Ricardo Franco-Duarte


People Detail

Research Area : Biodiversity

Position : Integrated members

Ongoing Projects

Team member:
- 2018-2021 TODOMICS: Omics approaches towards the industrial exploitation of Torulaspora delbrueckii: Elucidation of the molecular basis underlying complex cellular traits. FCT: POCI-01-0145-FEDER-030488. Member of team (15%). Coordinator: Maria João Sousa.

- 2018-2021 FATVAL: Production of high value fatty acids and derived molecules from inexpensive carbon sources using recombinant robust industrial strain of Saccharomyces cerevisiae. FCT: PTDC/EAM-AMB/32506/2017. Member of team (15%). Coordinator: Bjorn Johansson.

- 2018-2021 STREAMECO: Biodiversity and ecosystem functioning under climate change: from the gene to the stream. FCT: PTDC/CTA-AMB/31245/2017. Member of team (20%). Coordinator: Cláudia Pascoal.

Concluded Projects

- 2017-2020 VOLATILE: Biowaste derived volatile fatty acid platform for biopolymers, bioactive compounds and chemical building blocks; Call ID “H2020-NMBP-2016-2017; Horizon 2020; Proposal 720777-1. Coordinator of the Portuguese work-package: Célia Pais.

- 2017-2019 BIOPROSPECT: Valorising CBMA biobanks: characterization and bioprospection for novel value added products. Research project funded by CBMA. Coordinator: Tony Collins.

- 2015-2017. Strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569). Member of team (100%). Coordinator: Margarida Casal.

- 2014-2015. TRANSBIO: Biotransformation of by-products from fruit and vegetable processing industry into valuable bioproducts; Call ID “FP7-KBBE-2011-5; Proposal N289603. Coordinators of the Portuguese work-package: Dorit Schuller and Célia Pais.

- 2011-2012. WINEMETRICS: Revealing the volatile molecular feature responsible for the wine like aroma: a critical task toward the Wine Quality Definition. FCT PTDC/AGR-ALI/121062/2010. Member of team (10%). Coordinator: César Ferreira.

- 2010-2011. Effect of interactions between yeasts on expression of genes responsible for wine aroma. Cooperation FCT/Slovenia. Coordinators: Dorit Schuller and Peter Raspor.

- 2010-2013. PHENOMET: Integrative pheno-metabolomic and genomic approaches for Saccharomyces cerevisiae winemaking yeasts. Fundação para a Ciência e Tecnologia PTDC/AGR-ALI/103392/2008. Member of team (80%). Coordinator: Dorit Schuller.


