Wilkinson E, Correia D, Dávila Felipe M, De Oliveira T, Gascuel O.

Nature. 2018 Apr;556(7702):452-456. doi: 10.1038/s41586-018-0043-0. Epub 2018 Apr 18.

PMID:
29670290
3.

Improving pairwise comparison of protein sequences with domain co-occurrence.

Menichelli C, Gascuel O, Bréhélin L.

PLoS Comput Biol. 2018 Jan 2;14(1):e1005889. doi: 10.1371/journal.pcbi.1005889. eCollection 2018 Jan.

4.

The Role of Phylogenetics as a Tool to Predict the Spread of Resistance.

Zhukova A, Cutino-Moguel T, Gascuel O, Pillay D.

J Infect Dis. 2017 Dec 1;216(suppl_9):S820-S823. doi: 10.1093/infdis/jix411. Review.

PMID:
29029155
5.

[The tenth gene of HIV].

Cassan É, Arigon-Chifolleau AM, Mesnard JM, Gros A, Gascuel O.

Med Sci (Paris). 2017 May;33(5):484-485. doi: 10.1051/medsci/20173305008. Epub 2017 Jun 14. French. No abstract available.

6.

SMS: Smart Model Selection in PhyML.

Lefort V, Longueville JE, Gascuel O.

Mol Biol Evol. 2017 Sep 1;34(9):2422-2424. doi: 10.1093/molbev/msx149.

7.

Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study.

Saulnier E, Gascuel O, Alizon S.

PLoS Comput Biol. 2017 Mar 6;13(3):e1005416. doi: 10.1371/journal.pcbi.1005416. eCollection 2017 Mar.

8.

Special Issue: Mathematical and Computational Evolutionary Biology-2015.

Bryant D, Gascuel O.

Syst Biol. 2017 Jan 1;66(1):1-2. doi: 10.1093/sysbio/syw111. No abstract available.

9.

In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa.

Villabona-Arenas CJ, Vidal N, Guichet E, Serrano L, Delaporte E, Gascuel O, Peeters M.

AIDS. 2016 Nov 13;30(17):2577-2589.

PMID:
27603287
10.

The combinatorics of overlapping genes.

Lèbre S, Gascuel O.

J Theor Biol. 2017 Feb 21;415:90-101. doi: 10.1016/j.jtbi.2016.09.018. Epub 2016 Oct 11.

PMID:
27737786
11.

Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic.

Cassan E, Arigon-Chifolleau AM, Mesnard JM, Gross A, Gascuel O.

Proc Natl Acad Sci U S A. 2016 Oct 11;113(41):11537-11542. Epub 2016 Sep 28.

12.

Fast and accurate branch lengths estimation for phylogenomic trees.

Binet M, Gascuel O, Scornavacca C, Douzery EJ, Pardi F.

BMC Bioinformatics. 2016 Jan 7;17:23. doi: 10.1186/s12859-015-0821-8.

13.

Fast Dating Using Least-Squares Criteria and Algorithms.

To TH, Jung M, Lycett S, Gascuel O.

Syst Biol. 2016 Jan;65(1):82-97. doi: 10.1093/sysbio/syv068. Epub 2015 Sep 30.

14.

A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK.

Mourad R, Chevennet F, Dunn DT, Fearnhill E, Delpech V, Asboe D, Gascuel O, Hue S; UK HIV Drug Resistance Database & the Collaborative HIV, Anti-HIV Drug Resistance Network.

AIDS. 2015 Sep 24;29(15):1917-25. doi: 10.1097/QAD.0000000000000768.

PMID:
26355570
15.

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program.

Lefort V, Desper R, Gascuel O.

Mol Biol Evol. 2015 Oct;32(10):2798-800. doi: 10.1093/molbev/msv150. Epub 2015 Jun 30.

16.

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

Chang JM, Di Tommaso P, Lefort V, Gascuel O, Notredame C.

Nucleic Acids Res. 2015 Jul 1;43(W1):W3-6. doi: 10.1093/nar/gkv310. Epub 2015 Apr 8.

17.

Mathematical and computational evolutionary biology (2013).

Gascuel O, Stadler T.

Syst Biol. 2015 Jan;64(1):1-2. doi: 10.1093/sysbio/syu086. No abstract available.

PMID:
25504791
18.

FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets.

Dang CC, Le VS, Gascuel O, Hazes B, Le QS.

BMC Bioinformatics. 2014 Oct 24;15:341. doi: 10.1186/1471-2105-15-341.

19.

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.

20.

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
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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
29.

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.

30.

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
31.

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
32.

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.

33.
34.

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
35.

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.

36.

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
37.

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
38.

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
39.

Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial.

Le SQ, Gascuel O.

Syst Biol. 2010 May;59(3):277-87. doi: 10.1093/sysbio/syq002. Epub 2010 Mar 10.

PMID:
20525635
40.

Robustness of phylogenetic inference based on minimum evolution.

Pardi F, Guillemot S, Gascuel O.

Bull Math Biol. 2010 Oct;72(7):1820-39. doi: 10.1007/s11538-010-9510-y. Epub 2010 May 7.

PMID:
20449671
41.

FLU, an amino acid substitution model for influenza proteins.

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

BMC Evol Biol. 2010 Apr 12;10:99. doi: 10.1186/1471-2148-10-99.

42.

Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum.

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

BMC Genomics. 2010 Jan 15;11:35. doi: 10.1186/1471-2164-11-35.

43.

SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.

Gouy M, Guindon S, Gascuel O.

Mol Biol Evol. 2010 Feb;27(2):221-4. doi: 10.1093/molbev/msp259. Epub 2009 Oct 23.

PMID:
19854763
44.

Detection of new protein domains using co-occurrence: application to Plasmodium falciparum.

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

Bioinformatics. 2009 Dec 1;25(23):3077-83. doi: 10.1093/bioinformatics/btp560. Epub 2009 Sep 28.

PMID:
19786484
45.

A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism.

Florent I, Porcel BM, Guillaume E, Da Silva C, Artiguenave F, Maréchal E, Bréhélin L, Gascuel O, Charneau S, Wincker P, Grellier P.

BMC Genomics. 2009 May 19;10:235. doi: 10.1186/1471-2164-10-235.

46.

Estimating maximum likelihood phylogenies with PhyML.

Guindon S, Delsuc F, Dufayard JF, Gascuel O.

Methods Mol Biol. 2009;537:113-37. doi: 10.1007/978-1-59745-251-9_6.

PMID:
19378142
47.

Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference.

Bordewich M, Gascuel O, Huber KT, Moulton V.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jan-Mar;6(1):110-7. doi: 10.1109/TCBB.2008.37.

PMID:
19179704
48.

PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data.

Bréhélin L, Dufayard JF, Gascuel O.

BMC Bioinformatics. 2008 Oct 16;9:440. doi: 10.1186/1471-2105-9-440.

49.

Phylogenetic mixture models for proteins.

Le SQ, Lartillot N, Gascuel O.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3965-76. doi: 10.1098/rstb.2008.0180.

50.

Bioinformatics of African Pathogens and Vectors conference. Editorial.

Gascuel O, BenKahla A, Hidde W, Masiga D, Shah T.

Infect Genet Evol. 2009 May;9(3):305-7. doi: 10.1016/j.meegid.2008.09.002. Epub 2008 Sep 20. No abstract available.

PMID:
18848911

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