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Identification

Personal identification

Full name
Paulo Jorge Moura Pinto da Costa Dias

Author identifiers

Ciência ID
031C-B4B2-0B2E

Knowledge fields

  • Natural sciences - Biological Sciences
  • Natural sciences - Biological Sciences
Education
Degree Classification
2011 - 2018
Concluded
 Multi-resistance to chemical stresses: studies using the yeast model and functional genomics strategies (Pós-doutoramento)
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2006 - 2010
Concluded
 Biotecnologia (Doutoramento)
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
"Yeast Toxicogenomics focused on the Agricultural Fungicide Mancozeb: involvement of the drug:H+ antiporter Flr1p" (THESIS/DISSERTATION)
 Approved, with distinction
2002 - 2006
Concluded
 Probabilidades e Estatística (Mestrado)
Universidade de Lisboa Centro de Estatística e Aplicações, Portugal
"Transmembrane proteins topology prediction: non-homogenous hidden Markov models under a Bayesian perspective" (THESIS/DISSERTATION)
 Máxima
1995 - 2001
Concluded
 Microbial Biology and Genetics (Licenciatura)
Universidade de Lisboa Centro de Biotecnologia Vegetal, Portugal
"Taxonomic analysis in Candida albicans: from isolation and phenotypic identification to molecular typing" (THESIS/DISSERTATION)
 16
Affiliation

Science

Category
Host institution 		Employer
2020 - Current Contracted Researcher (Research) Associate Laboratory Institute for Health and Bioeconomy, Portugal
Associate Laboratory Institute for Health and Bioeconomy, Portugal
2018/12/01 - Current Contracted Researcher (Research) Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
Projects

