Francisco Ayala - Publications

Affiliations: 
University of California, Irvine, Irvine, CA 
Area:
molecular clock evolution, evolution of introns
Website:
http://www.faculty.uci.edu/profile.cfm?faculty_id=2134

152 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Tibayrenc M, Ayala FJ. Genomics and High-Resolution Typing Confirm Predominant Clonal Evolution Down to a Microevolutionary Scale in . Pathogens (Basel, Switzerland). 9. PMID 32397142 DOI: 10.3390/pathogens9050356  0.56
2019 Tibayrenc M, Ayala FJ. Are the multiple Trypanosoma cruzi infections in Louisiana rodents caused by independent genetic clones? Journal of Microbiology, Immunology, and Infection = Wei Mian Yu Gan Ran Za Zhi. PMID 31558357 DOI: 10.1016/j.jmii.2019.04.014  0.56
2018 Tibayrenc M, Ayala FJ. How clonal is Trypanosoma congolense? A necessary clarification of the predominant clonal evolution model. Acta Tropica. 190: 28-29. PMID 30391231 DOI: 10.1016/j.actatropica.2018.10.013  0.56
2018 Tibayrenc M, Ayala F. Hybridization in Trypanosoma congolense does not challenge the predominant clonal evolution model. A comment on Tihon et al., 2017, Mol. Ecol. Molecular Ecology. 27: 3421-3424. PMID 30146716 DOI: 10.1111/mec.14714  0.56
2018 Tibayrenc M, Ayala FJ. A misleading description of the predominant clonal evolution model in Trypanosoma cruzi. Acta Tropica. 187: 13-14. PMID 30048630 DOI: 10.1016/j.actatropica.2018.07.015  0.56
2018 Giribets MP, Guerreiro MPG, Santos M, Ayala FJ, Tarrío R, Rodríguez-Trelles F. Chromosomal inversions promote genomic islands of concerted evolution of Hsp70 genes in the Drosophila subobscura species subgroup. Molecular Ecology. PMID 29412486 DOI: 10.1111/mec.14511  0.44
2017 Tibayrenc M, Ayala FJ. Relevant units of analysis for applied and basic research dealing with neglected transmissible diseases: The predominant clonal evolution model of pathogenic microorganisms. Plos Neglected Tropical Diseases. 11: e0005293. PMID 28448491 DOI: 10.1371/journal.pntd.0005293  0.56
2016 Avise JC, Bowen BW, Ayala FJ. In the light of evolution X: Comparative phylogeography. Proceedings of the National Academy of Sciences of the United States of America. PMID 27432955 DOI: 10.1073/pnas.1604338113  0.92
2016 Zhou Q, Gu J, Lun ZR, Ayala FJ, Li Z. Two distinct cytokinesis pathways drive trypanosome cell division initiation from opposite cell ends. Proceedings of the National Academy of Sciences of the United States of America. PMID 26929336 DOI: 10.1073/pnas.1601596113  0.92
2015 Balakirev ES, Romanov NS, Ayala FJ. Complete mitochondrial genome of the Kamchatka grayling Thymallus mertensii (Salmoniformes, Salmonidae). Mitochondrial Dna. 1-2. PMID 26709442 DOI: 10.3109/19401736.2015.1111358  1
2015 Tibayrenc M, Ayala FJ. Reproductive clonality in protozoan pathogens-truth or artifact? A comment on Ramírez and Llewellyn. Molecular Ecology. 24: 5778-81. PMID 26607214 DOI: 10.1111/mec.13443  0.92
2015 Balakirev ES, Parensky VA, Kovalev MY, Ayala FJ. Complete mitochondrial genome of the white char Salvelinus albus (Salmoniformes, Salmonidae). Mitochondrial Dna. 1-2. PMID 26358825 DOI: 10.3109/19401736.2015.1079890  1
2015 Lun ZR, Lai DH, Wen YZ, Zheng LL, Shen JL, Yang TB, Zhou WL, Qu LH, Hide G, Ayala FJ. Cancer in the parasitic protozoans Trypanosoma brucei and Toxoplasma gondii. Proceedings of the National Academy of Sciences of the United States of America. 112: 8835-42. PMID 26195778 DOI: 10.1073/pnas.1502599112  1
2015 Tibayrenc M, Ayala FJ. How clonal are Neisseria species? The epidemic clonality model revisited. Proceedings of the National Academy of Sciences of the United States of America. 112: 8909-13. PMID 26195766 DOI: 10.1073/pnas.1502900112  1
2015 Tibayrenc M, Avise JC, Ayala FJ. In the light of evolution IX: Clonal reproduction: Alternatives to sex. Proceedings of the National Academy of Sciences of the United States of America. 112: 8824-6. PMID 26195755 DOI: 10.1073/pnas.1508087112  1
2015 Ayala FJ. Cloning humans? Biological, ethical, and social considerations. Proceedings of the National Academy of Sciences of the United States of America. 112: 8879-86. PMID 26195738 DOI: 10.1073/pnas.1501798112  1
2015 Tibayrenc M, Ayala FJ. The population genetics of Trypanosoma cruzi revisited in the light of the predominant clonal evolution model. Acta Tropica. 151: 156-65. PMID 26188332 DOI: 10.1016/j.actatropica.2015.05.006  1
2015 Tibayrenc M, Ayala FJ. Response to Rougeron et al.: Leishmania population genetics: clonality, selfing and aneuploidy. Trends in Parasitology. 31: 279-80. PMID 26142921 DOI: 10.1016/j.pt.2015.04.002  0.56