Master Thesis
- 2021 – José Carvalho. A search tool for identifying homologous proteins or protein-coding sequences in a database of extended pan-genomes. Master in Bioinformatics. Co-supervision with Pedro Soares. Underway.
- 2021 – Cláudio Monteiro. A bioinformatics tool for defining gene content profile within a group of organisms. Master in Bioinformatics. Co-supervision with Pedro Soares. Underway.
- 2021- Helena Santos. Inclusion of markers for detection of Candida auris species and resistance markers in a multiplex-PCR assay for Candida species. Master in Molecular Genetics. Co-supervision with Paula Sampaio. Underway
- 2021 - Alexandre Mendonça. Development of a real-time PCR methodology for the detection of systemic fungal detection. Master in Applied Biochemistry. Co-supervision with Paula Sampaio. Underway
- 2021 - Fábio Pereira. Exploitation of Torulaspora delbrueckii for winemaking focusing on biochemical and phenotypic traits. Master in Molecular Genetics. Co-supervision with Maria João Sousa. Underway
- 2020 - Carolina Santiago. Exploitation and annotation of Torulaspora delbrueckii genomes: comparison with biotechnological data. Master in Bioinformatics. Co-supervision with Pedro Soares. Underway
- 2020 Joana Mariz. “Análise de genes funcionais em espécies de fungos aquáticos como ferramenta para avaliar o impacto de alterações climáticas nos ecossistemas”. Master in Molecular Genetics. Co-supervision with Isabel Fernandes. Underway
- 2020 Ticiana Fernandes. “Exploitation of Torulaspora delbrueckii for winemaking”. Master in Molecular Genetics. Co-supervision with Maria João Sousa. Underway
- 2019 Rita Rocha. “Improved succinic acid production by non-Saccharomyces species via fermentation”. Master in Molecular Genetics. Co-supervision with Célia Pais. Underway.
- 2018 Soraia Esteves. “Establishment of a detailed mitochondrial DNA phylogenetic tree of Saccharomyces cerevisiae and assessment of purifying selection profiles throughout the phylogeny”. Master in Forensic Genetics. Co-supervision with Pedro Soares. Concluded.
- 2018 Catarina Miranda. “Screening of single cell oils producing yeasts using volatile fatty acids as carbon sources: optimization of Fourier transform infrared spectroscopy as a method to study lipid accumulation”. Master in Molecular Genetics. Co-supervision with Célia Pais. Concluded.
- 2018 Sara Pereira. “Oleaginous yeast selection for the production of lipidic compounds: development of an optimized fermentation protocol regarding nutrient requirements and growth conditions”. Master in Applied Biochemistry. Co-supervision with Célia Pais. Concluded.
- 2018 Irene Fugalli. “Caracterização da diversidade fúngica em golfinhos da costa portuguesa”. Master in Ecology. Co-supervision with Célia Pais. Concluded.

BSc Projects
- 2019 Carolina Santiago. “Exploração do genoma da levedura Torulaspora delbrueckii: exploração de dados bioquímicos, moleculares e genómicos”. Degree in Bioinformatics. Underway.
- 2019 Brian Pereira. “Modelo computacional de evolução de uma população microbiana com dependência de fatores ambientais”. Degree in Applied Biology. Underway.
- 2018 Ticiana Fernandes. “Produção de ácido succínico por leveduras: otimização de condições experimentais com vista à melhoria da sua produção fermentativa”. Degree in Applied Biochemistry. Concluded.
- 2018 Catarina Baltazar. “Estrutura populacional de Saccharomyces cerevisiae: análise filogenética através do estudo de DNA mitocontrial”. Degree in Applied Biochemistry. Concluded.
- 2018 Diana Rocha. “Produção de ácido succínico por leveduras: optimização de condições experimentais com vista à melhoria da sua produção fermentativa”. Degree in Applied Biology. Concluded.
- 2018 Bárbara Nunes. “Gordura é formusura: avaliação da produção de compostos lipídicos por leveduras oleaginosas”. Degree in Applied Biochemistry. Concluded.
- 2017 Rita Rocha. “Seleção de leveduras oleaginosas para a produção de compostos lipídicos”. Degree in Environmental Sciences. Concluded.
- 2016 Catarina Miranda. “Seleção de leveduras oleaginosas para a produção de compostos lipídicos”. Degree in Applied Biology. Concluded.


Papers in International Scientific Periodicals with Referees
25. Bettencourt S, Miranda C, Pozdniakova T, Sampaio P, Pais C, FRANCO-DUARTE R (2020) Single cell oil production by oleaginous yeasts grown in synthetic and waste-derived volatile fatty acids. Microorganisms 2020, 8, 1809. DOI:10.3390/microorganisms8111809.

24. Drumonde-Neves J, Čadež N, Domínguez YR, Gallmetzer A, Schuller D, Lima T, Pais C, FRANCO-DUARTE R (2020) Clavispora santaluciensis f.a., sp. nov., a novel ascomycetous yeast species isolated from vineyards. International Journal of Systematic and Evolutionary Microbiology. DOI: 10.1099/ijsem.0.004531.

23. Gerós-Mesquita A, Carvalho-Pereira J, FRANCO-DUARTE R, Alves A, Gerós H, Pais C, Sampaio P (2020) Oral Candida albicans colonization in healthy individuals: prevalence, genotypic diversity, stability along time and transmissibility. Journal of Oral Microbiology. DOI: 10.1080/20002297.2020.1820292. Impact factor (2019): 3.250.

