Cubillos Riffo Francisco Alberto

Email: 
francisco.cubillos.r@usach.cl
Teléfono: 
227 181 083
Sitio web: 
Elsevier

Abstract:

Dr. Francisco A. Cubillos is a distinguished scientist with a strong background in Genetics, Molecular Biology, and Ecology. He earned his PhD in 2010 from the University of Nottingham, UK, working under the esteemed supervision of Prof. Edward J. Louis and Dr. Gianni Liti. During his doctoral studies, Dr. Cubillos focused on unraveling the genetic architecture of complex traits in the model organism Saccharomyces cerevisiae. His research played a pivotal role in identifying key genes responsible for phenotypic variations among strains. This work led to the publication of nine impactful manuscripts, showcasing his expertise and contributions to the field.

After completing his PhD, Dr. Cubillos pursued postdoctoral research at the INRA-Versailles Research Centre in Paris, France. Under the mentorship of Dr. Olivier Loudet, he explored the model organism Arabidopsis thaliana, investigating natural variation in expression traits and the role of non-coding regions in plant adaptation to extreme environments, specifically drought stress. Driven by his passion for understanding the molecular basis of expression differences, he employed cutting-edge 'omics' approaches such as RNA-Seq, DNA-Seq, and epigenome sequencing. It was during this time that Dr. Cubillos received a prestigious returning grant from CONICYT, allowing him to return to Chile and establish his own research group.

Currently, Dr. Cubillos leads a dynamic research line that combines Ecology, Genetics, and Molecular Biology. His primary focus lies in studying native ethanol-tolerant yeast from Patagonia, with an emphasis on species such as S. eubayanus, S. uvarum, and L. cidri. The Cubillos lab is actively engaged in multiple ongoing projects aimed at generating novel lager hybrids by leveraging the vast genetic diversity of S. eubayanus from Patagonia. These initiatives involve utilizing diverse genetic improvement techniques, transitioning from studying yeast ecology in the wild to exploring their biotechnological applications.

Dr. Cubillos' exceptional research contributions have been recognized through numerous research and international collaboration grants. His notable accolades include being named an EMBO Global Investigator, a TWAS Young Affiliate, and receiving the distinguished titles of 2022 Best Chilean Young Scientist and Ciencia de Frontera Researcher by the National Science Academy. So far, Dr Cubillos has published over 50 WoS Manuscripts.

Dr. Cubillos' research endeavors continue to push the boundaries of knowledge in his field, fostering collaborations, and driving advancements in Ecology, Genetics, and Molecular Biology.

Línea(s) de investigación: 
Genética Molecular
Jerarquía: 
Asociado
Grados académicos /educación: 
PhD en Genética, Universidad de Nottingham
Magister en Cs Biológicas c/m Microbiología, Universidad de Chile
Licenciado en Ingenería en Biotecnología Molecular, Universidad de Chile
Publicaciones: 

Visit: https://scholar.google.cl/citations?user=fZpiENAAAAAJ&hl=es&authuser=1

Research Publications (2018 – 2023)

