CV Dr. Francisco Cubillos

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Francisco Cubillos




2007                Molecular Engineering Biotechnology B.Sc degree, University of Chile.

2008                Master in Microbiology University of Chile, Yeast Population Genetics, Advisor: Claudio Martínez

2010                PhD in Genetics University of Nottingham, 2010, Multi-parent populations in yeast, Advisor: Prof Ed Louis

2013                Postdoctoral Fellow INRA-Versailles, 2013, Natural variation in non-coding regions in Arabidopsis thaliana, Advisor: Olivier Loudet

APPOINTMENTS (2015-2022)

2013–present Associate Professor at Universidad de Santiago de Chile, Chile

2022 – present Associate Researcher Millenium Nucleus LiLi

2017 –present Associate Researcher Millenium Institute for Integrative Biology.

2016                 Young investigator of the Millennium Nucleus for Fungal Integrative and Synthetic Biology


2020-2022     President of the Chilean Genetics Society
2020-2021      Ministerial Advisory Committee Genomic Sequencing SARS-CoV-2. Ministerio de Ciencias.
2021                President Organizer Latin American Congress of Genetics ALAG2021.
2020                Organizing Committee Genetic Annual Meeting 2020. Virtual, Chile
2018                Congress Regional Organizing Committee ISSY34, Bariloche, Argentina
2018                Organizing Committee Genetic Annual Meeting 2018. Puerto Varas, Chile.
2016 – 2018    Accreditation Committee of the Doctoral Program in Biotechnology. Universidad de Santiago de Chile


2022 – present    Luis Saona
2022 – present    Felipe Muñoz
2021 – present    Macarena Araya
2020 – present    Pablo Villarreal
2020 – present    Jennifer Molinet
2019 – 2022       Wladimir Mardones
2017 – 2020       Carlos Villarroel


Current           Franco Vega
Current           Tomas Peña
Current           Vasni Zavaleta
Current           Pablo Quintrel
Current           Chrisitan Oporto
Current           Agustin Cofré


2020                Leonor Alvarado
2016                Mara Cuevas.


Current           Lucas Araya
Current           Javier del Pino
Current           Marlene Leal
Current           Sebastian Espinoza
Current           Felipe Sandoval
Current           Juan Navarrete
Current           Francisco Torres
Current           Martin Domeyko
Current           Dario Gonzalez
2022              Antonio Molina
2022              Constanza Acuña
2022              José Benavides
2022              Alex Valenzuela
2021              Camila Venegas
2021              Javier Herrara
2021              Alonso Marquez
2021              Constanza Vidal
2021              Sebastián Olivares
2021              Daniela Escobar
2021              Carolina Leiva
2020              Sebastián Flores
2020              Tomás Peña
2018              Kamila Urbina
2018              Pablo Quintrel


2021                TWAs Young Investigator
2020                EMBO Global Investigator
2016                Beca Santander for internship in Jose Manuel Guillamon’s laboratory, Valencia, Spain.

GRANTS as PI (2015-2022)

2022 – 2026    FONDECYT Regular 1220026 ‘Genomic and transcriptional profiling of fermentative vigor in laboratory lager yeast hybrids.. Investigador Principal.

2022 – 2025    Associated researcher Grant Millennium Nucelus LiLi.

2021-2025      EMBO Global Investigator. Phylogenomic studies in ethanol-tolerant yeast from Patagonia. Principal Investigator.

2020 – 2022    Networking Grant CONICYT-PCI REDES for International Scientific Cooperation Universidad de Santiago de Chile – University of Madison Wisconsin – TU Delft. ‘The SynVAR Collaborative Network: Yeast genetics for Synthetic Biology and Natural Variation advances innative Patagonian yeasts’. Principal Investigator.

2019 – 2022    Research Grant for International Scientific Cooperation ECOS/CONICYT C18B03 ‘Genomic and physiological Characterization of ethanol-producing yeast populations from Patagonia’. Principal Researcher.

2018 – 2020    FIC Región de los Rios. ‘Hacia la denominación de origen de la cerveza de Los Ríos: descubriendo una levadura nativa’. Co-Researcher

2018 – 2022    FONDECYT Regular 1180161 ‘Decoding the genomic and phenomic complexity of the cryotolerant yeast Saccharomyces eubayanus’. Principal Investigator.