Contract

Designation Funders
2023/05/25 - 2023/11/24 Construction of the Graph-based Pangenome of the model-organism Saccharomyces cerevisiae (3rd edition of Advanced Computing Projects: A1 Preparatory or Development Access - round C)
2023.05807.CPCA.A1
Principal investigator
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2023/03/03 - 2023/09/02 Construction of the Gene-based Pangenome of the model-organism Saccharomyces cerevisiae (3rd edition of Advanced Computing Projects: A0 Experimental Access - round B)
2022.42199.CPCA.A0
Principal investigator
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2019/06/01 - 2021/12/31 LACTOSYNT- Lactic acid bacteria as cell factories: Synthetic Biology approach for plasmid DNA and recombinant protein production
PTDC/BTM-SAL/28624/2017
Researcher
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2011 - 2018 INTACT - Integral engineering of acetic acid tolerance in yeast (Contract: ERA-IB/0002/2010)
ERA-IB/0002/2010
Post-doc Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2011 - 2018 PEst-OE/EQB/LA0023/2011_research line: Systems and Synthetic Biology.
PEst-OE/EQB/LA0023/2011_research line
Post-doc Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2011 - 2018 From small bioactive molecules to an integrated OMICS approach: Mass Spectrometry tools for mechanistic insights into drug-like and functional properties, toxicity, and stress responses (Contract: RECI/QEQ-MED/0330/2012).
RECI/QEQ-MED/0330/2012
Post-doc Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2011 - 2018 MFS-stress-Major Facilitator Superfamily transporters in the context of modern agriculture constraints: exploratory studies (Contract: EXPL/AGR-PRO/1013/2013).
EXPL/AGR-PRO/1013/2013
Post-doc Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2011 - 2018 Structural and functional analysis of the Haa1 transcription factor required for yeast response and resistance to acetic acid (Contract: PTDC/MAR-BIO/1547/2014)
PTDC/BBB-BEP/0385/2014
Post-doc Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2011 - 2018 YEASTPEC - Engineering of the yeast Saccharomyces cerevisiae for bioconversion of pectin- containing agro-industrial side-streams (Contract: ERA-IB-2/0003/2015)
ERA-IB-2/0003/2015
Post-doc Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2011 - 2012 Systems and Synthetic Biology
PEst-OE/EQB/LA0023/2011_research line
Post-doc Fellow
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2006 - 2010 DBYeast: Infrastructure and algorithms for analysis and identification of gene regulatory networks (Contract: POSI/EIA/57398/2004)
POSI/EIA/57398/2004
PhD Student Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2006 - 2010 Insights into the complex regulatory network acting in yeast cells challenged with drugs/chemical stresses: genome-wide expression approaches supported by bioinformatics (Contract: PDCT/BIO/56838/2004)
PDCT/BIO/56838/2004
PhD Student Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2006 - 2010 Dyablo: models for the dynamic behaviour of Biological Networks (Contract: PTDC/EIA/71587/2006)
PTDC/EIA/71587/2006
PhD Student Fellow
Fundação para a Ciência e a Tecnologia
Concluded
2006 - 2010 Characterization and modeling of a specific transcriptional regulatory network required for multidrug resistance in yeast (Contract: PTDC/BIO/72063/2006).
PTDC/BIO/72063/2006
PhD Student Fellow
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Conference abstract
  1. Dias, Paulo Jorge; Santos, JM; Antunes, DL; Duarte, Sofia de Oliveira Dias; Leonilde Morais Moreira; Gabriel António Amaro Monteiro. "Graph-based and Gene-based Pangenome of Lactococcus lactis and Lactococcus cremoris". Paper presented in Genome Informatics conference at Cold Spring Harbour Laboratory (CSHL), Cold Spring Harbour, NY, 2023.
    Accepted