2015 Jirk? M, Votýpka J, Petrželková KJ, Jirk?-Pomajbíková K, Kriegová E, Vodi?ka R, Lankester F, Leendertz SA, Wittig RM, Boesch C, Modrý D, Ayala FJ, Leendertz FH, Lukeš J. Wild chimpanzees are infected by Trypanosoma brucei. International Journal For Parasitology. Parasites and Wildlife. 4: 277-82. PMID 26110113 DOI: 10.1016/j.ijppaw.2015.05.001  1
2015 Ayala FJ. Science, evolution and natural selection: in praise of Darwin at the Stazione Zoologica Anton Dohrn of Naples. History and Philosophy of the Life Sciences. 36: 444-55. PMID 26013200 DOI: 10.1007/s40656-014-0031-0  1
2015 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. Malaria continues to select for sickle cell trait in Central Africa. Proceedings of the National Academy of Sciences of the United States of America. 112: 7051-4. PMID 25941403 DOI: 10.1073/pnas.1505665112  1
2015 Guo HM, Gao JM, Luo YL, Wen YZ, Zhang YL, Hide G, Zhou WL, Ayala FJ, Lun ZR. Infection by Toxoplasma gondii, a severe parasite in neonates and AIDS patients, causes impaired anion secretion in airway epithelia. Proceedings of the National Academy of Sciences of the United States of America. 112: 4435-40. PMID 25831498 DOI: 10.1073/pnas.1503474112  1
2015 Tibayrenc M, Ayala FJ. Response to Rougeron et al.: Leishmania population genetics: Clonality, selfing and aneuploidy Trends in Parasitology. DOI: 10.1016/j.pt.2015.04.002  1
2014 Liao JY, Guo YH, Zheng LL, Li Y, Xu WL, Zhang YC, Zhou H, Lun ZR, Ayala FJ, Qu LH. Both endo-siRNAs and tRNA-derived small RNAs are involved in the differentiation of primitive eukaryote Giardia lamblia. Proceedings of the National Academy of Sciences of the United States of America. 111: 14159-64. PMID 25225396 DOI: 10.1073/pnas.1414394111  1
2014 Skyrms B, Avise JC, Ayala FJ. In the light of evolution VIII: Darwinian thinking in the social sciences. Introduction. Proceedings of the National Academy of Sciences of the United States of America. 111: 10781-4. PMID 25202765 DOI: 10.1073/pnas.1411483111  1
2014 Arnaud-Haond S, Moalic Y, Barnabé C, Ayala FJ, Tibayrenc M. Discriminating micropathogen lineages and their reticulate evolution through graph theory-based network analysis: the case of Trypanosoma cruzi, the agent of Chagas disease. Plos One. 9: e103213. PMID 25148574 DOI: 10.1371/journal.pone.0103213  1
2014 Tomasini N, Lauthier JJ, Ayala FJ, Tibayrenc M, Diosque P. How often do they have sex? A comparative analysis of the population structure of seven eukaryotic microbial pathogens. Plos One. 9: e103131. PMID 25054834 DOI: 10.1371/journal.pone.0103131  1
2014 Séré M, Kaboré J, Jamonneau V, Belem AM, Ayala FJ, De Meeûs T. Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes. Parasites & Vectors. 7: 331. PMID 25027508 DOI: 10.1186/1756-3305-7-331  1
2014 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, ... ... Ayala FJ, et al. Patterns of selection on Plasmodium falciparum erythrocyte-binding antigens after the colonization of the New World. Molecular Ecology. 23: 1979-93. PMID 24834503 DOI: 10.1111/mec.12696  1
2014 Balakirev ES, Chechetkin VR, Lobzin VV, Ayala FJ. Computational methods of identification of pseudogenes based on functionality: entropy and GC content. Methods in Molecular Biology (Clifton, N.J.). 1167: 41-62. PMID 24823770 DOI: 10.1007/978-1-4939-0835-6_4  1
2014 Machin A, Telleria J, Brizard JP, Demettre E, Séveno M, Ayala FJ, Tibayrenc M. Trypanosoma cruzi: gene expression surveyed by proteomic analysis reveals interaction between different genotypes in mixed in vitro cultures. Plos One. 9: e95442. PMID 24748035 DOI: 10.1371/journal.pone.0095442  1
2014 Tibayrenc M, Ayala FJ. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades? Plos Pathogens. 10: e1003908. PMID 24722548 DOI: 10.1371/journal.ppat.1003908  1
2014 Tibayrenc M, Ayala FJ. New insights into clonality and panmixia in Plasmodium and toxoplasma. Advances in Parasitology. 84: 253-68. PMID 24480316 DOI: 10.1016/B978-0-12-800099-1.00005-3  1
2014 Sainz de Baranda P, Rodríguez-Iniesta M, Ayala F, Santonja F, Cejudo A. Determination of the criterion-related validity of hip joint angle test for estimating hamstring flexibility using a contemporary statistical approach. Clinical Journal of Sport Medicine : Official Journal of the Canadian Academy of Sport Medicine. 24: 320-5. PMID 24451690 DOI: 10.1097/JSM.0000000000000079  0.01
2014 Ayala F, De Ste Croix M, Sainz de Baranda P, Santonja F. Acute effects of static and dynamic stretching on hamstrings' response times. Journal of Sports Sciences. 32: 817-25. PMID 24405028 DOI: 10.1080/02640414.2013.861606  0.01
