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Identificação

Identificação pessoal

Nome completo
Paulo Jorge Moura Pinto da Costa Dias

Identificadores de autor

Ciência ID
031C-B4B2-0B2E

Endereços de correio eletrónico

  • pjdias00@gmail.com (Pessoal)

Domínios de atuação

  • Ciências Naturais - Ciências Biológicas
  • Ciências Naturais - Ciências Biológicas
  • Ciências Exatas - Física - Física Atómica
Formação
Grau Classificação
2011 - 2018
Concluído
 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
Concluído
 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" (TESE/DISSERTAÇÃO)
 Approved, with distinction
2002 - 2006
Concluído
 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" (TESE/DISSERTAÇÃO)
 Maximum Classification
1995 - 2001
Concluído
 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" (TESE/DISSERTAÇÃO)
 16
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2020 - Atual Investigador Contratado (Investigação) Associate Laboratory Institute for Health and Bioeconomy, Portugal
Associate Laboratory Institute for Health and Bioeconomy, Portugal
2018/12/01 - Atual Investigador Contratado (Investigação) Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
Projetos

Projeto

Designação Financiadores
2021/01/01 - 2025/12/31 Institute for Health and Bioeconomy
LA/P/0140/2020
10.54499/LA/P/0140/2020
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal

Universidade Nova de Lisboa, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Unidade de Ciências Biomoleculares Aplicadas, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

INESC Microsistemas e Nanotecnologias, Portugal

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Em curso
2024/08/02 - 2025/09/30 Construction and analysis of the Graph-based Pangenome of the Model-Organism Saccharomyces cerevisiae, of Nakaseomyces glabratus and of pathogenic bacteria belonging to the Burkholderia genus (Contract: 2024.07061.CPCA.A3)
10.54499/2024.07061.CPCA.A3
Investigador responsável
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2023/06/01 - 2023/12/31 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) (Contract: 2023.05807.CPCA.A1)
10.54499/2023.05807.CPCA.A1
Investigador responsável
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2019/01/01 - 2023/12/31 Applied Molecular Biosciences Unit
UIDP/04378/2020
10.54499/UIDP/04378/2020
UIDB/04378/2020
10.54499/UIDB/04378/2020
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal

Universidade Nova de Lisboa, Portugal

Rede de Química e Tecnologia Laboratório Associado para a Química Verde, Portugal

Universidade do Porto, Portugal

Unidade de Ciências Biomoleculares Aplicadas, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

INESC Microsistemas e Nanotecnologias, Portugal

Universidade Nova de Lisboa Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2023/03/01 - 2023/08/31 Construction of the Gene-based Pangenome of the model-organism Saccharomyces cerevisiae (3rd edition of Advanced Computing Projects: A0 Experimental Access) (round B) (Contract: 2022.42199.CPCA.A0)
10.54499/2022.42199.CPCA.A0
Investigador responsável
Associate Laboratory Institute for Health and Bioeconomy, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
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
Investigador
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2015/01/01 - 2018/12/31 Institute for Bioengineering and Biosciences
UID/BIO/04565/2013
grant.Provided by PTCRIS: 147338
UIDB/04565/2020
10.54499/UIDB/04565/2020
UIDP/04565/2020
10.54499/UIDP/04565/2020
UIDB/04565//2020 + UIDP/04565/2020
UID/BIO/04565/2019
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2011 - 2018 INTACT - Integral engineering of acetic acid tolerance in yeast (Contract: ERA-IB/0002/2010)
ERA-IB/0002/2010
Bolseiro de Pós-Doutoramento
Fundação para a Ciência e a Tecnologia
Concluído
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
Bolseiro de Pós-Doutoramento
Fundação para a Ciência e a Tecnologia
Concluído
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
Bolseiro de Pós-Doutoramento
Fundação para a Ciência e a Tecnologia
Concluído
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
Bolseiro de Pós-Doutoramento
Fundação para a Ciência e a Tecnologia
Concluído
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
Bolseiro de Pós-Doutoramento
Fundação para a Ciência e a Tecnologia
Concluído
2013/06/01 - 2016/12/31 Do desenvolvimento de novos produtos bioactivos à descoberta de novos materiais funcionais: uma abordagem estrutural em áreas emergentes
RECI/QEQ-QIN/0189/2012
Universidade de Lisboa Centro de Química Estrutural, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2011 - 2012 Systems and Synthetic Biology
PEst-OE/EQB/LA0023/2011_research line
Bolseiro de Pós-Doutoramento
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2008/01/01 - 2010/12/31 ARN - Algoritmos para a identificação de redes de regulação genética
PTDC/EIA/67722/2006
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluído
2006 - 2010 DBYeast: Infrastructure and algorithms for analysis and identification of gene regulatory networks (Contract: POSI/EIA/57398/2004)
POSI/EIA/57398/2004
Bolseiro de Doutoramento
Fundação para a Ciência e a Tecnologia
Concluído
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
Bolseiro de Doutoramento
Fundação para a Ciência e a Tecnologia
Concluído
2006 - 2010 Dyablo: models for the dynamic behaviour of Biological Networks (Contract: PTDC/EIA/71587/2006)
PTDC/EIA/71587/2006
Bolseiro de Doutoramento
Fundação para a Ciência e a Tecnologia
Concluído
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
Bolseiro de Doutoramento
Fundação para a Ciência e a Tecnologia
Concluído
Produções