  2. Sofia de Oliveira Dias Duarte; Furtado, Alexandre; Dias, Paulo Jorge; Leonilde Moreira 401D-32AD-2FA6; Prazeres, Duarte; Monteiro, Gabriel António Amaro. "A sustainable alternative for cheese production – a synthetic biology approach for chymosin production using recombinant Lactic Acid Bacteria". Paper presented in Microbiotec21, Lisbon, 2021.
    Published
  3. Palma, Margarida; Dias, Paulo Jorge; Luzia, Laura; Guerreiro, Joana F.; Roque, Filipa de Canaveira; Isabel Sá-Correia. "Functional and evolutionary analysis of the Zygosaccharomyces bailii ortholog of Saccharomyces cerevisiae Haa1 suggest its subfunctionalization in post-whole genome duplication species". Paper presented in 6th Conference on Physiology of Yeast and Filamentous Fungi (PYFF6), Lisbon, 2016.
  4. Dias, Paulo Jorge; Isabel Sá-Correia. "A common phylogenetic origin links the DHA2, ARN and GEX transporters: phylogenetic characterization and proposal of the new DAG protein family". Paper presented in XX Jornadas de Biologia de Leveduras "Nicolau van Uden", Lisbon, 2014.
    Published
  5. Dias, Paulo Jorge; Isabel Sá-Correia. "The major facilitator superfamily multidrug resistance transporters (mfs-mdr) in hemiascomycetous yeasts: phylogenetic and syntenic analyses". Paper presented in Microbiotec13, Lisbon, 2013.
    Published
  6. Dias, Paulo Jorge; Isabel Sá-Correia. "Evolution of the 12-spanner drug:H+ antiporters of family 1 (DHA1) in the pathogenic Candida species: phylogenetic analysis of Mdr1 and Flu1 proteins". Paper presented in XIX Jornadas de Biologia de Leveduras "Nicolau van Uden", Lisbon, 2012.
    Published
  7. Dias, Paulo Jorge; Pedro T Monteiro; Arlindo Limede de Oliveira; Ana Teresa Correia de Freitas; Isabel Sá-Correia; Teixeira, Miguel Cacho. "Insights into the transcription regulatory network controlling the multidrug resistance gene FLR1: a systems biology approach". Paper presented in 25th International Conference on Yeast Genetics and Molecular Biology, Olsztyn- Kortowo, 2011.
    Accepted
  8. Dias, Paulo Jorge; Seret M-L; Goffeau, André; Isabel Sá-Correia; Baret, Philippe V.. "Evolution of the 12-spanner drug:H+ antiporter DHA1 family in hemiascomycete yeasts". Paper presented in XVIII Jornadas de Biologia de Leveduras "Nicolau van Uden", Lisbon, 2010.
    Published
  9. Teixeira, Miguel Cacho; Pedro T Monteiro; Dias, Paulo Jorge; Costa, Catarina P; Ropers, D.; Arlindo Limede de Oliveira; Ana Teresa Correia de Freitas; Isabel Sá-Correia. "Refining current knowledge on the regulatory network underlying the transcriptional control of the multidrug resistance gene FLR1 combining experimental and computational approaches". Paper presented in XVIII Jornadas de Biologia de Leveduras "Nicolau van Uden", Lisbon, 2010.
    Published
  10. Dias, Paulo Jorge; Teixeira, Miguel Cacho; Pedro Miguel Santos; João Paulo Cabral Telo; Artur Pedro Duarte Reis Bastos Lourenço; Isabel Sá-Correia. "Mechanistic insights into the response and resistance to the agricultural fungicide mancozeb using Omics approaches". Paper presented in 4th Conference on Physiology of Yeast and Filamentous Fungi (PYFF4), Rotterdam, 2010.
  11. Pedro T Monteiro; Dias, Paulo Jorge; Ropers, D.; Arlindo Limede de Oliveira; Ana Teresa Correia de Freitas; Isabel Sá-Correia; Teixeira, Miguel Cacho. "The regulatory network underlying the transcriptional upregulation of the FLR1 gene in mancozeb stressed yeast cells: qualitative modeling and simulation". Paper presented in Microbiotec09, Vilamoura, 2009.
    Published
  12. Dias, Paulo Jorge; João Paulo Cabral Telo; Teixeira, Miguel Cacho; Isabel Sá-Correia. "Use of chemogenomics to identify genes involved in yeast resistance to the agricultural fungicide mancozeb". Paper presented in XVII Jornadas de Biologia de Leveduras "Nicolau van Uden", Braga, 2009.
    Published
  13. Teixeira, Miguel Cacho; Dias, Paulo Jorge; Simões, Tânia; Isabel Sá-Correia. "Coordinate control of the transcriptional up-regulation of FLR1 in yeast response to the fungicide mancozeb involves Yap1p, Pdr3p, Yrr1p and Rpn4p". Paper presented in 26th conference of Small Meeting on Yeast Transport and Energetics (SMYTE26), Braga, 2008.