2014 Cela-Conde CJ, Ayala FJ. Brain keys in the appreciation of beauty: A tale of two worlds Rendiconti Lincei. 25: 277-284. DOI: 10.1007/s12210-014-0299-8  1
2014 Ayala FJ. What light does biology shed on the social sciences and the humanities? Forms of Truth and the Unity of Knowledge. 140-159.  0.92
2013 Balakirev ES, Romanov NS, Mikheev PB, Ayala FJ. Mitochondrial DNA variation and introgression in Siberian taimen Hucho taimen. Plos One. 8: e71147. PMID 23951096 DOI: 10.1371/journal.pone.0071147  1
2013 Cela-Conde CJ, Gutiérrez Lombardo R, Avise JC, Ayala FJ. In the light of evolution VII: The human mental machinery. Proceedings of the National Academy of Sciences of the United States of America. 110: 10339-42. PMID 23754413 DOI: 10.1073/pnas.1307207110  1
2013 Zheng LL, Wen YZ, Yang JH, Liao JY, Shao P, Xu H, Zhou H, Wen JZ, Lun ZR, Ayala FJ, Qu LH. Comparative transcriptome analysis of small noncoding RNAs in different stages of Trypanosoma brucei. Rna (New York, N.Y.). 19: 863-75. PMID 23704326 DOI: 10.1261/rna.035683.112  1
2013 Prugnolle F, Rougeron V, Becquart P, Berry A, Makanga B, Rahola N, Arnathau C, Ngoubangoye B, Menard S, Willaume E, Ayala FJ, Fontenille D, Ollomo B, Durand P, Paupy C, et al. Diversity, host switching and evolution of Plasmodium vivax infecting African great apes. Proceedings of the National Academy of Sciences of the United States of America. 110: 8123-8. PMID 23637341 DOI: 10.1073/pnas.1306004110  1
2013 Tibayrenc M, Ayala FJ. How clonal are Trypanosoma and Leishmania? Trends in Parasitology. 29: 264-9. PMID 23602631 DOI: 10.1016/j.pt.2013.03.007  1
2013 Telleria J, Barnabé C, Ayala FJ, Tibayrenc M. Phylogenetic character mapping of RADES Probing, a new marker for exploring the clonal evolution of expressed coding sequences in Trypanosoma cruzi, the agent of Chagas disease. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 19: 287-91. PMID 23541409 DOI: 10.1016/j.meegid.2013.03.027  1
2012 Ayala FJ. Walter Monroe Fitch (May 21, 1929 - March 10, 2011): a memorial tribute. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 12: 1587-9. PMID 23087917  1
2012 Tibayrenc M, Ayala FJ. Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proceedings of the National Academy of Sciences of the United States of America. 109: E3305-13. PMID 22949662 DOI: 10.1073/pnas.1212452109  1
2012 Balakirev ES, Krupnova TN, Ayala FJ. DNA variation in the phenotypically-diverse brown alga Saccharina japonica. Bmc Plant Biology. 12: 108. PMID 22784095 DOI: 10.1186/1471-2229-12-108  1
2012 Balakirev ES, Krupnova TN, Ayala FJ. Symbiotic associations in the phenotypically-diverse brown alga Saccharina japonica. Plos One. 7: e39587. PMID 22745792 DOI: 10.1371/journal.pone.0039587  1
2012 Striedter GF, Avise JC, Ayala FJ. In the light of evolution VI: brain and behavior. Proceedings of the National Academy of Sciences of the United States of America. 109: 10607-11. PMID 22723364 DOI: 10.1073/pnas.1206166109  1
2012 Li Z, Zhao ZJ, Zhu XQ, Ren QS, Nie FF, Gao JM, Gao XJ, Yang TB, Zhou WL, Shen JL, Wang Y, Lu FL, Chen XG, Hide G, Ayala FJ, et al. Differences in iNOS and arginase expression and activity in the macrophages of rats are responsible for the resistance against T. gondii infection. Plos One. 7: e35834. PMID 22558235 DOI: 10.1371/journal.pone.0035834  1
2012 Kořený L, Sobotka R, Kovářová J, Gnipová A, Flegontov P, Horváth A, Oborník M, Ayala FJ, Lukeš J. Aerobic kinetoplastid flagellate Phytomonas does not require heme for viability. Proceedings of the National Academy of Sciences of the United States of America. 109: 3808-13. PMID 22355128 DOI: 10.1073/pnas.1201089109  1
2012 Wen YZ, Zheng LL, Qu LH, Ayala FJ, Lun ZR. Pseudogenes are not pseudo any more. Rna Biology. 9: 27-32. PMID 22258143 DOI: 10.4161/rna.9.1.18277  1
2012 Yalcindag E, Elguero E, Arnathau C, Durand P, Akiana J, Anderson TJ, Aubouy A, Balloux F, Besnard P, Bogreau H, Carnevale P, D'Alessandro U, Fontenille D, Gamboa D, Jombart T, ... ... Ayala FJ, et al. Multiple independent introductions of Plasmodium falciparum in South America. Proceedings of the National Academy of Sciences of the United States of America. 109: 511-6. PMID 22203975 DOI: 10.1073/pnas.1119058109  1
2012 Ayala FJ. Darwin and Intelligent Design The Blackwell Companion to Science and Christianity. 283-294. DOI: 10.1002/9781118241455.ch25  1
