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Are the multiple Trypanosoma cruzi infections in Louisiana rodents caused by independent genetic clones?

Tibayrenc M, Ayala FJ.

J Microbiol Immunol Infect. 2019 Sep 14. pii: S1684-1182(19)30081-7. doi: 10.1016/j.jmii.2019.04.014. [Epub ahead of print] No abstract available.


How clonal is Trypanosoma congolense? A necessary clarification of the predominant clonal evolution model.

Tibayrenc M, Ayala FJ.

Acta Trop. 2019 Feb;190:28-29. doi: 10.1016/j.actatropica.2018.10.013. Epub 2018 Nov 1. No abstract available.


A misleading description of the predominant clonal evolution model in Trypanosoma cruzi.

Tibayrenc M, Ayala FJ.

Acta Trop. 2018 Nov;187:13-14. doi: 10.1016/j.actatropica.2018.07.015. Epub 2018 Jul 23. No abstract available.


Encephalitis is mediated by ROP18 of Toxoplasma gondii, a severe pathogen in AIDS patients.

An R, Tang Y, Chen L, Cai H, Lai DH, Liu K, Wan L, Gong L, Yu L, Luo Q, Shen J, Lun ZR, Ayala FJ, Du J.

Proc Natl Acad Sci U S A. 2018 Jun 5;115(23):E5344-E5352. doi: 10.1073/pnas.1801118115. Epub 2018 May 21.


Art and brain coevolution.

Cela-Conde CJ, Ayala FJ.

Prog Brain Res. 2018;237:41-60. doi: 10.1016/bs.pbr.2018.03.013. Epub 2018 Apr 25. Review.


Chromosomal inversions promote genomic islands of concerted evolution of Hsp70 genes in the Drosophila subobscura species subgroup.

Puig Giribets M, García Guerreiro MP, Santos M, Ayala FJ, Tarrío R, Rodríguez-Trelles F.

Mol Ecol. 2019 Mar;28(6):1316-1332. doi: 10.1111/mec.14511. Epub 2018 Mar 1.


Extensive flagellar remodeling during the complex life cycle of Paratrypanosoma, an early-branching trypanosomatid.

Skalický T, Dobáková E, Wheeler RJ, Tesařová M, Flegontov P, Jirsová D, Votýpka J, Yurchenko V, Ayala FJ, Lukeš J.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):11757-11762. doi: 10.1073/pnas.1712311114. Epub 2017 Oct 16.


Nitric oxide blocks the development of the human parasite Schistosoma japonicum.

Shen J, Lai DH, Wilson RA, Chen YF, Wang LF, Yu ZL, Li MY, He P, Hide G, Sun X, Yang TB, Wu ZD, Ayala FJ, Lun ZR.

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10214-10219. doi: 10.1073/pnas.1708578114. Epub 2017 Sep 5.


The extension of biology through culture.

Whiten A, Ayala FJ, Feldman MW, Laland KN.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):7775-7781. doi: 10.1073/pnas.1707630114. Epub 2017 Jul 24. No abstract available.


Relevant units of analysis for applied and basic research dealing with neglected transmissible diseases: The predominant clonal evolution model of pathogenic microorganisms.

Tibayrenc M, Ayala FJ.

PLoS Negl Trop Dis. 2017 Apr 27;11(4):e0005293. doi: 10.1371/journal.pntd.0005293. eCollection 2017 Apr. Review.


Tracking zoonotic pathogens using blood-sucking flies as 'flying syringes'.

Bitome-Essono PY, Ollomo B, Arnathau C, Durand P, Mokoudoum ND, Yacka-Mouele L, Okouga AP, Boundenga L, Mve-Ondo B, Obame-Nkoghe J, Mbehang-Nguema P, Njiokou F, Makanga B, Wattier R, Ayala D, Ayala FJ, Renaud F, Rougeron V, Bretagnolle F, Prugnolle F, Paupy C.

Elife. 2017 Mar 28;6. pii: e22069. doi: 10.7554/eLife.22069.


Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

Tibayrenc M, Ayala FJ.

Adv Parasitol. 2017;97:243-325. doi: 10.1016/bs.apar.2016.08.007. Epub 2016 Oct 21. Review.


Guanylate-binding protein 1 (GBP1) contributes to the immunity of human mesenchymal stromal cells against Toxoplasma gondii.

Qin A, Lai DH, Liu Q, Huang W, Wu YP, Chen X, Yan S, Xia H, Hide G, Lun ZR, Ayala FJ, Xiang AP.

Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):1365-1370. doi: 10.1073/pnas.1619665114. Epub 2017 Jan 25.


Highly rearranged mitochondrial genome in Nycteria parasites (Haemosporidia) from bats.

Karadjian G, Hassanin A, Saintpierre B, Gembu Tungaluna GC, Ariey F, Ayala FJ, Landau I, Duval L.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9834-9. doi: 10.1073/pnas.1610643113. Epub 2016 Aug 15.


Medical Informatics and the "Three Long, One Short" Problem of Large Urban Hospitals in China.

Dai J, Wang X, Ayala FJ.