Conference paper
  1. Dias, P.J.; Costa, C.P.; Sá-Correia, I.; Teixeira, M.C.; Monteiro, P.T.; Oliveira, A.L.; Freitas, A.T.. "Using systems biology approaches to study a multidrug resistance network". 2011.
    10.1109/ENBENG.2011.6026073
  2. Dos Santos, S.C.; Teixeira, M.C.; Mira, N.P.; Cabrito, T.R.; Palma, M.; Lourenço, A.B.; Dias, P.J.; et al. "Response and resistance to drugs and chemical stress in the yeast model: A genome-wide view". 2011.
    10.1109/ENBENG.2011.6026076
  3. Dias, Paulo Jorge; Sa-Correia, Isabel. "Reconstruction of the evolutionary history of the DHA1 family of yeast multidrug resistance transporters of the major facilitator superfamily". 2011.
    10.1109/enbeng.2011.6026075
Conference poster
  1. Dias, Paulo Jorge; Santos, JM; Antunes, DL; Sofia de Oliveira Dias Duarte; Leonilde Moreira 401D-32AD-2FA6; Monteiro, Gabriel António Amaro. "Graph-based and Gene-based Pangenome of Lactococcus lactis and Lactococcus cremoris". Paper presented in 3rd iBB Workshop, 2023.
  2. Dias, Paulo Jorge. "Genome annotation of two thousand hemiascomycete yeast strains: towards the development of an information system dedicated to Yeast Comparative Genomics and Pangenomics". Paper presented in 3rd iBB Workshop, 2023.
  3. Dias, Paulo Jorge. "Genome annotation of two thousand hemiascomycete yeast strains: towards the development of an information system dedicated to Yeast Comparative Genomics and Pangenomics". Paper presented in 31st International Conference on Yeast Genetics and Molecular Biology (ICYGMB), 2023.
  4. Dias, Paulo Jorge. Corresponding author: Dias, Paulo Jorge. "Evolution of the Pleiotropic Drug Resistance (Pdr) Snq2/Pdr18 gene subfamily in the hemiascomycete yeasts". Paper presented in Yeast Genetics Meeting 2022, 2022.
  5. "Exometabolome analysis of Lactococcus lactis LMG19460 – Focus on the characterization of a novel ferulic acid pathway". Paper presented in 3rd BioIberoAmerica - Congresso Ibero-Americano de Biotecnologia, 2022.
  6. Dias, Paulo Jorge. "Genome Sequence and Annotation of Lactococcus lactis Strain LMG 19460 and Novel Strains IST-LL01 and IST-LL02". Paper presented in Microbiotec’21, 2021.
  7. Dias, Paulo Jorge. "Reconstruction of the Metabolic Network of Lactococcus lactis strains IL1403 and LMG 19460". Paper presented in Microbiotec’21, 2021.
  8. Dias, Paulo Jorge. "Characterization of a novel ferulic acid pathway in Lactococcus lactis". Paper presented in Microbiotec’21, 2021.
  9. Dias, Paulo Jorge. "Reconstruction of the Metabolic Network of Lactococcus lactis LMG 19460". Paper presented in 13th International Symposium on Lactic Acid Bacteria, 2021.
  10. Dias, Paulo Jorge. "Identification of the ferulic acid metabolism in Lactococcus lactis". Paper presented in 13th International Symposium on Lactic Acid Bacteria, 2021.
  11. Dias, Paulo Jorge; Machado, André. "New insights into the evolution of members of the drug: H+ Antiporters Gene Family 1 (DHA1) in Hemiascomycete Yeasts". Paper presented in International Congress on Yeasts (ICY) meets the International Conference on Yeast Genetics and Molecular Biology (ICYGMB), 2021.
  12. Dias, Paulo Jorge. "Molecular Evolution of the members of Snq2/Pdr18 subfamily of PDR transporters in Hemiascomycete yeasts". Paper presented in ICYGMB2019, 2019.
  13. Dias, Paulo Jorge. "Evolutionary and physiological insights into Saccharomyces cerevisiae multidrug/multixenobiotic resistance ABC transporter genes PDR18 and SNQ2". Paper presented in 6th Conference on Physiology of Yeast and Filamentous Fungi (PYFF6), 2016.
  14. Dias, Paulo Jorge. "Zygosaccharomyces bailii adaptation to acetic acid stress involves the transcription factor ZbHaa1 through the activation of genes homologous to genes of ScHaa1-regulon". Paper presented in 6th Conference on Physiology of Yeast and Filamentous Fungi, 2016.