2011 Prugnolle F, Durand P, Ollomo B, Ayala FJ, Renauda F. Reply to Sharp et al.: Host species sampling bias and Plasmodium falciparum origin paradigm shifts. Proceedings of the National Academy of Sciences of the United States of America. 108: E873. PMID 22141155 DOI: 10.1073/pnas.1112821108  1
2011 Tarrío R, Ayala FJ, Rodríguez-Trelles F. The Vein Patterning 1 (VEP1) gene family laterally spread through an ecological network. Plos One. 6: e22279. PMID 21818306 DOI: 10.1371/journal.pone.0022279  1
2011 Balakirev ES, Anisimova M, Ayala FJ. Complex interplay of evolutionary forces in the ladybird homeobox genes of Drosophila melanogaster. Plos One. 6: e22613. PMID 21799919 DOI: 10.1371/journal.pone.0022613  1
2011 Prugnolle F, Ollomo B, Durand P, Yalcindag E, Arnathau C, Elguero E, Berry A, Pourrut X, Gonzalez JP, Nkoghe D, Akiana J, Verrier D, Leroy E, Ayala FJ, Renaud F. African monkeys are infected by Plasmodium falciparum nonhuman primate-specific strains. Proceedings of the National Academy of Sciences of the United States of America. 108: 11948-53. PMID 21730135 DOI: 10.1073/pnas.1109368108  1
2011 Strassmann JE, Queller DC, Avise JC, Ayala FJ. In the light of evolution V: cooperation and conflict. Proceedings of the National Academy of Sciences of the United States of America. 108: 10787-91. PMID 21690379 DOI: 10.1073/pnas.1100289108  1
2011 Wen YZ, Zheng LL, Liao JY, Wang MH, Wei Y, Guo XM, Qu LH, Ayala FJ, Lun ZR. Pseudogene-derived small interference RNAs regulate gene expression in African Trypanosoma brucei. Proceedings of the National Academy of Sciences of the United States of America. 108: 8345-50. PMID 21531904 DOI: 10.1073/pnas.1103894108  1
2011 Ayala FJ. Elixir of life: In vino veritas. Proceedings of the National Academy of Sciences of the United States of America. 108: 3457-8. PMID 21292988 DOI: 10.1073/pnas.1019729108  1
2011 Wang Y, Kaneko O, Sattabongkot J, Chen JH, Lu F, Chai JY, Takeo S, Tsuboi T, Ayala FJ, Chen Y, Lim CS, Han ET. Genetic polymorphism of Plasmodium vivax msp1p, a paralog of merozoite surface protein 1, from worldwide isolates. The American Journal of Tropical Medicine and Hygiene. 84: 292-7. PMID 21292901 DOI: 10.4269/ajtmh.2011.10-0432  1
2011 Prugnolle F, Ayala F, Ollomo B, Arnathau C, Durand P, Renaud F. Plasmodium falciparum is not as lonely as previously considered. Virulence. 2: 71-6. PMID 21224722 DOI: 10.4161/viru.2.1.14608  1
2011 Tazi L, Ayala FJ. Unresolved direction of host transfer of Plasmodium vivax v. P. simium and P. malariae v. P. brasilianum. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 209-21. PMID 20849978 DOI: 10.1016/j.meegid.2010.08.007  1
2011 Ayala FJ. Darwin in the Twenty-First Century: Natural Selection, Molecular Biology, and Species Concepts Handbook of Molecular Microbial Ecology Ii: Metagenomics in Different Habitats. 589-596. DOI: 10.1002/9781118010549.ch55  1
2010 Telleria J, Biron DG, Brizard JP, Demettre E, Séveno M, Barnabé C, Ayala FJ, Tibayrenc M. Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi. Proceedings of the National Academy of Sciences of the United States of America. 107: 20411-6. PMID 21059959 DOI: 10.1073/pnas.1015496107  1
2010 Lun ZR, Lai DH, Li FJ, Lukes J, Ayala FJ. Trypanosoma brucei: two steps to spread out from Africa. Trends in Parasitology. 26: 424-7. PMID 20561822 DOI: 10.1016/j.pt.2010.05.007  1
2010 Duval L, Fourment M, Nerrienet E, Rousset D, Sadeuh SA, Goodman SM, Andriaholinirina NV, Randrianarivelojosia M, Paul RE, Robert V, Ayala FJ, Ariey F. African apes as reservoirs of Plasmodium falciparum and the origin and diversification of the Laverania subgenus. Proceedings of the National Academy of Sciences of the United States of America. 107: 10561-6. PMID 20498054 DOI: 10.1073/pnas.1005435107  1
2010 Avise JC, Ayala FJ. Colloquium paper: in the light of evolution IV: the human condition. Proceedings of the National Academy of Sciences of the United States of America. 107: 8897-901. PMID 20460311 DOI: 10.1073/pnas.1003214107  1
2010 Gleick PH, Adams RM, Amasino RM, Anders E, Anderson DJ, Anderson WW, Anselin LE, Arroyo MK, Asfaw B, Ayala FJ, Bax A, Bebbington AJ, Bell G, Bennett MV, Bennetzen JL, et al. Climate change and the integrity of science. Science (New York, N.Y.). 328: 689-90. PMID 20448167 DOI: 10.1126/science.328.5979.689  1
2010 Ayala FJ. Colloquium paper: the difference of being human: morality. Proceedings of the National Academy of Sciences of the United States of America. 107: 9015-22. PMID 20445091 DOI: 10.1073/pnas.0914616107  1
