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Dr. Gabriela Aguileta

SNF Researcher- Bioinformatics and Integrative Genomics

Publications by type


→ Peer-reviewed articles

→ Book chapters

→ Theses

→ Popular science books

see also my non-science publications

Gabriela Aguileta

Publications

Peer-reviewed articles

  1. Branco, S., Badouin, H., Rodríguez de la Vega, R., Gouzy, J., Carpentier, F., Aguileta, G., ... and Giraud, T. (2017) Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism. PNAS 114:7067-7072.
  2. Badouin, H., Gladieux, P., Gouzy, J., Siguenza, S., Aguileta, G., Snirc, A., Le Prieur, S., Jeziorski, C., Branca, A. and Giraud, T. (2017) Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates. Molecular Ecology 26:2041-2062.
  3. Gladieux, P., Byrnes, E.J.III, Aguileta, G., Fisher, M., Billmyre, R.B., Heitman, J. and Giraud, T. (2017) Epidemiology and Evolution of Fungal Pathogens in Plants and Animals. Genetics and Evolution of Infectious diseases, 2nd ed. 71-98.
  4. Aguileta, G., Badouin, H., Hood, M.E., Moller, A.P., Le Prieur, S., Snirc, A., Siguenza, S., Mousseau, T.A., Shykoff, J.A., Cuomo, C.A. and Giraud, T. (2016) Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl. Molecular Ecology 25:3370-3383.
  5. Chiapello, H. ,Mallet, L., Guérin, C., Aguileta, G. et al. (2015) Deciphering genome content and evolutionary relationships of isolates from the fungus Magnaporthe oryzae attacking different host plants. Genome Biology and Evolution 7:2896-2912.
  6. Badouin, H., Hood, M.E., Gouzy, J., Aguileta, G., Siguenza, S., Perlin, M.H., Cuomo, C.A., Fairhead, C., Branca, A. and Giraud, T. (2015). Chaos of rearrangements in the mating-type chromosomes of the anther-smut fungus of Microbotryum lychnidis-dioicae. Genetics 200:1275-1284.
  7. Perlin, M.H., Amselem, J., Fontanillas, E., Toh, S.S., Chen, Z., Goldberg, J., Duplessis, S., Henrissat, B., Young, S., Zeng, Q., Aguileta, G., et al. (2015). Sex and Parasites: Genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics 16:461.
  8. Fontanillas, E,.Hood, M.E., Badouin, H., Petit, E., Barbe, V., Gouzy, J., de Vienne, D.M., Aguileta, G. et al. (2015) Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi. Molecular Biology and Evolution 32 :928–943.
  9. Ropars, J., Aguileta, G., de Vienne D.M. and Tatiana Giraud (2014) Massive gene swamping among cheese-making Penicillium fungi. Microbial Cell 1:107-109.
  10. Aguileta, G., de Vienne, D.M., Ross, O.N., et al. (2014) High variability of mitochondrial gene order in fungi. Genome Biology and Evolution 6:451-465.
  11. Gladieux, P., Ropars, J. Badouin, H., Branca, A. Aguileta, G. et al. (2014) Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Molecular Ecology, DOI: 10.1111/mec.12631
  12. Gladieux, P., Devier, B. Aguileta, G., Cruaud, C. and Giraud, T. (2013) Purifying selection after episodes of recurrent adaptive diversification in fungal pathogens. Infections, Genetics and Evolution 17:123-131.
  13. Gabaldon, T., Martin,T., Marcet-Houben,M., Durrens,P., Bolotin-Fukuhara,M., Lespinet,O., Aguileta,G., et al. (2013) Comparative genomics of emerging pathogens in the Candida glabrata clade. BMC Genomics 14:623.
  14. Petit, E., Giraud, T., de Vienne, D.M., Coelho, M.A., Aguileta, G., et al. (2012) Linkage to the mating-type locus across the genus Microbotryum: insights into non-recombining chromosomes. Evolution. 66:3519-3533.
  15. Aguileta, G., Lengellé, J., Chiapello, et al. (2012) Genes under positive selection in a model plant pathogenic fungus, Botrytis. Infections, Genes and Evolution. 12:987-996.
  16. De Vienne, D.M., Ollier, S. and Aguileta, G. (2012) Phylo-MCOA : A fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis. Molecular Biology and Evolution. 29:1587- 1598.
  17. De Vienne, D.M., Aguileta, G., Ollier, S. (2011) The Euclidian nature of phylogenetic distance matrices. Systematic Bology. 60:826-832.
  18. López-Villavicencio M.1, Aguileta G.1, Giraud T. et al. (2010) Sex in Penicillium : combined phylogenetic and experimental approaches. Fungal Genetics and Biology. 47:693-706. 1These authors contributed equally to this work.
  19. Devier B, Aguileta G., Hood ME, Giraud T. (2010) Using phylogenies of pheromone receptor genes in the Microbotryum violaceum species complex to investigate possible speciation by hybridization. Mycologia. 102:689-696.
  20. Aguileta, G., Lengelle, J., Marthey, S., et al. (2010) Finding candidate genes under positive selection in Non-model species : examples of genes involved in host specialization in pathogens. Molecular Ecology. 19:292-306.
  21. Giraud F, Giraud T, Aguileta G., et al. (2010) Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing. Int Journal of Food Microbiology. 137:204-213.
  22. Aguileta, G., Refregier, G., Yockteng, R., et al. (2009) Rapidly evolving genes in pathogens: methods for detecting positive selection and examples among fungi, bacteria, viruses and protists. Invited review for Infections, Genetics and Evolution. 9:656-670.
  23. Devier, B.1, Aguileta, G.1, Hood, M.E., Giraud, T. (2009) Ancient trans-specific polymorphism at pheromone receptor genes in basidiomycetes. Genetics. 181:1-15. 1These authors contributed equally to this work.
  24. Aguileta G., Hood ME, Refrégier G, Giraud T. (2009) Genome evolution in pathogenic and symbiotic fungi. Advances in Botanical Research. 49: 157-199.
  25. Marthey S., Aguileta, G., Rodolphe, F., et al. (2008) FUNYBASE : a FUNgal phYlogenomic dataBASE. BMC Bioinformatics. 9:456.
  26. Aguileta, G., Marthey, S., Chiapello, H., et al. (2008) Assesing the per- formance of single-copy genes for recovering robust phylogenies. Systematic Biology 57: 613-627.
  27. Aguileta, G., Bielawski, J.P., Yang, Z. (2006) Proposed standard nomenclature for the alpha- and b–globin gene families. Genes and Genetic Systems 81: 367-371.
  28. Aguileta, G., Bielawski, J.P., Yang, Z. (2006) Evolutionary rate variation among vertebrate beta globin genes : implications for dating gene family duplication events. Gene 380: 21-29.
  29. Aguileta, G., Bielawski, J.P., Yang, Z. (2004) Gene conversion and functional divergence in the beta–globin gene family. J. Mol. Evol. 59: 177-189.

