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Items: 1 to 50 of 162

1.

The functional convergence of antibiotic resistance in β-lactamases is not conferred by a simple convergent substitution of amino acid.

Keshri V, Arbuckle K, Chabrol O, Rolain JM, Raoult D, Pontarotti P.

Evol Appl. 2019 Jul 18;12(9):1812-1822. doi: 10.1111/eva.12835. eCollection 2019 Oct.

2.

Human metallo-β-lactamase enzymes degrade penicillin.

Diene SM, Pinault L, Keshri V, Armstrong N, Khelaifia S, Chabrière E, Caetano-Anolles G, Colson P, La Scola B, Rolain JM, Pontarotti P, Raoult D.

Sci Rep. 2019 Aug 21;9(1):12173. doi: 10.1038/s41598-019-48723-y.

3.

HLAIb worldwide genetic diversity: New HLA-H alleles and haplotype structure description.

Paganini J, Abi-Rached L, Gouret P, Pontarotti P, Chiaroni J, Di Cristofaro J.

Mol Immunol. 2019 Aug;112:40-50. doi: 10.1016/j.molimm.2019.04.017. Epub 2019 May 8.

PMID:
31078115
4.

Transposon molecular domestication and the evolution of the RAG recombinase.

Zhang Y, Cheng TC, Huang G, Lu Q, Surleac MD, Mandell JD, Pontarotti P, Petrescu AJ, Xu A, Xiong Y, Schatz DG.

Nature. 2019 May;569(7754):79-84. doi: 10.1038/s41586-019-1093-7. Epub 2019 Apr 10.

5.

An Integrative Database of β-Lactamase Enzymes: Sequences, Structures, Functions, and Phylogenetic Trees.

Keshri V, Diene SM, Estienne A, Dardaillon J, Chabrol O, Tichit L, Rolain JM, Raoult D, Pontarotti P.

Antimicrob Agents Chemother. 2019 Apr 25;63(5). pii: e02319-18. doi: 10.1128/AAC.02319-18. Print 2019 May.

6.

Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes.

Colson P, Levasseur A, La Scola B, Sharma V, Nasir A, Pontarotti P, Caetano-Anollés G, Raoult D.

Front Microbiol. 2018 Nov 27;9:2668. doi: 10.3389/fmicb.2018.02668. eCollection 2018.

7.

Why do arthropods secrete β-lactams?

Pontarotti P, Raoult D.

Int J Antimicrob Agents. 2019 Apr;53(4):370. doi: 10.1016/j.ijantimicag.2018.11.006. Epub 2018 Nov 23. No abstract available.

PMID:
30476573
8.

Amphioxus functional genomics and the origins of vertebrate gene regulation.

Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M.

Nature. 2018 Dec;564(7734):64-70. doi: 10.1038/s41586-018-0734-6. Epub 2018 Nov 21.

9.

Immune diversity sheds light on missing variation in worldwide genetic diversity panels.

Abi-Rached L, Gouret P, Yeh JH, Di Cristofaro J, Pontarotti P, Picard C, Paganini J.

PLoS One. 2018 Oct 26;13(10):e0206512. doi: 10.1371/journal.pone.0206512. eCollection 2018.

10.

Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium.

Panda A, Drancourt M, Tuller T, Pontarotti P.

Sci Rep. 2018 Oct 4;8(1):14817. doi: 10.1038/s41598-018-33261-w.

11.

A Phylogenomic Study of Acanthamoeba polyphaga Draft Genome Sequences Suggests Genetic Exchanges With Giant Viruses.

Chelkha N, Levasseur A, Pontarotti P, Raoult D, Scola B, Colson P.

Front Microbiol. 2018 Sep 6;9:2098. doi: 10.3389/fmicb.2018.02098. eCollection 2018.

12.

In silico analysis of Schmidtea mediterranea TIR domain-containing proteins.

Tsoumtsa LL, Sougoufara S, Torre C, Lemichez E, Pontarotti P, Ghigo E.

Dev Comp Immunol. 2018 Sep;86:214-218. doi: 10.1016/j.dci.2018.05.004. Epub 2018 May 7.

PMID:
29746980
13.

Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members.

Keshri V, Panda A, Levasseur A, Rolain JM, Pontarotti P, Raoult D.

Genome Biol Evol. 2018 Apr 1;10(4):1106-1114. doi: 10.1093/gbe/evy028.

14.

Evolutionary and expression analyses reveal a pattern of ancient duplications and functional specializations in the diversification of the Downstream of Kinase (DOK) genes.

Guittard G, Pontarotti P, Granjeaud S, Rodrigues M, Abi-Rached L, Nunès JA.

Dev Comp Immunol. 2018 Jul;84:193-198. doi: 10.1016/j.dci.2018.02.011. Epub 2018 Feb 15.

PMID:
29453999
15.

The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes.

Levasseur A, Merhej V, Baptiste E, Sharma V, Pontarotti P, Raoult D.

Genome Biol Evol. 2017 Oct 1;9(10):2635-2639. doi: 10.1093/gbe/evx208.

16.

The RAG transposon is active through the deuterostome evolution and domesticated in jawed vertebrates.

Morales Poole JR, Huang SF, Xu A, Bayet J, Pontarotti P.

Immunogenetics. 2017 Jun;69(6):391-400. doi: 10.1007/s00251-017-0979-5. Epub 2017 Apr 28.

PMID:
28451741
17.

Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral (Corallium rubrum).

Pratlong M, Haguenauer A, Chenesseau S, Brener K, Mitta G, Toulza E, Bonabaud M, Rialle S, Aurelle D, Pontarotti P.

R Soc Open Sci. 2017 Mar 1;4(3):160880. doi: 10.1098/rsos.160880. eCollection 2017 Mar.

18.

MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales.

Jain S, Panda A, Colson P, Raoult D, Pontarotti P.

Viruses. 2017 Apr 7;9(4). pii: E72. doi: 10.3390/v9040072.

19.

Evolutionary and polymorphism analyses reveal the central role of BTN3A2 in the concerted evolution of the BTN3 gene family.

Afrache H, Pontarotti P, Abi-Rached L, Olive D.

Immunogenetics. 2017 Jun;69(6):379-390. doi: 10.1007/s00251-017-0980-z. Epub 2017 Apr 5.

PMID:
28382515
20.

Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum.

Pinos S, Pontarotti P, Raoult D, Merhej V.

BMC Evol Biol. 2017 Mar 9;17(1):75. doi: 10.1186/s12862-017-0921-3.

21.

Convergent evolution of the adaptive immune response in jawed vertebrates and cyclostomes: An evolutionary biology approach based study.

Morales Poole JR, Paganini J, Pontarotti P.

Dev Comp Immunol. 2017 Oct;75:120-126. doi: 10.1016/j.dci.2017.02.011. Epub 2017 Feb 21. Review.

PMID:
28232131
22.

Compartmentalization in PVC super-phylum: evolution and impact.

Pinos S, Pontarotti P, Raoult D, Baudoin JP, Pagnier I.

Biol Direct. 2016 Aug 9;11:38. doi: 10.1186/s13062-016-0144-3.

23.

Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination.

Huang S, Tao X, Yuan S, Zhang Y, Li P, Beilinson HA, Zhang Y, Yu W, Pontarotti P, Escriva H, Le Petillon Y, Liu X, Chen S, Schatz DG, Xu A.

Cell. 2016 Jun 30;166(1):102-14. doi: 10.1016/j.cell.2016.05.032. Epub 2016 Jun 9.

24.

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.

Pasquier J, Cabau C, Nguyen T, Jouanno E, Severac D, Braasch I, Journot L, Pontarotti P, Klopp C, Postlethwait JH, Guiguen Y, Bobe J.

BMC Genomics. 2016 May 18;17:368. doi: 10.1186/s12864-016-2709-z.

25.

MIMIVIRE is a defence system in mimivirus that confers resistance to virophage.

Levasseur A, Bekliz M, Chabrière E, Pontarotti P, La Scola B, Raoult D.

Nature. 2016 Mar 10;531(7593):249-52. doi: 10.1038/nature17146. Epub 2016 Feb 29.

PMID:
26934229
26.