  15. Dias, Paulo Jorge. "Yeast Drug:H+ antiporters: comparative genomic and phylogenetic analyses and design and implementation of a dedicated database". Paper presented in Microbiotec’15, 2015.
  16. Dias, Paulo Jorge. "Evolution of the 12-spanner drug:H+ antiporter family 1 (DHA1) in pathogenic Candida species: phylogenetic and comparative genomic analyses of Mdr1 and Flu1 proteins". Paper presented in XX Jornadas de Biologia de Leveduras "Nicolau van Uden", 2014.
  17. Dias, Paulo Jorge. "New Insights on the Evolution of the Hemiascomycete Yeasts Major Facilitator Superfamily Multidrug Resistance Transporters". Paper presented in Experimental Approaches to Evolution and Ecology using Yeast, 2012.
  18. Dias, Paulo Jorge. "Computational modeling and analysis of the yeast FLR1 regulatory network in mancozeb-challenged cells". Paper presented in 11th International Conference on Systems Biology (ICSB’10), 2010.
  19. Dias, Paulo Jorge. "Insights into the mechanisms of toxicity and tolerance to the thiol-reactive agricultural fungicide mancozeb in yeast, as suggested by a chemogenomic approach". Paper presented in Microbiotec09, 2009.
  20. Dias, Paulo Jorge. "Use of toxicogenomics and chemogenomics to identify genes involved in yeast response and resistance to the agricultural fungicide mancozeb". Paper presented in Yeast2008, 2008.
  21. Dias, Paulo Jorge. "New insights into the biological function of the drug-H+ antiporter encoded by the FLR1 gene revealed by H1-NMR-based metabolomics and expression proteomics". Paper presented in Yeast2008, 2008.
  22. Dias, Paulo Jorge. "Global analysis of the mechanism underlying yeast resistance and response to the fungicide mancozeb". Paper presented in 3rd Conference on Physiology of Yeasts and Filamentous Fungi (PYFF3), 2007.
  23. Dias, Paulo Jorge. "Insights into the mechanisms underlying yeast response and resistance to the fungicide mancozeb using expression proteomics and chemogenomics". Paper presented in Micro’07-Biotec’07-XXXIII JPG, 2007.
  24. Dias, Paulo Jorge. "Increased expression of the multidrug resistance transporter Flr1 in response to the fungicide mancozeb: the underlying transcriptional regulatory network". Paper presented in Micro’07-Biotec’07-XXXIII JPG, 2007.
  25. Dias, Paulo Jorge. "Predição da topologia de proteínas transmembranares: modelos de Markov escondidos não-homogéneos numa perspectiva bayesiana". Paper presented in XIII Annual Conference of the Statistical Portuguese Society (SPE), 2005.
  26. Dias, Paulo Jorge. "Tipificação de estirpes de Candida albicans e Candida parapsilosis utilizando as técnicas de MSP-PCR e PFGE". Paper presented in Micro2001, 2001.
  27. Dias, Paulo Jorge. "Epidemiological survey of Tinea capitis and introduction of molecular techniques in an elementary school in the outskirts of Lisbon during 1987/88 and 1998/99". Paper presented in 6th Medical Mycology European Congress, 2000.
Journal article
  1. Dias, Paulo Jorge. "Molecular Evolution of the members of the Snq2/Pdr18 subfamily of Pdr transporters in the Hemiascomycete yeasts". Frontiers in Genetics (2024):
    Under revision
  2. Ferreira, Mirela R.; Gomes, Sara C.; Dias, Paulo Jorge; DePas, William H. ; Cooper, Vaughn S; Leonilde Moreira 401D-32AD-2FA6. "Bep polysaccharide is essential for macroscopic multicellular aggregates formation in Burkholderia multivorans". (2024):
  3. Dias, Paulo Jorge; Satyanarayana Tulasi; Digvijay Verma. "Why does Comparative Genomics play a central role in the Biology and Biotechnology of the 21st century?". Frontiers in Genetics and Frontiers in Microbiology - Section Evolutionary and Genomic Microbiology (2024): https://www.frontiersin.org/research-topics/50431/microbial-comparative-genomics-and-pangenomics-new-tools-approaches-and-insights-into-gene-and-genome-evolution/magazine.