2018 – present Associate researcher Millennium Institute for Integrative Systems and Synthetic Biology (iBio).

2016-2017      Research Grant Millennium Nucleus in Synthetic Fungi Biology MNFISB. Associate Researcher.

2017                Grant Proyectos Extraordinarios USACH 021771CR_CONT ‘Genetic and phenotypic variability in S. cerevisiae natural populations of industrial interest’.

2016 – 2017    PCI-Conicyt. Redes 150077. Networking Grant for International Scientific Cooperation Universidad de Santiago de Chile – INRA Montpellier, France with Prof Sylvie Dequin. ‘Applied yeast genetics for high quality food products’.

2014 – 2017    FONDECYT 11140097. Research Grant FONDECYT de Iniciación ‘Quantitative genetic analysis of the response to mycotoxins in yeast’.

2013 – 2016    ECOS-CONICYT CB1302. Research Grant for International Scientific Cooperation ECOS/CONICYT 2013 ‘Identification of allelic variants underlying Nitrogen Metabolism in yeast through an integrative BS-RNA seq approach’ together with Dr. Gianni Liti, IRCAN, France.

2013 – 2015    CONICYT-PAI 82130010: Research Returning Grant ‘Study of the regulatory variants underlying natural diversity in Saccharomyces cerevisiae’ Program ‘Apoyo al Retorno de Investigadores/as desde el Extranjero – Convocatoria 2012’.


2020-2022      FIC Región de los Rios-Chile. Supporting economic re-activation of the brewing Industry in the Rios Region. Co-researcher.

2017-2020      INACH Regular Project RT_09_16 to Dr. Claudio Saez. ‘Biochemical and molecular responses disclose mechanisms of Antarctic macroalgae to thrive under Climate Change’. Co-PI

2016                Millennium Nucleus MN-FISB. Research Grant Millennium Nucleus in Synthetic Fungi Biology. Young Researcher. 2016.

2015-2019      FONDECYT 1150522. Research Grant FONDECYT Regular to Dr. Claudio Martínez. ‘Identification of natural genetic variants underlying nitrogen assimilation diversity in yeast’. Co-PI

2013-2015      Fic Gore Atacama 33 03 248 Establishment of sustainable systems for process control Pajarete Wine production in the province of Huasco to strengthen their local identity to Angélica Ganga. Co-PI


During the Millenium Institute Dr Cubillos has developed a series of outreach activities with brewers, teaching them about yeast microbiology and bacteria spoilage in the brewery environment. Cubillos organized over four events, involving more than 300 beer producers across different cities in the country.


Dr Cubillos has a series of international collaborations, mostly within Europe and USA. Among other, Dr Cubillos actively collaborates with Dr Gianni Liti (IRCAN-France) through an ECOS – CONICYT GRANT and Dr. Gilles Fischer, fundend by another ECOS-CONICYT Grant. Moreover, recently Dr Cubillos got another international grant awarded to collaborate beer yeast specialist from the Nethederlands and US. Dr Cubillos also collaborates with Dr Amparo Querol from IATA – Valencia with whom he has been collaborating for the past years in Spain. Similarly, Dr Cubillos has a series of informal collaborations with teams in Finland (Dr Brian Gibson, VTT Technical Research Centre Espoo), Dr Rike Stelkens (Stockholm University, Sweden), Dr Diego Libkind (Universidad Nacional del Comahue, Argentina), Dr Duncan Greig (UCL, UK) and Dr Jonas Warringer (Gothenburg University, Sweden).