2010 Nam DH, Oh JS, Nam MH, Park HC, Lim CS, Lee WJ, Sattabongkot J, Klein TA, Ayala FJ. Emergence of new alleles of the MSP-3alpha gene in Plasmodium vivax isolates from Korea. The American Journal of Tropical Medicine and Hygiene. 82: 522-4. PMID 20348492 DOI: 10.4269/ajtmh.2010.08-0332  1
2010 Prugnolle F, Durand P, Neel C, Ollomo B, Ayala FJ, Arnathau C, Etienne L, Mpoudi-Ngole E, Nkoghe D, Leroy E, Delaporte E, Peeters M, Renaud F. African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum. Proceedings of the National Academy of Sciences of the United States of America. 107: 1458-63. PMID 20133889 DOI: 10.1073/pnas.0914440107  1
2010 Ayala FJ. Darwin's explanation of design: from natural theology to natural selection. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 10: 840-3. PMID 19800418 DOI: 10.1016/j.meegid.2009.09.014  1
2010 Ayala FJ. Am I a monkey?: Six big questions about evolution Am I a Monkey?: Six Big Questions About Evolution. 1-85.  1
2009 Rich SM, Leendertz FH, Xu G, LeBreton M, Djoko CF, Aminake MN, Takang EE, Diffo JL, Pike BL, Rosenthal BM, Formenty P, Boesch C, Ayala FJ, Wolfe ND. The origin of malignant malaria. Proceedings of the National Academy of Sciences of the United States of America. 106: 14902-7. PMID 19666593 DOI: 10.1073/pnas.0907740106  1
2009 Ayala FJ. Darwin and the scientific method. Proceedings of the National Academy of Sciences of the United States of America. 106: 10033-9. PMID 19528662 DOI: 10.1073/pnas.0901404106  1
2009 Avise JC, Ayala FJ. In the light of evolution III: two centuries of Darwin. Proceedings of the National Academy of Sciences of the United States of America. 106: 9933-8. PMID 19528649 DOI: 10.1073/pnas.0903381106  1
2009 Rougeron V, De Meeûs T, Hide M, Waleckx E, Bermudez H, Arevalo J, Llanos-Cuentas A, Dujardin JC, De Doncker S, Le Ray D, Ayala FJ, Bañuls AL. Extreme inbreeding in Leishmania braziliensis. Proceedings of the National Academy of Sciences of the United States of America. 106: 10224-9. PMID 19497885 DOI: 10.1073/pnas.0904420106  1
2009 Ayala FJ. One hundred fifty years without Darwin are enough! Genome Research. 19: 693-9. PMID 19411593 DOI: 10.1101/gr.084285.108  1
2009 Haag KL, Gottstein B, Ayala FJ. The EG95 antigen of Echinococcus spp. contains positively selected amino acids, which may influence host specificity and vaccine efficacy. Plos One. 4: e5362. PMID 19401778 DOI: 10.1371/journal.pone.0005362  1
2009 Cela-Conde CJ, Ayala FJ, Munar E, Maestú F, Nadal M, Capó MA, del Río D, López-Ibor JJ, Ortiz T, Mirasso C, Marty G. Sex-related similarities and differences in the neural correlates of beauty. Proceedings of the National Academy of Sciences of the United States of America. 106: 3847-52. PMID 19237562 DOI: 10.1073/pnas.0900304106  1
2009 Ayala FJ, Avise JC. Darwin at 200. Proceedings of the National Academy of Sciences of the United States of America. 106: 2475-6. PMID 19211793 DOI: 10.1073/pnas.0900798106  1
2009 Koffi M, De Meeûs T, Bucheton B, Solano P, Camara M, Kaba D, Cuny G, Ayala FJ, Jamonneau V. Population genetics of Trypanosoma brucei gambiense, the agent of sleeping sickness in Western Africa. Proceedings of the National Academy of Sciences of the United States of America. 106: 209-14. PMID 19106297 DOI: 10.1073/pnas.0811080106  1
2009 Ayala FJ. There is no Place for Intelligent Design in the Philosophy of Biology: Intelligent Design is not Science Contemporary Debates in Philosophy of Biology. 364-390. DOI: 10.1002/9781444314922.ch20  1
2009 Ayala FJ. What the Biological Sciences can and cannot Contribute to Ethics Contemporary Debates in Philosophy of Biology. 316-336. DOI: 10.1002/9781444314922.ch18  1
2009 Ayala FJ, Arp R. Contemporary Debates in Philosophy of Biology Contemporary Debates in Philosophy of Biology. 1-426. DOI: 10.1002/9781444314922  1
2009 Ayala FJ. GEN's interview with Dr. Francisco J. Ayala Genetic Engineering and Biotechnology News. 29.  1
2008 Cachón V, Barahona A, Ayala FJ. The rhetorical construction of Eldredge and Gould's article on the theory of punctuated equilibria in 1972. History and Philosophy of the Life Sciences. 30: 317-37. PMID 19579708  1
2008 Ayala FJ. Where is Darwin 200 years later? Journal of Genetics. 87: 321-5. PMID 19147921 DOI: 10.1007/s12041-008-0054-y  1
2008 Balakirev ES, Pavlyuchkov VA, Ayala FJ. DNA variation and symbiotic associations in phenotypically diverse sea urchin Strongylocentrotus intermedius. Proceedings of the National Academy of Sciences of the United States of America. 105: 16218-23. PMID 18852450 DOI: 10.1073/pnas.0807860105  1