Publicações

Artigo em conferência
  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
Artigo em revista
  1. Dias, Paulo Jorge. "Molecular Evolution of the members of the Snq2/Pdr18 subfamily of Pdr transporters in the Hemiascomycete yeasts". FEMS Yeast Research (2025): https://doi.org/10.1093/femsyr/foaf026.
    10.1093/femsyr/foaf026
  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". (2025):
    Submetido
  3. Verma, Digvijay; Satyanarayana, Tulasi; Dias, Paulo Jorge. "Editorial: Microbial comparative genomics and pangenomics: new tools, approaches and insights into gene and genome evolution". Frontiers in Genetics 15 (2024): https://doi.org/10.3389/fgene.2024.1490645.
    10.3389/fgene.2024.1490645
  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): https://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
Livro
  1. Dias, Paulo Jorge; Satyanarayana, Tulasi; Verma, Digvijay. Autor correspondente: Dias, Paulo Jorge. Microbial Comparative Genomics and Pangenomics: New Tools, Approaches And Insights Into Gene and Genome Evolution. 2024.
    Publicado • 10.3389/978-2-8325-5650-4
Poster em conferência
  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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 31st International Conference on Yeast Genetics and Molecular Biology (ICYGMB), 2023.
  4. Dias, Paulo Jorge. Autor correspondente: Dias, Paulo Jorge. "Evolution of the Pleiotropic Drug Resistance (Pdr) Snq2/Pdr18 gene subfamily in the hemiascomycete yeasts". Trabalho apresentado em Yeast Genetics Meeting 2022, 2022.
  5. Ana Sofia Direito dos Santos Duarte; Costa B; Dias, Paulo Jorge; Moreira, Leonilde M; Duarte Miguel de França Teixeira dos Prazeres; Pedro Boto Pereira Franco Pinheiro; José Gonçalo Deira Duarte de Campos Justino; Monteiro, Gabriel António Amaro. "Exometabolome analysis of Lactococcus lactis LMG19460 – Focus on the characterization of a novel ferulic acid pathway". Trabalho apresentado em 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". Trabalho apresentado em Microbiotec’21, 2021.
  7. Dias, Paulo Jorge. "Reconstruction of the Metabolic Network of Lactococcus lactis strains IL1403 and LMG 19460". Trabalho apresentado em Microbiotec’21, 2021.
  8. Dias, Paulo Jorge. "Characterization of a novel ferulic acid pathway in Lactococcus lactis". Trabalho apresentado em Microbiotec’21, 2021.
  9. Dias, Paulo Jorge. "Reconstruction of the Metabolic Network of Lactococcus lactis LMG 19460". Trabalho apresentado em 13th International Symposium on Lactic Acid Bacteria, 2021.
  10. Dias, Paulo Jorge. "Identification of the ferulic acid metabolism in Lactococcus lactis". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em ICYGMB2019, 2019.
  13. Dias, Paulo Jorge. "Evolutionary and physiological insights into Saccharomyces cerevisiae multidrug/multixenobiotic resistance ABC transporter genes PDR18 and SNQ2". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em Yeast2008, 2008.