  1. Boynton, P., Patil, K.R., Stefanini, I., Stelkens, R., Cubillos, F.A., 2022. Yeast ecology and communities. Yeast 39, 3.
  2. Mardones, W., Villarroel, C.A., Abarca, V., Urbina, K., Peña, T.A., Molinet, J., Nespolo, R.F., Cubillos, F.A., 2022. Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing conditions. Microb Biotechnol 15, 967–984.
  3. Molinet, J., Urbina, K., Villegas, C., Abarca, V., Oporto, C.I., Villarreal, P., Villarroel, C.A., Salinas, F., Nespolo, R.F., Cubillos, F.A., 2022. A Saccharomyces eubayanus haploid resource for research studies. Sci Rep 12, 5976.
  4. Mozzachiodi, S., Bai, F.-Y., Baldrian, P., Bell, G., Boundy-Mills, K., Buzzini, P., ?adež, N., Cubillos, F.A., Dashko, S., Dimitrov, R., Fisher, K.J., Gibson, B., Gouliamova, D., Greig, D., Heistinger, L., Hittinger, C.T., Jecmenica, M., Koufopanou, V., Landry, C.R., Mašínová, T., Naumova, E.S., Opulente, D., Peña, J.J., Petrovi?, U., Tsai, I.J., Turchetti, B., Villarreal, P., Yurkov, A., Liti, G., Boynton, P., 2022. Yeasts from temperate forests. Yeast 39, 4–24.
  5. Vaishnav, E.D., de Boer, C.G., Molinet, J., Yassour, M., Fan, L., Adiconis, X., Thompson, D.A., Levin, J.Z., Cubillos, F.A., Regev, A., 2022. The evolution, evolvability and engineering of gene regulatory DNA. Nature 603, 455–463.
  6. Villarreal, P., Quintrel, P.A., Olivares-Muñoz, S., Ruiz, J.J., Nespolo, R.F., Cubillos, F.A., 2022a. Identification of new ethanol-tolerant yeast strains with fermentation potential from central Patagonia. Yeast 39, 128–140.
  7. Villarreal, P., Villarroel, C.A., O’Donnell, S., Agier, N., Quintero-Galvis, J.F., Peña, T.A., Nespolo, R.F., Fischer, G., Varela, C., Cubillos, F.A., 2022b. Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri. Environ Microbiol.
  8. Villarroel, C.A., González-González, A., Alvarez-Baca, J.K., Villarreal, P., Ballesteros, G.I., Figueroa, C.C., Cubillos, F.A., Ramírez, C.C., 2022. Genome sequencing of a predominant clonal lineage of the grain aphid Sitobion avenae. Insect Biochem Mol Biol 143, 103742.
  9. Del Campo, A., Salamanca, C., Fajardo, A., Díaz-Castro, F., Bustos, C., Calfío, C., Troncoso, R., Pastene-Navarrete, E.R., Acuna-Castillo, C., Milla, L.A., Villarroel, C.A., Cubillos, F.A., Aranda, M., Rojo, L.E., 2021. Anthocyanins from Aristotelia chilensis Prevent Olanzapine-Induced Hepatic-Lipid Accumulation but Not Insulin Resistance in Skeletal Muscle Cells. Molecules 26.
  10. Pérez-Torrado, R., Cubillos, F.A., 2021. Editorial: New Advances in Genetic Studies to Understand Yeast Adaptation to Extreme and Fermentative Environments. Front Genet 12, 663641.
  11. Villarroel, C.A., Bastías, M., Canessa, P., Cubillos, F.A., 2021. Uncovering Divergence in Gene Expression Regulation in the Adaptation of Yeast to Nitrogen Scarcity. mSystems 6, e0046621.
  12. Libkind, D., Peris, D., Cubillos, F.A., Steenwyk, J.L., Opulente, D.A., Langdon, Q.K., Rokas, A., Hittinger, C.T., 2020. Into the wild: new yeast genomes from natural environments and new tools for their analysis. FEMS Yeast Res 20.
  13. Mandakovic, D., Pulgar, R., Maldonado, J., Mardones, W., González, M., Cubillos, F.A., Cambiazo, V., 2020. Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures. Microorganisms 8.
  14. Mardones, W., Villarroel, C.A., Krogerus, K., Tapia, S.M., Urbina, K., Oporto, C.I., O’Donnell, S., Minebois, R., Nespolo, R., Fischer, G., Querol, A., Gibson, B., Cubillos, F.A., 2020. Molecular profiling of beer wort fermentation diversity across natural Saccharomyces eubayanus isolates. Microb Biotechnol 13, 1012–1025.
  15. Molinet, J., Cubillos, F.A., 2020. Wild Yeast for the Future: Exploring the Use of Wild Strains for Wine and Beer Fermentation. Front Genet 11, 589350.
