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Dinka Mandakovic, Rodrigo Pulgar, Jonathan Maldonado, Wladimir Mardones, Mauricio González, Francisco A. Cubillos* and Verónica Cambiazo*. Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures. Microorganisms20208(6), 956; [Article]

Urbina K*, Villarreal P*, Nespolo RF, Salazar R, Santander R, Cubillos FAVolatile compound screening using HS-SPME-GC/MS on Saccharomyces eubayanus strains under low-temperature pilsner wort fermentation. Microorganisms 20208(5), 755; [Article]

Nespolo RF*, Villarroel CA*, Oporto CI, Tapia SM, Vega F, Urbina K, De Chiara M, Mozzachiodi S, Mikhalev E, Thompson D, Saenz-Agudelo P, Larrondo LF, Liti G, Cubillos FA. An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages. PLoS Genetics. 2020. 10.1371/journal.pgen.1008777 [Article].

Devia J., Bastias C., Kessi-Perez EI., Villarroel CA, Cubillos FA, Liti G., Martínez C & Salinas F. Transcriptional activity and protein levels for horizontally acquired genes in yeast reveal hallmarks of adaptation to fermentative environments. Frontiers in Genetics 2020. doi: 10.3389/fgene.2020.00293 [Article].

Roberto F. Nespolo, Jaiber J. Solano-Iguaran, Rocío Paleo-López, Julian F. Quintero-Galvis, Francisco A. Cubillos, Francisco Bozinovic. Performance, genomic rearrangements and signatures of adaptive evolution: lessons from fermentative yeasts. Ecology and Evolution. 2020. Doi: 10.1002/ece3.6208.

Mardones W, Villarroel CA, Krogerus K, Tapia SM, Urbina K, Oporto CI, O’Donnell S, Minebois R, Nespolo R, Fischer G, Querol A, Gibson B, Cubillos FA*. Molecular profiling of beer wort fermentation diversity across natural Saccharomyces eubayanus isolates. Microb Biotechnol. 2020 Feb 25. doi: 10.1111/1751-7915.13545 [Article]

Libkind D, Peris D, Cubillos FA, Steenwyk JL, Opulente DA, Langdon QK, Rokas A, Hittinger CT. Into the wild: new yeast genomes from natural environments and new tools for their analysis. FEMS Yeast Res. 2020 Feb 3. pii: foaa008. doi: 10.1093/femsyr/foaa008 [Article]


Oporto, C. I., Villarroel, C. A., Tapia, S. M., Garcia, V., and Cubillos, F. A. 2019. Distinct Transcriptional Changes in Response to Patulin Underlie Toxin Biosorption Differences in Saccharomyces Cerevisiae. Toxins (Basel). 11 [Article]?

Molinet, J., Cubillos, F. A., Salinas, F., Liti, G., and Martinez, C. 2019. Genetic variants of TORC1 signaling pathway affect nitrogen consumption in Saccharomyces cerevisiae during alcoholic fermentation. PLoS One. 14:e0220515 [Article]?

Cubillos, F. A., Gibson, B., Grijalva-Vallejos, N., Krogerus, K., and Nikulin, J. 2019. Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers. Yeast. [Article]???


Brice C, Cubillos FA, Dequin S, Camarasa C, Martínez C 2018. Adaptability of the Saccharomyces cerevisiaeyeasts to wine fermentation conditions relies on their strong ability to consume nitrogen. PLoS 2018 Feb 12;13(2):e0192383. doi: 10.1371/journal.pone.0192383. eCollection 2018.[Pubmed]

Tapia, S. M., Cuevas, M., Abarca, V., Delgado, V., Rojas, V., García, V., Brice, C., Martínez, C., Salinas, F., Larrondo, L. F., and Cubillos, F. A. 2018. GPD1 and ADH3 natural variants underlie glycerol yield differences in wine fermentation. Front. Microbiol. 9:1–13 [Article]?


?Quispe X, Tapia SM, Villarroel C, Oporto C, Abarca V, García V, Martínez C, Cubillos FA. 2017. Genetic basis of mycotoxin susceptibility differences between budding yeast isolates. Scientific Reports. 2017 Aug 23;7(1):9173. doi: 10.1038/s41598-017-09471-z.

Godoy L, Silva-Moreno E, Mardones W, Guzman D, Cubillos FA, Ganga A. 2017. Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensisLAMAP2480. J Mol Microbiol Biotechnol. 2017 Jun 9;27(3):147-158.

Cubillos FA, Brice C, Molinet J, Tisné S, Abarca V, Tapia SM, Oporto C, García V, Liti G & Martínez C. 2017. Identification of nitrogen consumption genetic variants in yeast through QTL mapping and Bulk segregant RNA-seq analyses. G3(Bethesda). 2017 Jun 7;7(6):1693-1705.

Thompson DA & Cubillos FA. 2017. Natural gene expression variation studies in yeast. Yeast Jan;34(1):3-17.