  22. Dias, Paulo Jorge. "Global analysis of the mechanism underlying yeast resistance and response to the fungicide mancozeb". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 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". Trabalho apresentado em 6th Medical Mycology European Congress, 2000.
Resumo em conferência
  1. Dias, Paulo Jorge. "Construction and Analysis of the Graph-based Pangenomes of two Lactic Acid Bacteria (LAB), Lactococcus lactis and Lactococcus cremoris". Trabalho apresentado em Genome Graph Symposium (IGGSY 2024), Ascona, 2024.
    Publicado
  2. 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". Trabalho apresentado em Genome Informatics conference at Cold Spring Harbour Laboratory (CSHL), Cold Spring Harbour, NY, 2023.
    Publicado
  3. 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". Trabalho apresentado em Microbiotec21, Lisbon, 2021.
    Publicado
  4. 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". Trabalho apresentado em 6th Conference on Physiology of Yeast and Filamentous Fungi (PYFF6), Lisbon, 2016.
    Publicado
  5. 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". Trabalho apresentado em XX Jornadas de Biologia de Leveduras "Nicolau van Uden", Lisbon, 2014.
    Publicado
  6. Dias, Paulo Jorge; Isabel Sá-Correia. "The major facilitator superfamily multidrug resistance transporters (mfs-mdr) in hemiascomycetous yeasts: phylogenetic and syntenic analyses". Trabalho apresentado em Microbiotec13, Lisbon, 2013.
    Publicado
  7. 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". Trabalho apresentado em XIX Jornadas de Biologia de Leveduras "Nicolau van Uden", Lisbon, 2012.
    Publicado
  8. 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". Trabalho apresentado em 25th International Conference on Yeast Genetics and Molecular Biology, Olsztyn- Kortowo, 2011.
    Publicado
  9. 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". Trabalho apresentado em XVIII Jornadas de Biologia de Leveduras "Nicolau van Uden", Lisbon, 2010.
    Publicado
  10. 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". Trabalho apresentado em XVIII Jornadas de Biologia de Leveduras "Nicolau van Uden", Lisbon, 2010.
    Publicado
  11. 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". Trabalho apresentado em 4th Conference on Physiology of Yeast and Filamentous Fungi (PYFF4), Rotterdam, 2010.
    Publicado
  12. 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". Trabalho apresentado em Microbiotec09, Vilamoura, 2009.
    Publicado
  13. 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". Trabalho apresentado em XVII Jornadas de Biologia de Leveduras "Nicolau van Uden", Braga, 2009.
    Publicado
  14. 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". Trabalho apresentado em 26th conference of Small Meeting on Yeast Transport and Energetics (SMYTE26), Braga, 2008.
    Publicado