  16. Nespolo, R.F., Solano-Iguaran, J.J., Paleo-López, R., Quintero-Galvis, J.F., Cubillos, F.A., Bozinovic, F., 2020a. Performance, genomic rearrangements, and signatures of adaptive evolution: Lessons from fermentative yeasts. Ecol Evol 10, 5240–5250.
  17. Nespolo, R.F., Villarroel, C.A., Oporto, C.I., Tapia, S.M., Vega-Macaya, F., Urbina, K., De Chiara, M., Mozzachiodi, S., Mikhalev, E., Thompson, D., Larrondo, L.F., Saenz-Agudelo, P., Liti, G., Cubillos, F.A., 2020b. An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages. PLoS Genet 16, e1008777.
  18. Urbina, K., Villarreal, P., Nespolo, R.F., Salazar, R., Santander, R., Cubillos, F.A., 2020. Volatile Compound Screening Using HS-SPME-GC/MS on Saccharomyces eubayanus Strains under Low-Temperature Pilsner Wort Fermentation. Microorganisms 8.
  19. Devia, J., Bastías, C., Kessi-Pérez, E.I., Villarroel, C.A., De Chiara, M., Cubillos, F.A., Liti, G., Martínez, C., Salinas, F., 2020. Transcriptional Activity and Protein Levels of Horizontally Acquired Genes in Yeast Reveal Hallmarks of Adaptation to Fermentative Environments. Front Genet 11, 293.
  20. Cubillos, F.A., Gibson, B., Grijalva-Vallejos, N., Krogerus, K., Nikulin, J., 2019. Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers. Yeast 36, 383–398.
  21. Molinet, J., Cubillos, F.A., Salinas, F., Liti, G., Martínez, C., 2019. Genetic variants of TORC1 signaling pathway affect nitrogen consumption in Saccharomyces cerevisiae during alcoholic fermentation. PLoS One 14, e0220515.
  22. Oporto, C.I., Villarroel, C.A., Tapia, S.M., García, V., Cubillos, F.A., 2019. Distinct Transcriptional Changes in Response to Patulin Underlie Toxin Biosorption Differences in Saccharomyces Cerevisiae. Toxins (Basel) 11.
  23. Brice, C., Cubillos, F.A., Dequin, S., Camarasa, C., Martínez, C., 2018. Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen. PLoS One 13, e0192383.
  24. Tapia, S.M., Cuevas, M., Abarca, V., Delgado, V., Rojas, V., García, V., Brice, C., Martínez, C., Salinas, F., Larrondo, L.F., Cubillos, F.A., 2018. GPD1 and ADH3 Natural Variants Underlie Glycerol Yield Differences in Wine Fermentation. Front Microbiol 9, 1460.
  25. Cubillos, F.A., Brice, C., Molinet, J., Tisné, S., Abarca, V., Tapia, S.M., 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) 7, 1693–1705.
  26. Godoy, L., Silva-Moreno, E., Mardones, W., Guzman, D., Cubillos, F.A., Ganga, A., 2017. Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480. J Mol Microbiol Biotechnol 27, 147–158.
  27. Quispe, X., Tapia, S.M., Villarroel, C., Oporto, C., Abarca, V., García, V., Martínez, C., Cubillos, F.A., 2017. Genetic basis of mycotoxin susceptibility differences between budding yeast isolates. Sci Rep 7, 9173.
  28. Thompson, D.A., Cubillos, F.A., 2017. Natural gene expression variation studies in yeast. Yeast 34, 3–17.
  29. Cubillos, F.A., 2016. Exploiting budding yeast natural variation for industrial processes. Curr Genet 62, 745–751.
  30. Kessi-Pérez, E.I., Araos, S., García, V., Salinas, F., Abarca, V., Larrondo, L.F., Martínez, C., Cubillos, F.A., 2016. RIM15 antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast. FEMS Yeast Res 16, fow021.
  31. Salinas, F., de Boer, C.G., Abarca, V., García, V., Cuevas, M., Araos, S., Larrondo, L.F., Martínez, C., Cubillos, F.A., 2016. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. Sci Rep 6, 21849.
  32. Coustham, V., Vlad, D., Deremetz, A., Gy, I., Cubillos, F.A., Kerdaffrec, E., Loudet, O., Bouché, N., 2014. SHOOT GROWTH1 maintains Arabidopsis epigenomes by regulating IBM1. PLoS One 9, e84687.