JAMA. 2016 Jul 19;316(3):269-70. doi: 10.1001/jama.2016.5487. No abstract available.


In the light of evolution X: Comparative phylogeography.

Avise JC, Bowen BW, Ayala FJ.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):7957-61. doi: 10.1073/pnas.1604338113. No abstract available.


DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea).

Balakirev ES, Anisimova M, Pavlyuchkov VA, Ayala FJ.

BMC Genet. 2016 May 12;17(1):66. doi: 10.1186/s12863-016-0374-5.


Ape malaria transmission and potential for ape-to-human transfers in Africa.

Makanga B, Yangari P, Rahola N, Rougeron V, Elguero E, Boundenga L, Moukodoum ND, Okouga AP, Arnathau C, Durand P, Willaume E, Ayala D, Fontenille D, Ayala FJ, Renaud F, Ollomo B, Prugnolle F, Paupy C.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):5329-34. doi: 10.1073/pnas.1603008113. Epub 2016 Apr 11.


Two distinct cytokinesis pathways drive trypanosome cell division initiation from opposite cell ends.

Zhou Q, Gu J, Lun ZR, Ayala FJ, Li Z.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3287-92. doi: 10.1073/pnas.1601596113. Epub 2016 Feb 29.


Complete mitochondrial genome of the Kamchatka grayling Thymallus mertensii (Salmoniformes, Salmonidae).

Balakirev ES, Romanov NS, Ayala FJ.

Mitochondrial DNA A DNA Mapp Seq Anal. 2017 Jan;28(1):135-136. doi: 10.3109/19401736.2015.1111358. Epub 2015 Dec 28.


Reproductive clonality in protozoan pathogens--truth or artifact? A comment on Ramírez and Llewellyn.

Tibayrenc M, Ayala FJ.

Mol Ecol. 2015 Dec;24(23):5778-81. doi: 10.1111/mec.13443.


Complete mitochondrial genome of the white char Salvelinus albus (Salmoniformes, Salmonidae).

Balakirev ES, Parensky VA, Kovalev MY, Ayala FJ.

Mitochondrial DNA A DNA Mapp Seq Anal. 2016 Sep;27(5):3753-4. doi: 10.3109/19401736.2015.1079890. Epub 2015 Sep 10.


Cancer in the parasitic protozoans Trypanosoma brucei and Toxoplasma gondii.

Lun ZR, Lai DH, Wen YZ, Zheng LL, Shen JL, Yang TB, Zhou WL, Qu LH, Hide G, Ayala FJ.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):8835-42. doi: 10.1073/pnas.1502599112. Epub 2015 Jul 20.


How clonal are Neisseria species? The epidemic clonality model revisited.

Tibayrenc M, Ayala FJ.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):8909-13. doi: 10.1073/pnas.1502900112.


In the light of evolution IX: Clonal reproduction: Alternatives to sex.

Tibayrenc M, Avise JC, Ayala FJ.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):8824-6. doi: 10.1073/pnas.1508087112. No abstract available.


Cloning humans? Biological, ethical, and social considerations.

Ayala FJ.

Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):8879-86. doi: 10.1073/pnas.1501798112. Epub 2015 Jul 20. Review.


The population genetics of Trypanosoma cruzi revisited in the light of the predominant clonal evolution model.

Tibayrenc M, Ayala FJ.

Acta Trop. 2015 Nov;151:156-65. doi: 10.1016/j.actatropica.2015.05.006. Epub 2015 Jul 16.


Response to Rougeron et al.: Leishmania population genetics: clonality, selfing and aneuploidy.

Tibayrenc M, Ayala FJ.

Trends Parasitol. 2015 Jul;31(7):279-80. No abstract available.


Wild chimpanzees are infected by Trypanosoma brucei.

Jirků M, Votýpka J, Petrželková KJ, Jirků-Pomajbíková K, Kriegová E, Vodička R, Lankester F, Leendertz SA, Wittig RM, Boesch C, Modrý D, Ayala FJ, Leendertz FH, Lukeš J.

Int J Parasitol Parasites Wildl. 2015 Jun 16;4(3):277-82. doi: 10.1016/j.ijppaw.2015.05.001. eCollection 2015 Dec.


Malaria continues to select for sickle cell trait in Central Africa.

Elguero E, Délicat-Loembet LM, Rougeron V, Arnathau C, Roche B, Becquart P, Gonzalez JP, Nkoghe D, Sica L, Leroy EM, Durand P, Ayala FJ, Ollomo B, Renaud F, Prugnolle F.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):7051-4. doi: 10.1073/pnas.1505665112. Epub 2015 May 4.


Infection by Toxoplasma gondii, a severe parasite in neonates and AIDS patients, causes impaired anion secretion in airway epithelia.

Guo HM, Gao JM, Luo YL, Wen YZ, Zhang YL, Hide G, Zhou WL, Ayala FJ, Lun ZR.

Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4435-40. doi: 10.1073/pnas.1503474112. Epub 2015 Mar 23.


Complete mitochondrial genomes of the anadromous and resident forms of the lamprey Lethenteron camtschaticum.

Balakirev ES, Parensky VA, Ayala FJ.