Origin and Evolution of Rickettsial Plasmids.

El Karkouri K, Pontarotti P, Raoult D, Fournier PE.

PLoS One. 2016 Feb 11;11(2):e0147492. doi: 10.1371/journal.pone.0147492. eCollection 2016.

27.

Mimivirus inaugurated in the 21st century the beginning of a reclassification of viruses.

Sharma V, Colson P, Pontarotti P, Raoult D.

Curr Opin Microbiol. 2016 Jun;31:16-24. doi: 10.1016/j.mib.2015.12.010. Epub 2016 Jan 30. Review.

28.

Genomic resources and their influence on the detection of the signal of positive selection in genome scans.

Manel S, Perrier C, Pratlong M, Abi-Rached L, Paganini J, Pontarotti P, Aurelle D.

Mol Ecol. 2016 Jan;25(1):170-84. doi: 10.1111/mec.13468. Epub 2015 Dec 17. Review.

PMID:
26562485
29.

Pithovirus sibericum, a new bona fide member of the "Fourth TRUC" club.

Sharma V, Colson P, Chabrol O, Pontarotti P, Raoult D.

Front Microbiol. 2015 Aug 4;6:722. doi: 10.3389/fmicb.2015.00722. eCollection 2015.

30.

Welcome to pandoraviruses at the 'Fourth TRUC' club.

Sharma V, Colson P, Chabrol O, Scheid P, Pontarotti P, Raoult D.

Front Microbiol. 2015 May 18;6:423. doi: 10.3389/fmicb.2015.00423. eCollection 2015.

31.

The human gut microbiome, a taxonomic conundrum.

Sankar SA, Lagier JC, Pontarotti P, Raoult D, Fournier PE.

Syst Appl Microbiol. 2015 Jun;38(4):276-86. doi: 10.1016/j.syapm.2015.03.004. Epub 2015 Mar 25. Review.

PMID:
25864640
32.

The red coral (Corallium rubrum) transcriptome: a new resource for population genetics and local adaptation studies.

Pratlong M, Haguenauer A, Chabrol O, Klopp C, Pontarotti P, Aurelle D.

Mol Ecol Resour. 2015 Sep;15(5):1205-15. doi: 10.1111/1755-0998.12383. Epub 2015 Feb 22.

PMID:
25648864
33.

Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.

Huang S, Chen Z, Yan X, Yu T, Huang G, Yan Q, Pontarotti PA, Zhao H, Li J, Yang P, Wang R, Li R, Tao X, Deng T, Wang Y, Li G, Zhang Q, Zhou S, You L, Yuan S, Fu Y, Wu F, Dong M, Chen S, Xu A.

Nat Commun. 2014 Dec 19;5:5896. doi: 10.1038/ncomms6896.

34.

African relapsing Fever borreliae genomospecies revealed by comparative genomics.

Elbir H, Abi-Rached L, Pontarotti P, Yoosuf N, Drancourt M.

Front Public Health. 2014 May 14;2:43. doi: 10.3389/fpubh.2014.00043. eCollection 2014.

35.

Mycobacteriophage-drived diversification of Mycobacterium abscessus.

Sassi M, Gouret P, Chabrol O, Pontarotti P, Drancourt M.

Biol Direct. 2014 Sep 15;9:19. doi: 10.1186/1745-6150-9-19.

36.

The proto-MHC of placozoans, a region specialized in cellular stress and ubiquitination/proteasome pathways.

Suurväli J, Jouneau L, Thépot D, Grusea S, Pontarotti P, Du Pasquier L, Rüütel Boudinot S, Boudinot P.

J Immunol. 2014 Sep 15;193(6):2891-901. doi: 10.4049/jimmunol.1401177. Epub 2014 Aug 11.

37.

The genome of the white-rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown.

Levasseur A, Lomascolo A, Chabrol O, Ruiz-Dueñas FJ, Boukhris-Uzan E, Piumi F, Kües U, Ram AF, Murat C, Haon M, Benoit I, Arfi Y, Chevret D, Drula E, Kwon MJ, Gouret P, Lesage-Meessen L, Lombard V, Mariette J, Noirot C, Park J, Patyshakuliyeva A, Sigoillot JC, Wiebenga A, Wösten HA, Martin F, Coutinho PM, de Vries RP, Martínez AT, Klopp C, Pontarotti P, Henrissat B, Record E.