Cubillos F.A.Exploiting budding yeast natural variation for industrial processes. 2016. Current Genetics. Nov;62(4):745-75.

Kessi-Pérez EI, Araos S, García V, Salinas F, Abarca V, Larrondo LF, Martínez C & Cubillos FA. 2016. RIM15antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast. FEMS Yeast Research. pii: fow021. Epub 2016 Mar 4.

Salinas F, de Boer CG, Abarca V, García V, Cuevas M, Araos S, Larrondo LF, Martínez C, Cubillos FA. 2016. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. Scientific Reports, srep21849.


Cubillos FA*, Stegle O, Grondin C, Canut M, Tisne S, Gy I & Loudet O. 2014. Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis. Plant Cell 26(11):4298-4310.

Valdes J, Tapia P, Cepeda P, Varela J, Godoy L, Cubillos FA, Silva E, Martínez C & Ganga A. Draft genome sequence and transcriptome analysis of the wine spoilage yeast Dekkera bruxellensisLAMAP2480 provides insights into genetic diversity, metabolism and survival. FEMS microbiology letters361(2): 104-106.

Jara M*, Cubillos FA*, García V, Salinas F, Aguilera O, Liti G & Martínez C. 2014. Natural variation in the central nitrogen metabolism in fermenter yeasts. PLoS ONE9(1): e86533.

Coustham V, Vlad D, Deremetz A, Gy I, Cubillos FA, Kerdaffrec E, Loudet O & Bouché N. 2014. SHOOT GROWTH1 Maintains Arabidopsis Epigenomes by Regulating IBM1. PLoS ONE9  (1), e84687.


Cubillos FA*, Parts L*, Salinas F, Bergström A, Scovacicricchi E, Zia A, Illingworth CJ, Mustonen V, Ibstedt S, Warringer J, Louis EJ, Durbin R†& Liti G†. 2013. High-Resolution Mapping of Complex Traits with a Four-Parent Advanced Intercross Yeast Population. Genetics.195(3):1141-55

Liti G, Nguyen Ba A, Blythe M, Müller C, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, Siow C, Warringer J, Moses A, Louis EJ*& Nieduszynski C*. 2013. High Quality de novo Sequencing and Assembly of the Saccharomyces arboricolusgenome. BMC Genomics.14 (1), 69.


Salinas F, Cubillos FA, Soto D, García V, Bergström A, Warringer J, GangaA, Louis EJ, Liti G* & Martinez C*. 2012. The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiaePLoS ONE. 7 (11), e49640.

Cubillos FA*, Yansouni J*, Khalili H, Balzergue S, Elftieh S, Martin-Magniette ML, Serrand Y, Lepiniec L, Baud S, Dubreucq B, Renou JP, Camilleri C§& Loudet O§. 2012. Expression variation in connected recombinant populations of Arabidopsis thalianahighlights distinct transcriptome architectures. BMC Genomics. Mar 27;13:117.

Zörgö E, Gjuvsland A, Cubillos FA, Louis EJ, Liti G, Blomberg A, Omholt SW & Warringer J. 2012. Life history shapes trait heredity by promoting accumulation of loss-of-function alleles in yeast.Molecular Biology Evolution.Jul;29(7):1781-9.

Cubillos FA, Coustham V & Loudet O. 2012. Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants. Current Opinion in Plant Biology. Apr;15(2):192-8.


Warringer J, Zörgö E, Cubillos FA, Zia A, Gjuvsland A, Simpson J, Forsmark A, Durbin R, Omholt S, Louis EJ, Liti G, Moses A & Blomberg A. 2011. Trait variation in yeast is defined by population history. PLoS GeneticsJun;7(6):e1002111.

Parts L, Cubillos FA, Warringer J, Jain K, Salinas F, Bumpstead S, Molin M, Zia A, Simpson J, Quail M, Moses A, Louis EJ, Durbin R & Liti G. 2011. Revealing the genetic structure of a trait by sequencing a population under selection. Genome ResearchJul;21(7):1131-8. [Pubmed]

Cubillos FA, Billi E, Zörgö E, Parts L, Fargier P, Omholt S, Blomberg A, Warringer J, Louis EJ & Liti G. 2011. Assessing the complex architecture of polygenic traits in diverged yeast populations. Molecular Ecology, Apr;20(7):1401-13.


Cubillos FA, Louis EJ, Liti G*. 2009. Generation of a Large Set of Genetically Tractable Haploid and Diploid SaccharomycesStrains. FEMS Yeast Research. 9, 1217-1225.

Liti G*, Haricharan S, Cubillos FA, Tierney AL, Sharp S, Bertuch AA, Parts L, Bailes E, Louis EJ. 2009. Segregating YKU80and TLC1Alleles Underlying Natural Variation in Telomere Properties in Wild Yeast. PLoS Genetics.5 (9); e1000659.

Cubillos FA, Vásquez C, Faugeron S, Ganga A, Martínez C. 2009. Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations.FEMS Microbiology Ecology. Jan;67(1):162-70.

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