  1. Jennifer Molinet, Juan I. Eizaguirre, Pablo Quintrel, Nicolás Bellora, Carlos A. Villarroel, Pablo Villarreal, José Benavides-Parra, Roberto F. Nespolo, Diego Libkind, Francisco A. Cubillos. Natural Variation in Diauxic Shift between Patagonian Saccharomyces eubayanus Strains. mSystems. 2022 Dec 20;7(6):e0064022. doi: 10.1128/msystems.00640-22.
  2. Olguín V, Durán A, Las Heras M, Rubilar JC, Cubillos FA, Olguín P, Klein AD. Genetic Background Matters: Population-Based Studies in Model Organisms for Translational Research. International Journal of Molecular Sciences. 2022; 23(14):7570. https://doi.org/10.3390/ijms23147570.
  3. Villarreal P, Villarroel CA, O'Donnell S, Agier N, Quintero-Galvis JF, Peña TA, Nespolo RF, Fischer G, Varela C, Cubillos FA. Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri. Environ Microbiol. 2022 Jun 29. doi: 10.1111/1462-2920.16103. Epub ahead of print. PMID: 35769023.
  4. Molinet J, Urbina K, Villegas C, Abarca V, Oporto CI, Villarreal P, Villarroel CA, Salinas F, Nespolo RF, Cubillos FA. A Saccharomyces eubayanus haploid resource for research studies. Sci Rep. 2022 Apr 8;12(1):5976. doi: 10.1038/s41598-022-10048-8. PMID: 35396494; PMCID: PMC8993842.
  5. Vaishnav ED, de Boer CG, Molinet J, Yassour M, Fan L, Adiconis X, Thompson DA, Levin JZ, Cubillos FA, Regev A. The evolution, evolvability and engineering of gene regulatory DNA. Nature. 2022 Mar 9. doi: 10.1038/s41586-022-04506-6.
  6. Villarroel CA, González-González A, Alvarez-Baca JK, Villarreal P, Ballesteros GI, Figueroa CC, Cubillos FA, Ramírez CC. Genome sequencing of a predominant clonal lineage of the grain aphid Sitobion avenae. Insect Biochem Mol Biol. 2022 Feb 18;143:103742. doi: 10.1016/j.ibmb.2022.103742.
  7. Mozzachiodi S, Bai FY, Baldrian P, Bell G, Boundy-Mills K, Buzzini P, Čadež N, Cubillos FA, Dashko S, Dimitrov R, Fisher KJ, Gibson B, Gouliamova D, Greig D, Heistinger L, Hittinger CT, Jecmenica M, Koufopanou V, Landry CR, Mašínová T, Naumova ES, Opulente D, Peña JJ, Petrovič U, Tsai IJ, Turchetti B, Villarreal P, Yurkov A, Liti G, Boynton P. Yeasts from temperate forests. Yeast. 2022 Jan;39(1-2):4-24. doi: 10.1002/yea.3699. Epub 2022 Feb 17. PMID: 35146791.
  8. Villarreal P, Quintrel PA, Olivares-Muñoz S, Ruiz JI, Nespolo RF, Cubillos FA. Identification of new ethanol-tolerant yeast strains with fermentation potential from central Patagonia. Yeast. 2022 Jan;39(1-2):128-140. doi: 10.1002/yea.3662. Epub 2021 Sep 2.
  9. Wladimir Mardones, Carlos A. Villarroel, Valentina Abarca, Kamila Urbina, Tomás A. Peña, Jennifer Molinet, Roberto F. Nespolo and Francisco A. Cubillos*. Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing conditions. Microb Biotechnol. 2022 Mar;15(3):967-984. doi: 10.1111/1751-7915.13803. Epub 2021 Mar 23
  10. Del Campo A, Salamanca C, Fajardo A, Díaz-Castro F, Bustos C, Calfío C, Troncoso R, Pastene-Navarrete ER, Acuna-Castillo C, Milla LA, Villarroel CA, Cubillos FA, Aranda M, Rojo LE. Anthocyanins from Aristotelia chilensis Prevent Olanzapine-Induced Hepatic-Lipid Accumulation but Not Insulin Resistance in Skeletal Muscle Cells. Molecules. 2021 Oct 12;26(20):6149. doi: 10.3390/molecules26206149.
  11. Villarroel CA, Bastías M, Canessa P, Cubillos FA. Uncovering Divergence in Gene Expression regulation in the Adaptation of Yeast to Nitrogen Scarcity.  mSystems. 2021 Aug 31;6(4):e0046621. doi: 10.1128/mSystems.00466-21. Epub 2021 Aug 24.
  12. Jennifer Molinet and Francisco A. Cubillos. Wild yeast for the future: Exploring the use of wild strains for wine and beer fermentation. Front Genet. 2020 Nov 2;11:589350. doi: 10.3389/fgene.2020.589350. eCollection 2020.
  13. Mandakovic D, Pulgar R, Maldonado J, Mardones W, González M, Cubillos FA*, Cambiazo V*. Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures. Microorganisms. 2020 Jun 24;8(6):956. doi: 10.3390/microorganisms8060956.
  14. Urbina K*, Villarreal P*, Nespolo RF, Salazar R, Santander R, Cubillos FA. Volatile compound screening using HS-SPME-GC/MS on Saccharomyces eubayanus strains under low-temperature pilsner wort fermentation. Microorganisms 2020, 8(5), 755; https://doi.org/10.3390/microorganisms8050755.
  15. 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 Genet. 2020 May 1;16(5):e1008777. doi: 10.1371/journal.pgen.1008777. eCollection 2020 May.
  16. 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. Front Genet. 2020 Apr 30;11:293. doi: 10.3389/fgene.2020.00293. eCollection 2020
  17. 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. Ecol Evol. 2020 Jun 2;10(12):5240-5250. doi: 10.1002/ece3.6208. eCollection 2020 Jun.
  18. 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
  19. 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]
  20. Molinet, Jennifer; Cubillos, Francisco; Salinas, Francisco; Liti, Gianni; Martínez, Claudio. PLoS One. 2019 Jul 26;14(7):e0220515. doi: 10.1371/journal.pone.0220515. eCollection 2019.
  21. Oporto CI, Villarroel CA, Tapia SM, García V, Cubillos FA. Distinct Transcriptional Changes in Response to Patulin Underlie Toxin Biosorption Differences in Saccharomyces cerevisiae. Toxins (Basel). 2019 Jul 10;11(7):400. doi: 10.3390/toxins11070400.
  22. Cubillos FA, Gibson B, Grijalva-Vallejos N, Krogerus K, Nikulin J Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers. Yeast. 2019 Jun;36(6):383-398. doi: 10.1002/yea.3380. Epub 2019 Feb 1
  23. Tapia SM, Cuevas M, Abarca V, Delgado V, Rojas V, García V, Brice C, Martínez C, Salinas F, Larrondo LF, Cubillos FA*. 2018. GPD1 and ADH3 natural variants underlie glycerol yield differences in wine fermentation. Frontiers in Microbiology. 9:1460. doi: 10.3389/fmicb.2018.01460
  24. Brice C, Cubillos FA, 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 2018 Feb 12;13(2):e0192383. doi: 10.1371/journal.pone.0192383. eCollection 2018.
Premios y Honores: 

