CBMA

- Comparative analysis of yeast genomes by computational methods;

- Yeasts and their biotechnological importance;

- Study of the microbiome associated with by-products from fruit and vegetable processing industry;

- Interdisciplinary study of yeast biodiversity, applying techniques of genetic and phenotypic characterization in order to evaluate the variability within Saccharomyces cerevisiae strains;

- Holistic bioinformatic analysis to relate genetic and phenotypic analysis as a contribution to yeast phenomics;

- Characterization of the metabolic diversity of fermentative yeast strains;

- Development of computational models for data fusion;

- Genomic features of yeast patogenicity.

         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

      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.

      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.

     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.

ª     2017-present. 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. (Member of Team)

 Team member:

ª   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.

ª       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.

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

ª      2010-2012. 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. 

       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

      FRANCO-DUARTE R, Umek L, Mendes I, Castro CC, Silva J, Martins R, Silva-Ferreira AC, Pais C, Schuller D (2016) Saccharomyces cerevisiae pheno-metabolomic profile revealed by integrative computational approaches. Food Chemistry. DOI: 10.1016/j.foodchem.2016.05.080

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.

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

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

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

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

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

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

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

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

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 Supplement 1 (25th International Conference on Yeast Genetics and Molecular Biology, Poland). DOI: 10.1002/yea.1883.

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). Progress in Forensic Genetics 11, Elsevier. DOI: 10.1016/j.ics.2005.11.034.

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”. Elsevier.

FRANCO-DUARTE R, Mendes I, Castro CC, Silva JS, Xavier A, Drumonde-Neves J, Oliveira C, Martins RC, Oliveira JM, Ferreira AC, Schuller D. "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. 2011.

 Pereira L, FRANCO-DUARTE R, Ramos P, Alemão F, Gomes P, Sousa S, Santos M, Duarte FL, Casal M, Schuller D (2008) Populational analysis of Saccharomyces cerevisiae strains from different appellations of origin and grape varieties by microsatellite analysis. Nature Preceedings, 2290 (1). DOI: 10.1038/npre.2008.2290.1

FRANCO-DUARTE R, Umek L, Zupan B, Schuller D (2008) Bioinformatic approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection. Nature Preceedings, 2288 (1). DOI: 10.1038/npre.2008.2288.1

FRANCO-DUARTE R, Sampaio P, Pais C (2015) Genetic determinants responsible for the adaptation of Saccharomyces cerevisiae strains to different ecological niches. XXXIX Portuguese Genetics Conference, 25^th to 27^th May 2015, Braga, Portugal.

FRANCO-DUARTE R, Carreto L, Mendes I, Cambon B, Dequin S, Santos MAS, Casal M, Schuller D (2012) Intra-strain phenotypic and genomic variability of the commercial Saccharomyces cerevisiae strains Zymaflore VL1 recovered from vineyard environments. 13th International Congress on Yeasts, Madison, 26-30 August, 2012, Madison, USA.

FRANCO-DUARTE R, Carreto L, Cambon B, Dequin S, Santos MAS, Casal M, Schuller D (2011) Microevolutionary changes of commercial Saccharomyces cerevisiae strains recovered from vineyard environments identified by comparative genome hybridization on array. Microbiotec ´11, 1 -3 Dec, 2011, Braga, Portugal.

FRANCO-DUARTE R, Carreto L, Cambon B, Dequin S, Santos M, Casal M, Schuller D (2011) Comparative genomics of commercial Saccharomyces cerevisiae isolates recovered from vineyard environments. XXXVI Jornadas Portuguesas de Genética, 30 May – 1 June 2011, Coimbra, Portugal.

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. XXXIV World Congress of Vine and Wine, 20-27 June, 2011, Porto, Portugal.

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. 27th International Specialized Symposium on Yeasts (ISSY), 26-29 August 2009, Institut Pasteur, Paris, France.

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. XVII Jornadas de Biologia de leveduras Prof. Van Uden, 19-20 June 2009, Braga, Portugal.

FRANCO-DUARTE R, Casal M, Schuller D (2007) Bioinformatic approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection. XV Jornadas de Biologia de leveduras Prof. Van Uden, 15-16 June 2007, Porto, Portugal.