 

Book chapters

  1. Gladieux, P., Byrnes III, E.J., Aguileta, G., Fisher, M., Heitman, J., Giraud, T. (2013) Epidemiology and Evolution of Fungal Pathogens in Plants and Animals. In : Genetics and Evolution of Infectious Diseases. Michel Tibayrenc (ed.). Elsevier, Inc. London, 749p.
  2. Aguileta G., and Giraud T. (2012) Application of codon models to the study of fungal genome evolution. In : Codon Evolution. Mechanisms and Models. Gina M. Cannarozzi and Adrian Schneider (eds.) Oxford University Press. 296p.

 

Theses

  1. Aguileta, G. PhD Thesis. (2004) The evolution of the beta-globin gene family. Director : Professor Ziheng Yang. University College London, London, UK.
  2. Aguileta, G. BSc Thesis in Spanish. (1999) Construction, purification and kinetic characterization of two chimerical proteins of Triosephosphate Isomerase (TIM). Director : Alejandro Fernández Velasco. Universidad Nacional Autó- noma de México.

 

Popular science books (in Spanish)

Miguel Ángel & Gabriela Aguileta. (2006). "Las células madre", 24pp. Libros del escarabajo, México, D.F. ISBN 970-5775-20-6. (on stem cells)

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Gabriela Aguileta (2005). "El origen de la vida", 24pp. Libros del escarabajo, México, D.F. ISBN 970-5775-17-6 (on the origin of life)

Link

Gabriela Aguileta (2005). "Los virus", 24pp. Libros del escarabajo, México, D.F. ISBN 970-5775-15-X (on viruses)

Link