2008 Long S, Jirku M, Ayala FJ, Lukes J. Mitochondrial localization of human frataxin is necessary but processing is not for rescuing frataxin deficiency in Trypanosoma brucei. Proceedings of the National Academy of Sciences of the United States of America. 105: 13468-73. PMID 18768799 DOI: 10.1073/pnas.0806762105  1
2008 Avise JC, Hubbell SP, Ayala FJ. Colloquium paper: in the light of evolution II: biodiversity and extinction. Proceedings of the National Academy of Sciences of the United States of America. 105: 11453-7. PMID 18695213 DOI: 10.1073/pnas.0802504105  1
2008 Tarrío R, Ayala FJ, Rodríguez-Trelles F. Alternative splicing: a missing piece in the puzzle of intron gain. Proceedings of the National Academy of Sciences of the United States of America. 105: 7223-8. PMID 18463286 DOI: 10.1073/pnas.0802941105  1
2008 Alcaraz LD, Olmedo G, Bonilla G, Cerritos R, Hernández G, Cruz A, Ramírez E, Putonti C, Jiménez B, Martínez E, López V, Arvizu JL, Ayala F, Razo F, Caballero J, et al. The genome of Bacillus coahuilensis reveals adaptations essential for survival in the relic of an ancient marine environment. Proceedings of the National Academy of Sciences of the United States of America. 105: 5803-8. PMID 18408155 DOI: 10.1073/pnas.0800981105  1
2008 Badaraco JL, Ayala FJ, Bart JM, Gottstein B, Haag KL. Using mitochondrial and nuclear markers to evaluate the degree of genetic cohesion among Echinococcus populations Experimental Parasitology. 119: 453-459. PMID 18367173 DOI: 10.1016/j.exppara.2008.02.004  1
2008 Lai DH, Hashimi H, Lun ZR, Ayala FJ, Lukes J. Adaptations of Trypanosoma brucei to gradual loss of kinetoplast DNA: Trypanosoma equiperdum and Trypanosoma evansi are petite mutants of T. brucei. Proceedings of the National Academy of Sciences of the United States of America. 105: 1999-2004. PMID 18245376 DOI: 10.1073/pnas.0711799105  1
2008 Haag KL, Gottstein B, Ayala FJ. Taeniid history, natural selection and antigenic diversity: evolutionary theory meets helminthology. Trends in Parasitology. 24: 96-102. PMID 18182327 DOI: 10.1016/j.pt.2007.11.004  1
2008 Ayala FJ. Science, evolution, and creationism. Proceedings of the National Academy of Sciences of the United States of America. 105: 3-4. PMID 18178613 DOI: 10.1073/pnas.0711608105  1
2008 Ayala FJ. The Evolution of Organisms: A Synopsis Handbook of Evolution. 2: 1-26. DOI: 10.1002/9783527619719.ch1  1
2008 Wuketits FM, Ayala FJ. Preface Handbook of Evolution. 2: v-vi. DOI: 10.1002/9783527619719  1
2008 Ayala FJ. From Paley to Darwin: Intelligent design to natural selection Human Evolution. 23: 153-162.  1
2007 Ayala FJ. The Vatican and evolution. History and Philosophy of the Life Sciences. 29: 225-9. PMID 18564513  1
2007 Tatarenkov A, Ayala FJ. Nucleotide variation at the dopa decarboxylase (Ddc) gene in natural populations of Drosophila melanogaster. Journal of Genetics. 86: 125-37. PMID 17968140 DOI: 10.1007/s12041-007-0017-8  1
2007 Lukes J, Mauricio IL, Schönian G, Dujardin JC, Soteriadou K, Dedet JP, Kuhls K, Tintaya KW, Jirků M, Chocholová E, Haralambous C, Pratlong F, Oborník M, Horák A, Ayala FJ, et al. Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy. Proceedings of the National Academy of Sciences of the United States of America. 104: 9375-80. PMID 17517634 DOI: 10.1073/pnas.0703678104  1
2007 Ayala FJ. Darwin's greatest discovery: design without designer. Proceedings of the National Academy of Sciences of the United States of America. 104: 8567-73. PMID 17494753 DOI: 10.1073/pnas.0701072104  1
2007 Avise JC, Ayala FJ. From the Academy: Colloquium Perspective: In the light of evolution I: Adaptation and complex design. Proceedings of the National Academy of Sciences of the United States of America. 104: 8563-6. PMID 17494742 DOI: 10.1073/pnas.0702066104  1
2007 Annan Z, Durand P, Ayala FJ, Arnathau C, Awono-Ambene P, Simard F, Razakandrainibe FG, Koella JC, Fontenille D, Renaud F. Population genetic structure of Plasmodium falciparum in the two main African vectors, Anopheles gambiae and Anopheles funestus. Proceedings of the National Academy of Sciences of the United States of America. 104: 7987-92. PMID 17470800 DOI: 10.1073/pnas.0702715104  1
2007 Graichen DAS, Gottstein B, Matsumoto J, Müller N, Zanotto PMA, Ayala FJ, Haag KL. Expression and diversity of Echinococcus multilocularis AgB genes in secondarily infected mice: evaluating the influence of T-cell immune selection on antigenic variation Gene. 392: 98-105. PMID 17208391 DOI: 10.1016/j.gene.2006.11.015  1
2007 Ayala FJ. Human evolution: The three grand challenges of human biology The Cambridge Companion to the Philosophy of Biology. 233-254. DOI: 10.1017/CCOL9780521851282.012  1