22. Vieira D, Esteves S, Santiago C, Conde-Sousa E, Fernandes T, Pais C, Soares P, FRANCO-DUARTE R (2020) Population analysis and evolution of Saccharomyces cerevisiae mitogenomes. Microorganisms 8 (7): 1001.
DOI: 10.3390/microorganisms8071001. Impact factor (2020): 4.167. Quartile score: Q1 (Scimago SJR).

21. Čadež N, Drumonde-neves R, Sipiczki M, Dlauchy D, Lima T, Pais C, Schuller D, FRANCO-DUARTE R, Lachance M-A, Péter G (2020) Starmerella vitis f.a., sp. nov., a yeast species isolated from flowers and grapes. Antonie van Leeuwenhoek.
DOI: 10.1007/s10482-020-01438-x. Impact factor (2019): 1.934. Quartile score: Q1/Q2 (Scimago SJR).

20. Miranda C, Bettencourt S, Pozdniakova T, Pereira J, Sampaio P, Pais C, FRANCO-DUARTE R (2020) Modified high-throughput Nile red fluorescence assay for the rapid screening of oleaginous yeasts. BMC Microbiology 20:60.
DOI: 10.1186/s12866-020-01742-6. Impact factor (2019):3.287. Quartile score: Q2 (Scimago SJR).

19. FRANCO-DUARTE R, Černáková L, Kadam S, Kaushik KS, Salehi B, Bevilacqua A, Corbo MR, Antolak H, Dybka-Stępień K, Leszczewicz M, Tintino SR, Sousa VCA, Sharifi-Rad J, Coutinho HDM, Martins N, Rodrigues CF (2019) Advances in chemical and biological methods to identify microorganisms – from past to present. Microorganisms 7 (5), 130.
DOI: 10.3390/microorganisms7050130.

18. Legras JL, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T, Sanchez I, Couloux A, Guy J, FRANCO-DUARTE R, Schuller D, Sampaio JP, Dequin S (2018) Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication. Molecular Biology and Evolution.
DOI: 10.1093/molbev/msy066. Impact factor (2017):10.217. Quartile score: Q1 (Scimago SJR)

17. Drumonde-Neves J, FRANCO-DUARTE R, Vieira E, Mendes I, Lima T, Schuller D, Pais C (2018) Differentiation of Saccharomyces cerevisiae populations from vineyards of the Azores Archipelago: geography vs ecology. Food Microbiology 74: 151-162.
DOI: 10.1016/j.fm.2018.03.017. Impact factor (2017): 4.090. Quartile score: Q1 (Scimago SJR)

16. FRANCO-DUARTE R, Bessa D, Gonçalves F, Martins R, Silva-Ferreira AC, Schuller D, Sampaio P, Pais C (2017) Genomic and transcriptomic analysis of Saccharomyces cerevisiae isolates with focus in succinic acid production. FEMS Yeast Research, 17 (6): fox057.
DOI: 10.1093/femsyr/fox057. Impact factor (2017): 2.609. Quartile score: Q1 (Scimago SJR)

15. Mendes I, Sanchez I, FRANCO-DUARTE R, Camarasa C, Schuller D, Dequin S, Sousa MJ (2017) Integrating transcriptomics and metabolomic for the analysis of the aroma profiles of wine, sake, cachaça and laboratory Saccharomyces cerevisiae strains. BMC Genomics 18: 455.
DOI: 10.1186/s12864-017-3816-1. Impact factor (2017): 3.730. Quartile score: Q1 (Scimago SJR)

14. Kosel J, Čadež N, Schuller D, Carreto L, FRANCO-DUARTE R, Raspor P (2017) The influence of Dekkera bruxellensis on the transcriptome of Saccharomyces cerevisiae and on the aromatic profile of synthetic wine must. FEMS Yeast Research, 17 (4): fox018.
DOI: 10.1093/femsyr/fox018. Impact factor (2017): 2.609. Quartile score: Q1 (Scimago SJR)