  4. Godinho, Cláudia P.; Dias, Paulo J.; Ponçot, Elise; Sá-Correia, Isabel. "The Paralogous Genes PDR18 and SNQ2, Encoding Multidrug Resistance ABC Transporters, Derive From a Recent Duplication Event, PDR18 Being Specific to the Saccharomyces Genus". Frontiers in Genetics 9 (2018): http://dx.doi.org/10.3389/fgene.2018.00476.
    10.3389/fgene.2018.00476
  5. Palma, Margarida; Dias, Paulo Jorge; Roque, Filipa de Canaveira; Luzia, Laura; Guerreiro, Joana Fernandes; Sá-Correia, Isabel. "The Zygosaccharomyces bailii transcription factor Haa1 is required for acetic acid and copper stress responses suggesting subfunctionalization of the ancestral bifunctional protein Haa1/Cup2". BMC Genomics 18 1 (2017): http://dx.doi.org/10.1186/s12864-016-3443-2.
    10.1186/s12864-016-3443-2
  6. Dias, Paulo Jorge; Sá-Correia, Isabel. "Phylogenetic and syntenic analyses of the 12-spanner drug:H + antiporter family 1 (DHA1) in pathogenic Candida species: evolution of MDR1 and FLU1 genes". Genomics 104 1 (2014): 45-57. http://dx.doi.org/10.1016/j.ygeno.2014.05.005.
    10.1016/j.ygeno.2014.05.005
  7. Costa, Catarina; Dias, Paulo J.; Sá-Correia, Isabel; Teixeira, Miguel C.. "MFS multidrug transporters in pathogenic fungi: do they have real clinical impact?". Frontiers in Physiology 5 (2014): http://dx.doi.org/10.3389/fphys.2014.00197.
    10.3389/fphys.2014.00197
  8. dos Santos, Sandra C.; Teixeira, Miguel C.; Dias, Paulo J.; Sá-Correia, Isabel. "MFS transporters required for multidrug/multixenobiotic (MD/MX) resistance in the model yeast: understanding their physiological function through post-genomic approaches". Frontiers in Physiology 5 (2014): http://dx.doi.org/10.3389/fphys.2014.00180.
    10.3389/fphys.2014.00180
  9. Dias, Paulo; Sá-Correia, Isabel. "The drug:H+ antiporters of family 2 (DHA2), siderophore transporters (ARN) and glutathione:H+ antiporters (GEX) have a common evolutionary origin in hemiascomycete yeasts". BMC Genomics 14 1 (2013): 901. http://dx.doi.org/10.1186/1471-2164-14-901.
    10.1186/1471-2164-14-901
  10. Monteiro, P.T.; Sá-Correia, I.; Ropers, D.; Teixeira, M.C.; Dias, P.J.; Freitas, A.T.; Oliveira, A.L.. "Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae". IET Systems Biology 5 5 (2011): 308-316. http://dx.doi.org/10.1049/iet-syb.2011.0001.
    10.1049/iet-syb.2011.0001
  11. Dias, Paulo Jorge; Seret, Marie-Line; Goffeau, André; Correia, Isabel Sá; Baret, Philippe V.. "Evolution of the 12-Spanner Drug:H+ Antiporter DHA1 Family in Hemiascomycetous Yeasts". OMICS: A Journal of Integrative Biology 14 6 (2010): 701-710. http://dx.doi.org/10.1089/omi.2010.0104.
    10.1089/omi.2010.0104
  12. Dias, Paulo J.; Teixeira, Miguel C.; Telo, João P.; Sá-Correia, Isabel. "Insights into the Mechanisms of Toxicity and Tolerance to the Agricultural Fungicide Mancozeb in Yeast, as Suggested by a Chemogenomic Approach". OMICS: A Journal of Integrative Biology 14 2 (2010): 211-227. http://dx.doi.org/10.1089/omi.2009.0134.
    10.1089/omi.2009.0134
  13. Teixeira, M. C.; Dias, P. J.; Monteiro, P. T.; Sala, A.; Oliveira, A. L.; Freitas, A. T.; Sá-Correia, I.. "Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches". Molecular BioSystems 6 12 (2010): 2471. http://dx.doi.org/10.1039/c004881j.
    10.1039/c004881j
  14. Teixeira, Miguel Cacho; Dias, Paulo Jorge; Simões, Tânia; Sá-Correia, Isabel. "Yeast adaptation to mancozeb involves the up-regulation of FLR1 under the coordinate control of Yap1, Rpn4, Pdr3, and Yrr1". Biochemical and Biophysical Research Communications 367 2 (2008): 249-255. http://dx.doi.org/10.1016/j.bbrc.2007.12.056.
    10.1016/j.bbrc.2007.12.056
Journal issue
  1. Dias, Paulo Jorge; Satyanarayana Tulasi; Digvijay Verma. "Microbial Comparative Genomics and Pangenomics: New Tools, Approaches And Insights Into Gene and Genome Evolution". Frontiers in Genetics (2023): https://www.frontiersin.org/research-topics/50431/microbial-comparative-genomics-and-pangenomics-new-tools-approaches-and-insights-into-gene-and-genome-evolution.
    Published • Editor