2006 Ayala FJ. Evolution vs. creationism. History and Philosophy of the Life Sciences. 28: 71-82. PMID 17286042  1
2006 Rodríguez-Trelles F, Tarrío R, Ayala FJ. Origins and evolution of spliceosomal introns. Annual Review of Genetics. 40: 47-76. PMID 17094737 DOI: 10.1146/annurev.genet.40.110405.090625  1
2006 Haag KL, Gottstein B, Müller N, Schnorr A, Ayala FJ. Redundancy and recombination in the Echinococcus AgB multigene family: Is there any similarity with protozoan contingency genes? Parasitology. 133: 411-419. PMID 16817991 DOI: 10.1017/S0031182006000564  1
2006 Rodríguez-Trelles F, Tarrío R, Ayala FJ. Models of spliceosomal intron proliferation in the face of widespread ectopic expression. Gene. 366: 201-8. PMID 16288838 DOI: 10.1016/j.gene.2005.09.004  0.44
2006 Haag KL, Zanotto PMA, Alves-Junior L, Gasser RB, Zaha A, Ayala FJ. Searching for antigen B genes and their adaptive sites in distinct strains and species of the helminth Echinococcus Infection, Genetics and Evolution. 6: 251-261. PMID 16207536 DOI: 10.1016/j.meegid.2005.07.003  1
2003 Sáez AG, Tatarenkov A, Barrio E, Becerra NH, Ayala FJ. Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: unraveling the footprint of a recent selective sweep. Proceedings of the National Academy of Sciences of the United States of America. 100: 1793-8. PMID 12578968 DOI: 10.1073/pnas.242746799  1
2002 DeFilippis VR, Ayala FJ, Villarreal LP. Evidence of diversifying selection in human papillomavirus type 16 E6 but not E7 oncogenes. Journal of Molecular Evolution. 55: 491-9. PMID 12355268 DOI: 10.1007/s00239-002-2344-y  1
2002 Machado CA, Ayala FJ. Sequence variation in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) and trypanothione reductase (TR) genes of Trypanosoma cruzi. Molecular and Biochemical Parasitology. 121: 33-47. PMID 11985861 DOI: 10.1016/S0166-6851(02)00019-1  1
2001 Machado CA, Ayala FJ. Nucleotide sequences provide evidence of genetic exchange among distantly related lineages of Trypanosoma cruzi. Proceedings of the National Academy of Sciences of the United States of America. 98: 7396-401. PMID 11416213 DOI: 10.1073/pnas.121187198  1
1999 Tatarenkov A, Kwiatowski J, Skarecky D, Barrio E, Ayala FJ. On the evolution of Dopa decarboxylase (Ddc) and Drosophila systematics. Journal of Molecular Evolution. 48: 445-62. PMID 10079283  1
1997 Barrio E, Ayala FJ. Evolution of the Drosophila obscura species group inferred from the Gpdh and Sod genes. Molecular Phylogenetics and Evolution. 7: 79-93. PMID 9007023 DOI: 10.1006/mpev.1996.0375  1
1996 Ayala FJ, Barrio E, Kwiatowski J. Molecular clock or erratic evolution? A tale of two genes. Proceedings of the National Academy of Sciences of the United States of America. 93: 11729-34. PMID 8876205 DOI: 10.1073/pnas.93.21.11729  1
1995 Moya A, Galiana A, Ayala FJ. Founder-effect speciation theory: failure of experimental corroboration. Proceedings of the National Academy of Sciences of the United States of America. 92: 3983-6. PMID 7732017  1
1995 Escalante AA, Barrio E, Ayala FJ. Evolutionary origin of human and primate malarias: evidence from the circumsporozoite protein gene. Molecular Biology and Evolution. 12: 616-26. PMID 7659017  1
1994 Kwiatowski J, Latorre A, Skarecky D, Ayala FJ. Characterization of a Cu/Zn superoxide dismutase-encoding gene region in Drosophila willistoni. Gene. 147: 295-6. PMID 7926818 DOI: 10.1016/0378-1119(94)90085-X  1
1993 Galiana A, Moya A, Ayala FJ. FOUNDER-FLUSH SPECIATION IN DROSOPHILA PSEUDOOBSCURA: A LARGE-SCALE EXPERIMENT. Evolution; International Journal of Organic Evolution. 47: 432-444. PMID 28568735 DOI: 10.1111/j.1558-5646.1993.tb02104.x  1
1993 Tyler RH, Brar H, Singh M, Latorre A, Graves JL, Mueller LD, Rose MR, Ayala FJ. The effect of superoxide dismutase alleles on aging in Drosophila. Genetica. 91: 143-9. PMID 8125265 DOI: 10.1007/BF01435994  1
1992 Barrio E, Latorre A, Moya A, Ayala FJ. Phylogenetic reconstruction of the Drosophila obscura group, on the basis of mitochondrial DNA. Molecular Biology and Evolution. 9: 621-35. PMID 1630303  1
1991 Guo PZ, Mueller LD, Ayala FJ. Evolution of behavior by density-dependent natural selection. Proceedings of the National Academy of Sciences of the United States of America. 88: 10905-6. PMID 1961760  1
1991 Milosevic M, Moya A, Ayala FJ. Fertility and viability at the Sod locus in Drosophila melanogaster: non-additive and asymmetric selection. Genetical Research. 57: 267-72. PMID 1909679  1