13. Drumonde-Neves J, FRANCO-DUARTE R, Lima T, Schuller D, Pais C (2017) Association between grape yeast communities and vitivinicultural terroir. PLoS ONE 12(1): e0169883.
DOI: 10.1371/journal.pone.0169883. Impact factor (2016): 2.766. Quartile score: Q1 (Scimago SJR)

12. Lucas C, Ferreira C, Cazzanelli G, FRANCO-DUARTE R, Tulha J (2016) Yeast Gup1(2) Proteins Are Homologues of the Hedgehog Morphogens Acyltransferases HHAT(L): Facts and Implications . Journal of Developmental Biology 4 (4): 33.
DOI: 10.3390/jdb4040033. Impact factor (2016): 2.944.

11. Drumonde-Neves J, FRANCO-DUARTE R, Lima T, Schuller D, Pais C (2016) Yeast biodiversity in vineyard environments is increased by human intervention. Plos One 11(8): e0160579.
DOI: 10.1371/journal.pone.0160579. Impact factor (2016): 2.806. Quartile score: Q1 (Scimago SJR)

10. FRANCO-DUARTE R, Umek L, Mendes I, Castro CC, Fonseca N, Martins R, Silva-Ferreira AC, Sampaio P, Pais C, Schuller D (2016) New integrative computational approaches unveil the Saccharomyces cerevisiae pheno-metabolomic profile and allow strain selection for winemaking. Food Chemistry 211: 509-520.
DOI: 10.1016/j.foodchem.2016.05.080. Impact factor (2016): 4.529. Quartile score: Q1, top 5.7% (Scimago SJR)

9. FRANCO-DUARTE R, Carreto L, Mendes I, Dequin S, Santos MAS, Pais C, Schuller D (2015) Intra-strain phenotypic and genomic variability of the commercial Saccharomyces cerevisiae strain Zymaflore VL1 recovered from vineyard environments. FEMS Yeast Research 15 (6): fov063.
DOI: 10.1093/femsyr/fov063. Impact factor (2015): 2.479. Quartile score: Q1 (Scimago SJR)

8. Oliveira MM, FRANCO-DUARTE R, Romeo O, Pais C, Criseo G, Sampaio P, Zancope-Oliveira RM (2015) Evaluation of T3B fingerprinting for identification of clinical and environmental Sporothrix species. FEMS Microbiology Letters 362 (6): fnv027.
DOI: 10.1093/femsle/fnv027. Impact factor (2014): 2.121. Quartile score: Q2 (Scimago SJR)

7. FRANCO-DUARTE R*, Mendes I*, Umek L, Drumonde-Neves J, Zupan B, Schuller D (2014) Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae. Yeast 31 (7): 265-277.
* both authors contributed equally
DOI: 10.1002/yea.3016. Impact factor (2014): 1.634. Quartile score: Q2 (Scimago SJR)

6. FRANCO-DUARTE R*, Mendes I*, Umek L, Fonseca E, Drumonde-Neves J, Dequin S, Zupan B, Schuller D (2013) Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles. PLoS ONE 8 (7): e66523.
* both authors contributed equally
DOI: 10.1371/journal.pone.0066523. Impact factor (2013): 3.534. Quartile score: Q1 (Scimago SJR)

5. FRANCO-DUARTE R, Mendes I, Gomes A, Santos MAS, de Sousa B, Schuller D (2011) Genotyping of Saccharomyces cerevisiae strains by interdelta sequence typing using automated microfluidics. Electrophoresis 32 (12): 1447-55.
DOI: 10.1002/elps.201000640. Impact factor (2011): 3.303. Quartile score: Q1 (Scimago SJR)