Other

Dataset
  1. Dias, Paulo Jorge. GenomeDB and BlastDB focusing the hemiascomycete yeasts. 2024.
  2. Dias, Paulo Jorge. Pangenome Graph of Saccharomyces cerevisiae and of other Saccharomyces species. 2024.
  3. Dias, Paulo Jorge. Pangenome Graph of Lactococcus lactis and Lactococcus cremoris. 2023.
  4. Dias, Paulo Jorge. GenomeDB and BlastDB focusing the Burkholderiales. 2023.
  5. Dias, Paulo Jorge. Pangenome Graph of eight Burkholderia species. 2023.
  6. Dias, Paulo Jorge; Antunes, DL. Metabolic model of the Lactococcus lactis species. 2021.
  7. Dias, Paulo Jorge. MetaboliteDB and ReactionDB focusing bacterial species with available Metabolic models. 2020.
  8. Dias, Paulo Jorge. GenomeDB and BlastDB focusing the Lactobacillales. 2019.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/12/07 Graph-based and Gene-based Pangenome of Lactococcus lactis and Lactococcus cremoris Genome Informatics
Cold Spring Harbour Laboratory (CSHL) (Cold Spring Harbour, NY, United States)
2021/11/23 A sustainable alternative for cheese production – a synthetic biology approach for chymosin production using recombinant Lactic Acid Bacteria Microbiotec’21
(Lisbon, Portugal)
2014 A common phylogenetic origin links the DHA2, ARN and GEX transporters: phylogenetic characterization and proposal of the new DAG protein family XX Jornadas de Biologia de Leveduras "Nicolau van Uden"
(Lisboa, Portugal)
2013 The major facilitator superfamily multidrug resistance transporters (mfs-mdr) in hemiascomycetous yeasts: phylogenetic and syntenic analyses Microbiotec’13
(Aveiro, Portugal)
2012 Evolution of the 12-spanner drug:H+ antiporters of family 1 (DHA1) in the pathogenic Candida species: phylogenetic analysis of Mdr1 and Flu1 proteins XIX Jornadas de Biologia de Leveduras "Nicolau van Uden"
(Caparica, Portugal)
2011 Reconstruction of the evolutionary history of the DHA1 family of Yeast multidrug resistance transporters of the major facilitator superfamily 1st Portuguese Meeting in Bioengineering
(Oeiras, Portugal)
2010 Mechanistic insights into the response and resistance to the agricultural fungicide mancozeb using Omics approaches 4th Conference on Physiology of Yeast and Filamentous Fungi (PYFF4)
(Rotterdam, Netherlands)
2010 Evolution of the 12-spanner drug:H+ antiporter DHA1 family in hemiascomycete yeasts XVIII Jornadas de Biologia de Leveduras "Nicolau van Uden"
(Lisboa, Portugal)
2009 Use of chemogenomics to identify genes involved in yeast resistance to the agricultural fungicide mancozeb XVII Jornadas de Biologia de Leveduras "Nicolau van Uden"
(Braga, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023 - 2024 Evolution of two gene families of Adhesins in the Burkholderiales species (provisional title)
Supervisor
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - 2023/12 Gene-based and Graph-based Pangenomes of 8 Burkholderia Species: Construction, Visualization and Analysis
Supervisor
 Master of Science Degree in Biological Engineering (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2019/09/01 - 2021/01/22 Comparative Systems Biology analyses of Lactococcus lactis subsp. lactis strain LMG 19460
Co-supervisor
 Mestrado em Microbiologia Aplicada (Master)
Universidade de Lisboa, Portugal
2015 - 2016 Evolution and Bioinformatics Analysis of the Drug: H+ Antiporter Family 1 (DHA1) in the hemiascomycetes yeasts
Supervisor
 Master of Science in Biotecnology (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2014 - 2015/12 Functional analysis and evolution of Zygosaccharomyces bailii transcription factor Haa1, involved in acetic acid tolerance
Co-supervisor
 Master of Science in Biotecnology (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2016 - 2016 Member of the Organizing Commitee of the "6th Conference on Physiology of Yeast and Filamentous Fungi (PYFF6)" (2016 - 2016)
Conference (Member of the Organising Committee)
 Universidade de Lisboa Instituto Superior Técnico, Portugal
2014/06/11 - 2014/06/12 Member of the staff aiding the organization of the XX Jornadas de Biologia de Leveduras Nicolau van Uden (2014/06/11 - 2014/06/12)
Conference (Other)
 Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2007/11/30 - 2007/12/02 Member of the staff aiding the organization of the Micro'07-Biotec'07-XXXIII JPG meeting (2007/11/30 - 2007/12/02)
Conference (Other)
 Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
1999/08/18 - 1999/09/02 Member of the staff aiding the organization of the 14th Meeting of the European Cytoskeleton Forum (1999/08/18 - 1999/09/02)
Conference (Other)
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2022/09/12 - 2022/09/16 International Scientific Course lectured by Professors Lennart Martens and Lieven Clement
Other
 Proteomics Data Analysis (PDA22)
Instituto Gulbenkian de Ciência, Portugal
2019/09/09 - 2019/09/13 International Scientific Course lectured by Professors Erik Garrison and Mikko Rautiainen
Other
 Computational PANGenomics (CPANG19)
Instituto Gulbenkian de Ciência, Portugal
2014/10/06 - 2014/10/09 International Scientific Course lectured by professors Riccardo Cigliano and Stefan Götz
Other
 Transcriptome Assembly, Automatic Functional Annotation and Data Mining (TA-AFADM14)
Instituto Gulbenkian de Ciência, Portugal
2012/09/11 - 2012/09/14 International Scientific Course lectured by professors Rutger Vos and Darin London
Other
 Automated and reproducible analysis of NGS data (ARANGS12)
Instituto Gulbenkian de Ciência, Portugal
2011/09/12 - 2011/09/13 National Scientific Course lectured by Professor Hélio dos Santos Migon
Other
 Dynamic Bayesian Models in Time Series (short course)
Universidade de Lisboa Centro de Estatística e Aplicações, Portugal
2011/06/20 - 2011/06/24 International Scientific Course lectured by professors Bernhard Palsson, Ronan Fleming, Ines Thiele and Eivind Almaas
Other
 5th Systems Biology Short Course
University of Iceland, Center for Systems Biology, Iceland

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023/09 Evaluating the impact of horizontally acquired genes on the metabolism of non-conventional yeast lineage
(Thesis) Main arguer
 Victoria Helena Navas Gil (Master)
Universidade Nova de Lisboa, Portugal
2022/11/07 Upgrade of a Ustilaginomycetes's genome-scale metabolic model for MEL production by Moesziomyces antarcticus
(Thesis) Main arguer
 Fátima Mendes Costa (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 Identification and molecular characterization of the highly acetic acid tolerant Zygosaccharomyces bailii strain IST302
(Thesis) Main arguer
 Pessa J (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 Evolution and Bioinformatics Analysis of the Drug: H+ Antiporter Family 1 (DHA1) in the hemiascomycetes yeasts
Supervisor
 Machado A (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 Functional analysis and evolution of Zygosaccharomyces bailii transcription factor Haa1, involved in acetic acid tolerance
(Thesis) Main arguer
 Luzia L (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Association member