BMC Genomics. 2014 Jun 18;15:486. doi: 10.1186/1471-2164-15-486.

38.

DNA-dependent RNA polymerase detects hidden giant viruses in published databanks.

Sharma V, Colson P, Giorgi R, Pontarotti P, Raoult D.

Genome Biol Evol. 2014 Jun 13;6(7):1603-10. doi: 10.1093/gbe/evu128.

39.

Methods to study the occurrence and the evolution of pseudogenes through a phylogenetic approach.

Dainat J, Pontarotti P.

Methods Mol Biol. 2014;1167:87-99. doi: 10.1007/978-1-4939-0835-6_7.

PMID:
24823773
40.

Alphaproteobacteria species as a source and target of lateral sequence transfers.

Le PT, Pontarotti P, Raoult D.

Trends Microbiol. 2014 Mar;22(3):147-56. doi: 10.1016/j.tim.2013.12.006. Epub 2014 Jan 21. Review.

PMID:
24461455
41.

To tree or not to tree? Genome-wide quantification of recombination and reticulate evolution during the diversification of strict intracellular bacteria.

Hernández-López A, Chabrol O, Royer-Carenzi M, Merhej V, Pontarotti P, Raoult D.

Genome Biol Evol. 2013;5(12):2305-17. doi: 10.1093/gbe/evt178.

42.

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.

Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K.

Nature. 2013 Aug 22;500(7463):453-7. doi: 10.1038/nature12326. Epub 2013 Jul 21.

43.

Choosing the best ancestral character state reconstruction method.

Royer-Carenzi M, Pontarotti P, Didier G.

Math Biosci. 2013 Mar;242(1):95-109. doi: 10.1016/j.mbs.2012.12.003. Epub 2012 Dec 28.

PMID:
23276531
44.

Peptidoglycan: a post-genomic analysis.

Cayrou C, Henrissat B, Gouret P, Pontarotti P, Drancourt M.

BMC Microbiol. 2012 Dec 18;12:294. doi: 10.1186/1471-2180-12-294. Erratum in: BMC Microbiol. 2014;14:123.

45.

An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales.

Le PT, Ramulu HG, Guijarro L, Paganini J, Gouret P, Chabrol O, Raoult D, Pontarotti P.

BMC Evol Biol. 2012 Dec 12;12:243. doi: 10.1186/1471-2148-12-243.

46.

Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes.

Paganini J, Campan-Fournier A, Da Rocha M, Gouret P, Pontarotti P, Wajnberg E, Abad P, Danchin EG.

PLoS One. 2012;7(11):e50875. doi: 10.1371/journal.pone.0050875. Epub 2012 Nov 30.

47.

Oocyte-somatic cells interactions, lessons from evolution.

Charlier C, Montfort J, Chabrol O, Brisard D, Nguyen T, Le Cam A, Richard-Parpaillon L, Moreews F, Pontarotti P, Uzbekova S, Chesnel F, Bobe J.

BMC Genomics. 2012 Oct 19;13:560. doi: 10.1186/1471-2164-13-560.

48.

The butyrophilin (BTN) gene family: from milk fat to the regulation of the immune response.

Afrache H, Gouret P, Ainouche S, Pontarotti P, Olive D.

Immunogenetics. 2012 Nov;64(11):781-94. doi: 10.1007/s00251-012-0619-z. Epub 2012 Sep 23. Review.

PMID:
23000944
49.

The rhizome of life: what about metazoa?

Ramulu HG, Raoult D, Pontarotti P.

Front Cell Infect Microbiol. 2012 Apr 11;2:50. doi: 10.3389/fcimb.2012.00050. eCollection 2012. Review.

50.

The chordate proteome history database.

Levasseur A, Paganini J, Dainat J, Thompson JD, Poch O, Pontarotti P, Gouret P.

Evol Bioinform Online. 2012;8:437-47. doi: 10.4137/EBO.S9186. Epub 2012 Aug 1.

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