Mitochondrial DNA A DNA Mapp Seq Anal. 2016 May;27(3):1730-1. doi: 10.3109/19401736.2014.961143. Epub 2014 Sep 22.


Both endo-siRNAs and tRNA-derived small RNAs are involved in the differentiation of primitive eukaryote Giardia lamblia.

Liao JY, Guo YH, Zheng LL, Li Y, Xu WL, Zhang YC, Zhou H, Lun ZR, Ayala FJ, Qu LH.

Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):14159-64. doi: 10.1073/pnas.1414394111. Epub 2014 Sep 15.


In the light of evolution VIII: Darwinian thinking in the social sciences. Introduction.

Skyrms B, Avise JC, Ayala FJ.

Proc Natl Acad Sci U S A. 2014 Jul 22;111 Suppl 3:10781-4. No abstract available.


Discriminating micropathogen lineages and their reticulate evolution through graph theory-based network analysis: the case of Trypanosoma cruzi, the agent of Chagas disease.

Arnaud-Haond S, Moalic Y, Barnabé C, Ayala FJ, Tibayrenc M.

PLoS One. 2014 Aug 22;9(8):e103213. doi: 10.1371/journal.pone.0103213. eCollection 2014.


How often do they have sex? A comparative analysis of the population structure of seven eukaryotic microbial pathogens.

Tomasini N, Lauthier JJ, Ayala FJ, Tibayrenc M, Diosque P.

PLoS One. 2014 Jul 23;9(7):e103131. doi: 10.1371/journal.pone.0103131. eCollection 2014.


Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes.

Séré M, Kaboré J, Jamonneau V, Belem AM, Ayala FJ, De Meeûs T.

Parasit Vectors. 2014 Jul 15;7:331. doi: 10.1186/1756-3305-7-331.


Complete mitochondrial genome of Sakhalin taimen Parahucho perryi (Salmoniformes, Salmonidae) without two frame-disrupting indels in the ND4 gene.

Balakirev ES, Romanov NS, Ayala FJ.

Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27(2):1020-1. doi: 10.3109/19401736.2014.926534. Epub 2014 Jun 18.


Complete mitochondrial genomes of the Northern (Salvelinus malma) and Southern (Salvelinus curilus) Dolly Varden chars (Salmoniformes, Salmonidae).

Balakirev ES, Romanov NS, Ayala FJ.

Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27(2):1016-7. doi: 10.3109/19401736.2014.926531. Epub 2014 Jun 12.


Complete mitochondrial genome of blunt-snouted lenok Brachymystax tumensis (Salmoniformes, Salmonidae).

Balakirev ES, Romanov NS, Ayala FJ.

Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27(2):882-3. doi: 10.3109/19401736.2014.919487. Epub 2014 May 27.


Complete mitochondrial genome of Siberian taimen, Hucho taimen not introgressed by the lenok subspecies, Brachymystax lenok and B. lenok tsinlingensis.

Balakirev ES, Romanov NS, Mikheev PB, Ayala FJ.

Mitochondrial DNA A DNA Mapp Seq Anal. 2016;27(2):815-6. doi: 10.3109/19401736.2014.919455. Epub 2014 May 20.


Patterns of selection on Plasmodium falciparum erythrocyte-binding antigens after the colonization of the New World.

Yalcindag E, Rougeron V, Elguero E, Arnathau C, Durand P, Brisse S, Diancourt L, Aubouy A, Becquart P, D'Alessandro U, Fontenille D, Gamboa D, Maestre A, Ménard D, Musset L, Noya O, Veron V, Wide A, Carme B, Legrand E, Chevillon C, Ayala FJ, Renaud F, Prugnolle F.

Mol Ecol. 2014 Apr;23(8):1979-93.


Computational methods of identification of pseudogenes based on functionality: entropy and GC content.

Balakirev ES, Chechetkin VR, Lobzin VV, Ayala FJ.

Methods Mol Biol. 2014;1167:41-62. doi: 10.1007/978-1-4939-0835-6_4.


Trypanosoma cruzi: gene expression surveyed by proteomic analysis reveals interaction between different genotypes in mixed in vitro cultures.

Machin A, Telleria J, Brizard JP, Demettre E, Séveno M, Ayala FJ, Tibayrenc M.

PLoS One. 2014 Apr 18;9(4):e95442. doi: 10.1371/journal.pone.0095442. eCollection 2014.


Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

Tibayrenc M, Ayala FJ.

PLoS Pathog. 2014 Apr 10;10(4):e1003908. doi: 10.1371/journal.ppat.1003908. eCollection 2014 Apr. Review.


New insights into clonality and panmixia in Plasmodium and toxoplasma.

Tibayrenc M, Ayala FJ.

Adv Parasitol. 2014;84:253-68. doi: 10.1016/B978-0-12-800099-1.00005-3.


Mitochondrial DNA variation and introgression in Siberian taimen Hucho taimen.

Balakirev ES, Romanov NS, Mikheev PB, Ayala FJ.

PLoS One. 2013 Aug 12;8(8):e71147. doi: 10.1371/journal.pone.0071147. eCollection 2013.

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