Society Organization name Role
2005 - 2020 Portuguese Microbiology Society Membership, Associate

Consulting

Activity description Institution / Organization
2022 - Current Guest Associate Editor in Evolutionary and Genomic Microbiology, a section in Frontiers in Genetics and Frontiers in Microbiology journals Frontiers Media SA, Switzerland
2022 - Current Review Editor in Medical Mycology, a section in Frontiers in Fungal Biology journal Frontiers Media SA, Switzerland

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2009 - 2016 Introduction to key evolutionary concepts and to phylogenetic trees Master's programme in Biotechnology (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2009 - 2016 Gene and genomic duplications and the evolution of genomes PhD programme in Biotechnology (Doutoramento) Universidade de Lisboa Instituto Superior Técnico, Portugal
2009 - 2016 Inference of phylogenies: introduction to phylogenetic trees and evolutionary comparative genomics Master’s in Biotechnology (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2009 - 2016 Inference of phylogenies: introduction to phylogenetic trees and evolutionary comparative genomics PhD programme in Biotechnology (Doutoramento) Universidade de Lisboa Instituto Superior Técnico, Portugal

Mentoring / Tutoring

Topic Student name
2024/02/20 - Current Construction of the Gene-based and Graph-based Pangenome of Saccharomyces cerevisiae and of other Saccharomyces species Hugo Ramalho
2023 - Current Evolution of a carbohydrate gene cluster in Burkholderiales species Mirela Ferreira
2022/03/20 - 2022/07/22 Evolution of the endonuclease Nth in Lactobacillales species Beatriz De Jesus Louren ¸co Labiza
2021 - 2022 Characterization of the exo-metabolome of L. lactis strain LMG 19469 and studying the unknown peak produced by this strain in response to exposure to ferulic acid Bruno Costa
2021 - 2022 Development of a sustainable alternative for cheese production using a synthetic biology approach for chymosin production in Lactic Acid Bacteria Alexandre Furtado
2019 - 2022 Development of a Crispr-Cas9 system specifically for the L. lactis species José Miguel Miquelão Santos
2015 - 2016 Trehalose-6-Phosphate Synthase/Phosphatase (TPS/TPP) Complex in Saccharomyces cerevisiae - characterization and evolution Rui Pacheco (PhD student)
2015 - 2016 A yeast MFS-MDR Transporter Information System Anandashankar Anil (MSc student in the euSysBio Erasmus Mundus Master in Systems Biology)
2014 - 2016 Comparative genomics, Bioinformatics and Evolution Tools applied of MFS-Major Facilitator Superfamily in Saccharomycetaceae André Miguel Moreira Machado (MSc student)
2014 - 2015 Phylogenetic and syntenic analysis of the Pleiotropic Drug Resistance transporters: evolution of the Snq2/Pdr18 cluster Cláudia Godinho (PhD student)
2014 - 2015 Evolutionary and variational analysis of the drug:H+ antiporters family 1 (DHA1) in the Zygosaccharomyces genus Tineka Blake (MSc student in the euSysBio Erasmus Mundus Master in Systems Biology)
2014 - 2015 Design and Implementation of a MFS-MDR Transporters Information System Kaiyang Zhang (MSc student in the euSysBio Erasmus Mundus Master in Systems Biology)
2013 - 2014 Evolution of multidrug resistance transporters in the protoploid Saccharomycetaceae Tuan Nguyen (MSc student in the euSysBio Erasmus Mundus Master in Systems Biology)
2011 - 2012 Global responses of yeast to oxidative stress: mechanisms of activation of the transcription factor Yap1 in response to the agricultural fungicide Mancozeb Ana Almeida (MSc student)
2009 - 2010 Combined phylogenetic and gene neighbourhood analysis of the DHA2 family of hemiascomycetous MDR-MFS transporters Êunice Carrasquinha, Fátima Gil, Filipe Cardoso, José Pedro Amaral (Group project MSc students)
2008 - 2009 Exploiting phylogenetic analysis and comparative genomics to guide the functional characterization of fungal multidrug resistance transporters Cármen Ribeiro, Iracema Martinho, José Ribeiro, Maria Inês Lopes (Group project MSc students)
2007 - 2008 Analysis of a genome-wide screen of Saccharomyces cerevisiae disruptome to get insights into the biological targets and resistance mechanisms to the agricultural fungicide mancozeb linked to the development of Parkinson disease Joana Santos, Inês Vilalva, Daniel Freire, Ana Freitas (Group project MSc students)