4. Pereira L, Silva NM, FRANCO-DUARTE R, Fernandes V, Pereira JB, Costa MD, Martins H, Soares P, Behar DM, Richards MB, Macaulay V (2010) Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6. BMC Evolutionary Biology (BMCEvolBiol) 10(1): 390.
DOI: 10.1186/1471-2148-10-390. Impact factor (2010): 3.702. Quartile score: Q1 (Scimago SJR)

3. FRANCO-DUARTE R, Umek L, Zupan B, Schuller D (2009) Computational approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection. Yeast 26, 675-692.
DOI: 10.1002/yea.1728. Impact factor (2009): 1.805. Quartile score: Q1 (Scimago SJR)

2. Santos MM, Reis-Henriques MA, Guillot R, Lima D, FRANCO-DUARTE R, Mendes I, Queirós S, Castro LFC (2008) Anti-androgenic effects to sewage treatment plant effluents in the Prosobranch gastropod Nucella lapillus. Comp Biochem Physiol C Toxicol Pharmacol 148(1): 87-93.
DOI: 10.1016/j.cbpc.2008.03.012. Impact factor (2008): 2.530. Quartile score: Q1 (Scimago SJR)

1. Pereira L, Gonçalves J, FRANCO-DUARTE R, Silva J, Rocha T, Arnold C, Richards M, Macaulay V (2007) No evidence for an mtDNA role in sperm motility: data from complete sequencing of asthenozoospermic males. Molecular Biology and Evolution (MolBiolEvol) 24(3):868–874.
DOI: 10.1093/molbev/msm004. Impact factor (2007): 6.438. Quartile score: Q1 (top 1% Scimago SJR)

Papers in Conference Proceedings
2. Legras JL, Coi AL, Bigey F, Galeote V, Marsit S, Couloux A, Guy J, FRANCO-DUARTE R, Schuller D, Sampaio JP, Budroni M, Dequin S (2015) New insights into the adaptation of yeasts to anthropic environment using comparative genomics. Yeast 32, S89-S90 (27th International Conference on Yeast Genetics and Molecular Biology, Italy).
DOI: 10.1002/yea.3091

1. FRANCO-DUARTE R, Carreto L, Cambon B, Dequin S, Santos M, Casal M, Schuller D (2011) Genetic characterization of commercial Saccharomyces cerevisiae isolates recovered from vineyard environments using comparative genome hybridization on array (aCGH). Yeast 28, Issue S1 (25th International Conference on Yeast Genetics and Molecular Biology, Poland).
DOI: 10.1002/yea.1883

Book Chapters
3. Pais C, FRANCO-DUARTE R, Sampaio P, Wildner J, Carolas A, Figueira D, Ferreira BS (2016) Production of dicarboxylic acid platform chemicals using yeasts: focus on succinic acid. In: “BioTransformation of agricultural waste and by-products. The Food, Feed, Fibre, Fuel (4F) economy”.
Editora: Elsevier.
ISBN: 978-0-12-803622-8. DOI:10.1016/B978-0-12-803622-8.00009-4

2. FRANCO-DUARTE R, Mendes I, Castro CC, Silva JS, Xavier A, Drumonde-Neves J, Oliveira C, Martins RC, Oliveira JM, Ferreira AC, Schuller D (2011) Genotypic and pheno-metabolomic characterization of a Saccharomyces cerevisiae strain collection. In: "The Wine Construction: proceedings of the 34th World Congress of Vine and Wine". Editora: Um porto para o mundo.
ISBN 978-989-20-2449-3.

1. Pereira L, Morales AC, Goios A, FRANCO-DUARTE R, Rodrigues C, Endicott P, Alonso A, Martin R, Torres C, Amorim A (2006) The islamization of Iberian Peninsula: a demographic shift or a cultural change? Search for an answer using extant and ancient DNA from Mértola (Southeast Portugal). In: “Progress in Forensic Genetics 11, 1st edition”. Published by: Elsevier, Amsterdam Lausanne New York Oxford, 2006.
ISBN-13: 978-0444521026. DOI: 10.1016/j.ics.2005.11.034