  33. Cubillos, F.A., Stegle, O., Grondin, C., Canut, M., Tisné, S., Gy, I., Loudet, O., 2014. Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. Plant Cell 26, 4298–4310.
  34. Jara, M., Cubillos, F.A., García, V., Salinas, F., Aguilera, O., Liti, G., Martínez, C., 2014. Mapping genetic variants underlying differences in the central nitrogen metabolism in fermenter yeasts. PLoS One 9, e86533.
  35. Valdes, J., Tapia, P., Cepeda, V., Varela, J., Godoy, L., Cubillos, F.A., Silva, E., Martinez, C., Ganga, M.A., 2014. Draft genome sequence and transcriptome analysis of the wine spoilage yeast Dekkera bruxellensis LAMAP2480 provides insights into genetic diversity,  metabolism and survival. FEMS Microbiol Lett 361, 104–106.
  36. Cubillos, F.A., Parts, L., Salinas, F., Bergström, A., Scovacricchi, E., Zia, A., Illingworth, C.J.R., Mustonen, V., Ibstedt, S., Warringer, J., Louis, E.J., Durbin, R., Liti, G., 2013. High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics 195, 1141–1155.
  37. Liti, G., Nguyen Ba, A.N., Blythe, M., Müller, C.A., Bergström, A., Cubillos, F.A., Dafhnis-Calas, F., Khoshraftar, S., Malla, S., Mehta, N., Siow, C.C., Warringer, J., Moses, A.M., Louis, E.J., Nieduszynski, C.A., 2013. High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. BMC Genomics 14, 69.
  38. Cubillos, F.A., Billi, E., Zörgö, E., Parts, L., Fargier, P., Omholt, S., Blomberg, A., Warringer, J., Louis, E.J., Liti, G., 2011. Assessing the complex architecture of polygenic traits in diverged yeast populations. Mol Ecol 20, 1401–1413.
  39. Parts, L., Cubillos, F.A., Warringer, J., Jain, K., Salinas, F., Bumpstead, S.J., Molin, M., Zia, A., Simpson, J.T., Quail, M.A., Moses, A., Louis, E.J., Durbin, R., Liti, G., 2011. Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res 21, 1131–1138.
  40. Warringer, J., Zörgö, E., Cubillos, F.A., Zia, A., Gjuvsland, A., Simpson, J.T., Forsmark, A., Durbin, R., Omholt, S.W., Louis, E.J., Liti, G., Moses, A., Blomberg, A., 2011. Trait variation in yeast is defined by population history. PLoS Genet 7, e1002111.
  41. Cubillos, F.A., Coustham, V., Loudet, O., 2012a. Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants. Curr Opin Plant Biol 15, 192–198.
  42. Cubillos, F.A., Yansouni, J., Khalili, H., Balzergue, S., Elftieh, S., Martin-Magniette, M.-L., Serrand, Y., Lepiniec, L., Baud, S., Dubreucq, B., Renou, J.-P., Camilleri, C., Loudet, O., 2012b. Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures. BMC Genomics 13, 117.
  43. Salinas, F., Cubillos, F.A., Soto, D., Garcia, V., Bergström, A., Warringer, J., Ganga, M.A., Louis, E.J., Liti, G., Martinez, C., 2012. The genetic basis of natural variation in oenological traits in Saccharomyces cerevisiae. PLoS One 7, e49640.
  44. Zörgö, E., Gjuvsland, A., Cubillos, F.A., Louis, E.J., Liti, G., Blomberg, A., Omholt, S.W., Warringer, J., 2012. Life history shapes trait heredity by accumulation of loss-of-function alleles in yeast. Mol Biol Evol 29, 1781–1789.
  45. Cubillos, F.A., Louis, E.J., Liti, G., 2009a. Generation of a large set of genetically tractable haploid and diploid Saccharomyces strains. FEMS Yeast Res 9, 1217–1225.
  46. Cubillos, F.A., Vásquez, C., Faugeron, S., Ganga, A., Martínez, C., 2009b. Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations. FEMS Microbiol Ecol 67, 162–170.
  47. Liti, G., Haricharan, S., Cubillos, F.A., Tierney, A.L., Sharp, S., Bertuch, A.A., Parts, L., Bailes, E., Louis, E.J., 2009. Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast. PLoS Genet 5, e1000659.

h-index = 21

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