1991 Mueller LD, Guo PZ, Ayala FJ. Density-dependent natural selection and trade-offs in life history traits. Science (New York, N.Y.). 253: 433-5. PMID 1907401  1
1991 Peng TX, Moya A, Ayala FJ. Two modes of balancing selection in Drosophila melanogaster: overcompensation and overdominance. Genetics. 128: 381-91. PMID 1906418  1
1990 Milosevi? M, Moya A, Ayala FJ. Overcompensation as a mechanism for maintaining polymorphism: egg-to-adult viability in Drosophila. Genetica. 82: 183-7. PMID 2128629  1
1989 Bierbaum TJ, Mueller LD, Ayala FJ. DENSITY-DEPENDENT EVOLUTION OF LIFE-HISTORY TRAITS IN DROSOPHILA MELANOGASTER. Evolution; International Journal of Organic Evolution. 43: 382-392. PMID 28568549 DOI: 10.1111/j.1558-5646.1989.tb04234.x  1
1989 Lenski RE, Slatkin M, Ayala FJ. Mutation and selection in bacterial populations: alternatives to the hypothesis of directed mutation. Proceedings of the National Academy of Sciences of the United States of America. 86: 2775-8. PMID 2704747  1
1989 Lenski RE, Slatkin M, Ayala FJ. Another alternative to directed mutation. Nature. 337: 123-4. PMID 2643054 DOI: 10.1038/337123b0  1
1988 Latorre A, Barrio E, Moya A, Ayala FJ. Mitochondrial DNA evolution in the Drosophila obscura group. Molecular Biology and Evolution. 5: 717-28. PMID 3221793  1
1988 Smit-McBride Z, Moya A, Ayala FJ. Linkage disequilibrium in natural and experimental populations of Drosophila melanogaster. Genetics. 120: 1043-51. PMID 3147215  1
1987 Marinkovi? D, Tuci? N, Moya A, Ayala FJ. Genetic Diversity and Linkage Disequilibrium in Drosophila melanogaster with Different Rates of Development. Genetics. 117: 513-20. PMID 17246407  1
1986 Latorre A, Moya A, Ayala FJ. Evolution of mitochondrial DNA in Drosophila subobscura. Proceedings of the National Academy of Sciences of the United States of America. 83: 8649-53. PMID 16578796  1
1986 Tibayrenc M, Ward P, Moya A, Ayala FJ. Natural populations of Trypanosoma cruzi, the agent of Chagas disease, have a complex multiclonal structure. Proceedings of the National Academy of Sciences of the United States of America. 83: 115-9. PMID 3510428  1
1986 Peng TX, Moya A, Ayala FJ. Irradiation-resistance conferred by superoxide dismutase: possible adaptive role of a natural polymorphism in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 83: 684-7. PMID 3080745  1
1985 Mueller LD, Barr LG, Ayala FJ. Natural selection vs. random drift: evidence from temporal variation in allele frequencies in nature. Genetics. 111: 517-54. PMID 4054608  1
1982 Mueller LD, Ayala FJ. Estimation and interpretation of genetic distance in empirical studies. Genetical Research. 40: 127-37. PMID 7152254  1
1981 Mueller LD, Ayala FJ. Trade-off between r-selection and K-selection in Drosophila populations. Proceedings of the National Academy of Sciences of the United States of America. 78: 1303-5. PMID 16592964  1
1981 Mueller LD, Ayala FJ. Fitness and density-dependent population growth in Drosophila melanogaster. Genetics. 97: 667-77. PMID 6795084  1
1976 Avise JC, Ayala FJ. GENETIC DIFFERENTIATION IN SPECIOSE VERSUS DEPAUPERATE PHYLADS: EVIDENCE FROM THE CALIFORNIA MINNOWS. Evolution; International Journal of Organic Evolution. 30: 46-58. PMID 28565048 DOI: 10.1111/j.1558-5646.1976.tb00880.x  1
1975 Avise JC, Smith JJ, Ayala FJ. ADAPTIVE DIFFERENTIATION WITH LITTLE GENIC CHANGE BETWEEN TWO NATIVE CALIFORNIA MINNOWS. Evolution; International Journal of Organic Evolution. 29: 411-426. PMID 28563177 DOI: 10.1111/j.1558-5646.1975.tb00831.x  1
1975 Avise JC, Ayala FJ. Genetic change and rates of cladogenesis. Genetics. 81: 757-73. PMID 1213274  1
1975 Fontdevila A, Mendez J, Ayala FJ, McDonald J. Maintenance of allozyme polymorphisms in experimental populations of Drosophila. Nature. 255: 149-51. PMID 1128678  1
1973 Dobzhansky T, Ayala FJ. Temporal frequency changes of enzyme and chromosomal polymorphisms in natural populations of Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 70: 680-3. PMID 4514981  1
1971 Ayala FJ, Powell JR, Dobzhansky T. Polymorphisms in continental and island populations of Drosophila willistoni. Proceedings of the National Academy of Sciences of the United States of America. 68: 2480-3. PMID 5289881  1
1970 Ayala FJ, Mourão CA, Pérez-Salas S, Richmond R, Dobzhansky T. Enzyme variability in the Drosophila willistoni group. I. Genetic differentiation among sibling species. Proceedings of the National Academy of Sciences of the United States of America. 67: 225-32. PMID 5272313  1
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