2022. Premio Científico Joven Destacado 2022, Sociedad de Biología Celular de Chile y GrupoBios 2022.

2022.  Ciencia de Frontera Laureate, Academia Nacional de Ciencias de Chile (2022 – 2024)

2022.  TWAs Young Investigator

2021.  EMBO Global Investigator

2020. President of the Chilean Genetics Society

2018. Vice President of the Chilean Genetics Society

2016. Beca Santander Iberoamericana para estancia en España en laboratorio de José Manuel Guillamón, IATA-CSIC, Valencia.

2010. Premio ‘University Endowed Postgraduate Prize 2009/2010’ para los 10 alumnos más sobresalientes del programa PhD, University of Nottingham.

2010. Beca completa para asistir al Congreso ‘ECFG, 10th International European Conference on Fungal Genetics’, Amsterdam, Holanda.

2009. Beca Heredity Fieldwork de la Sociedad de Genética, Reino Unido para realizar pasantía en  ‘High throughput phenotyping’ en el laboratorio de Anders Blomberg, Gotemburgo, Suecia

2007. Beca Chile para estudios de doctorado en el extranjero (Universidad de Nottingham, Reino Unido) otorgada por el Gobierno de Chile.

Proyectos: 
  1. Junio 2023 – Junio 2025. FONDEF ID23|10260. Elaboración de whiskey a base de recursos nacionales y un modelo circular sustentable. Principal Investigator.
  2. April 2022 – March 2026. FONDECYT Regular 1220026 ‘Genomic and transcriptional profiling of fermentative vigor in laboratory lager yeast hybrids.’. Principal Investigator.
  3. January 2022 – January 2025. Millenium Nucleus of Patagonian Limit-of-Life. Associate Researcher
  4. January 2021 - December 2025. EMBO Global Investigator. Phylogenomic studies in ethanol-tolerant yeast from Patagonia. Principal Investigator.
  5. November 2020 - November 2022. FIC Región de los Rios-Chile. Supporting economic re-activation of the brewing Industry in the Rios Region. Co-researcher.
  6. January 2020 – December 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 in native Patagonian yeasts’. Principal Investigator.
  7. January 2019 – December 2022: Research Grant for International Scientific Cooperation ECOS/CONICYT C18B03 ‘Genomic and physiological Characterization of ethanol-producing yeast populations from Patagonia’. Principal Researcher.
  8. May 2018  - May 2020 FIC Región de los Rios. ‘Hacia la denominación de origen de la cerveza de Los Ríos: descubriendo una levadura nativa’. Co-Researcher
  9. April 2018 – March 2022. FONDECYT Regular 1180161 ‘Decoding the genomic and phenomic complexity of the cryotolerant yeast Saccharomyces eubayanus’. Principal Investigator.
  10. January 2018 – to date: Millennium Institute for Integrative Biology (iBio). Associate Researcher.
Otras actividades relevantes: 

Current Undergraduate students: 4

Former Undergraduate students: 28

Current Postgraduate students: 8

Former Postgraduate students: 1

Current Post-docs: 4

Former Post-docs: 3