Outros

Conjunto de dados
  1. Dias, Paulo Jorge. Pangenome Graph of Saccharomyces cerevisiae and of other species beloging to the Saccharomyces genus. 2024.
  2. Dias, Paulo Jorge. Pangenome Graph of Lactococcus lactis and Lactococcus cremoris. 2023.
  3. Dias, Paulo Jorge. GenomeDB and BlastDB focusing the Burkholderiales. 2023.
  4. Dias, Paulo Jorge. Pangenome Graph of eight Burkholderia species. 2023.
  5. Dias, Paulo Jorge; Antunes, DL. Metabolic model of the Lactococcus lactis species. 2021.
  6. Dias, Paulo Jorge. MetaboliteDB and ReactionDB focusing bacterial species with available Metabolic models. 2020.
  7. Dias, Paulo Jorge. GenomeDB and BlastDB focusing the Lactobacillales. 2019.
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
2024/06/30 Construction and Analysis of the Graph-based Pangenomes of two Lactic Acid Bacteria (LAB), Lactococcus lactis and Lactococcus cremoris Genome Graph Symposium (IGGSY 2024)
(Ascona, Suiça)
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, Estados Unidos)
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, Países Baixos)
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)

Orientação

Título / Tema
Papel desempenhado 		Curso (Tipo)
Instituição / Organização
2023 - 2024 Evolution of two gene families of Adhesins in the Burkholderiales species (provisional title)
Orientador
Universidade de Lisboa Instituto Superior Técnico, Portugal
2023 - 2023/12 Gene-based and Graph-based Pangenomes of 8 Burkholderia Species: Construction, Visualization and Analysis
Orientador
 Master of Science Degree in Biological Engineering (Mestrado)
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
Coorientador
 Mestrado em Microbiologia Aplicada (Mestrado)
Universidade de Lisboa, Portugal
2015 - 2016 Evolution and Bioinformatics Analysis of the Drug: H+ Antiporter Family 1 (DHA1) in the hemiascomycetes yeasts
Orientador
 Master of Science in Biotecnology (Mestrado)
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
Coorientador
 Master of Science in Biotecnology (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Organização de evento

Nome do evento
Tipo de evento (Tipo de participação) 		Instituição / Organização
2016 - 2016 Member of the Organizing Commitee of the "6th Conference on Physiology of Yeast and Filamentous Fungi (PYFF6)" (2016 - 2016)
Conferência (Membro da Comissão Organizadora)
 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)
Conferência (Outra)
 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)
Conferência (Outra)
 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)
Conferência (Outra)
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Participação em evento

Descrição da atividade
Tipo de evento 		Nome do evento
Instituição / Organização
2025/05/15 - 2026/01/31 Foundation of Quantum Technology Management, lectured by professors Fedja Orucevic, Peter Kruger, Niel De Beaudrap and Paul Nightingale (ongoing course), University of Sussex, Brighton, England Foundation of Quantum Technology Management
University of Sussex, Reino Unido
2024/10/28 - 2024/10/31 Horizon Europe Training Cycle – 4th Edition. Organized by the Training and Development Unit (NFD), Human Resources Directorate. Horizon Europe Training Cycle
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022/09/12 - 2022/09/16 International Scientific Course lectured by Professors Lennart Martens and Lieven Clement
Outro
 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
Outro
 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
Outro
 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
Outro
 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
Outro
 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
Outro
 5th Systems Biology Short Course
University of Iceland, Center for Systems Biology, Islândia
1992 - 1992 Technological Course in Informatics, training for Microsoft Certified Systems Engineer (MCSE) certification. Organized by TAP Air Portugal, Lisbon, Portugal. Technological Course in Informatics, training for Microsoft Certified Systems Engineer (MCSE) certification
TAP Air Portugal, Portugal

Júri de grau académico

Tema
Tipo de participação 		Nome do candidato (Tipo de grau)
Instituição / Organização
2023/09 Evaluating the impact of horizontally acquired genes on the metabolism of non-conventional yeast lineage
Arguente principal
 Victoria Helena Navas Gil (Mestrado)
Universidade Nova de Lisboa, Portugal
2022/11/07 Upgrade of a Ustilaginomycetes's genome-scale metabolic model for MEL production by Moesziomyces antarcticus
Arguente principal
 Fátima Mendes Costa (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 Identification and molecular characterization of the highly acetic acid tolerant Zygosaccharomyces bailii strain IST302
Arguente principal
 Pessa J (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 Evolution and Bioinformatics Analysis of the Drug: H+ Antiporter Family 1 (DHA1) in the hemiascomycetes yeasts
Orientador
 Machado A (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2016 Functional analysis and evolution of Zygosaccharomyces bailii transcription factor Haa1, involved in acetic acid tolerance
Arguente principal
 Luzia L (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Consultoria / Parecer

Descrição da atividade Instituição / Organização
2022 - Atual Guest Associate Editor in Evolutionary and Genomic Microbiology, a section in Frontiers in Genetics and Frontiers in Microbiology journals Frontiers Media SA, Suiça
2022 - Atual Review Editor in Medical Mycology, a section in Frontiers in Fungal Biology journal Frontiers Media SA, Suiça

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
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

Membro de associação

Nome da associação Tipo de participação
2005 - 2020 Portuguese Microbiology Society Membership, Associate

Tutoria

Tópico Nome do aluno
2024/02/20 - Atual Construction of the Gene-based and Graph-based Pangenome of Saccharomyces cerevisiae and of other Saccharomyces species Hugo Ramalho
2023 - Atual 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)