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Francisco Dionisio has been an Associate Professor (with Habilitation) at the Faculty of Sciences, University of Lisbon, since 2023 and an Assistant Professor before that (since 2006). He has been passionate about plasmids for more than 25 years. Plasmids are intriguing, from origins to diversity, evolution, or their role as carriers of virulence or antibiotic resistance genes. He has combined bioinformatics with computational models, laboratory experiments, and mathematical models to understand plasmids and why most bacteria carry them. He has a PhD in Microbiology (2000, Université Paris VII Denis Diderot) and a 5-years degree in Physics Engineering from Universidade Técnica de Lisboa - Instituto Superior Técnico. Until Jan/2025, he has published 45 scientific papers (Scopus), 29 as the corresponding or co-corresponding author and 11 as the first author. According to the Scopus database, F. Dionisio has been cited more than 1595 times and has four papers with over a hundred citations. He also published a book about the evolution of genetic conflicts (this book is in Portuguese to the general public) and three book chapters. He has been an advisor or co-advisor of several PhD theses and MSc theses. F. Dionisio belonged to the comité of coordinators for both Ph.D. programs at the Plant Biology Department of the Faculty of Sciences, Univ. Lisbon between 2008 and 2019. He has been the Coordinator of the Master's Molecular Biology and Genetics course since 6/2019. Before, he was the Coordinator or co-Coordinator of the Master's in Bioinformatics and Computational Biology between 2010 and 6/2019. Since 2006, F. Dionisio has taught several courses comprising about 230 hours/year at the bachelor's, master's, and PhD levels. These courses include bioinformatics, evolutionary biology of microorganisms, evolutionary biology in medicine, and computational methods in evolution and ecology.
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Identification

Personal identification

Full name
Francisco André de Campos Pereira Dionísio

Citation names

  • Dionísio, Francisco
  • Dionisio, Francisco
  • Dionisio, F

Author identifiers

Ciência ID
7413-DB46-16E0
ORCID iD
0000-0002-3653-1511
Google Scholar ID
bI2KRKQAAAAJ
Researcher Id
A-2129-2009
Scopus Author Id
6506790127

Email addresses

  • francisco.dionisio@gmail.com (Professional)
  • dionisio@fc.ul.pt (Professional)
  • fadionisio@fc.ul.pt (Professional)

Addresses

  • Faculdade de Ciências da Universidade de Lisboa. Dep. Biologia Vegetal, Edifício C2, Piso 2, Campo Grande, 1749-016, Lisboa, Lisboa, Portugal (Professional)

Websites

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Advanced (C1) Advanced (C1) Intermediate (B1) Advanced (C1)
Spanish; Castilian Intermediate (B1) Advanced (C1) Beginner (A1) Intermediate (B1)
Education
Degree Classification
2019/05/14
Concluded
 Biologia (Título de Agregado)
Major in Especialidade: Evolução
Universidade de Lisboa Faculdade de Ciências, Portugal
"Harmful behavior mediated by pathogens and parasites" (THESIS/DISSERTATION)
 Approved with distinction
2000/12/15
Concluded
 Microbiologia (Doctor of Philosophy)
Université Paris VII Denis Diderot UFR Sciences du Vivant, France
"Horizontal Gene Transfer in Enterobacteria: Homologous Recombination and Dynamics of Conjugative Plasmids" (THESIS/DISSERTATION)
 Mention Très Honorable et les félicitations du jury
1995/07
Concluded
 Engenharia Física Tecnológica (Licenciatura)
Major in Não Aplicável
Universidade de Lisboa Instituto Superior Técnico, Portugal
 16/20
Affiliation

Teaching in Higher Education

Category
Host institution 		Employer
2023/05 - Current Associate Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2006/04 - 2023/05 Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal

Positions / Appointments

Category
Host institution 		Employer
2019/06/01 - Current Coordinator of the Master's Degree in Molecular Biology and Genetics Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Faculdade de Ciências, Portugal
2007 - Current Coordinator or director of Research Group Universidade de Lisboa, Portugal
2016 - 2019 Director of the Master Degree in Bioinformatics and Computationa Biology Universidade de Lisboa, Portugal
2010 - 2019 Co-coordination of Doctoral Program Universidade de Lisboa Faculdade de Ciências, Portugal
Faculty of Sciences, University of Lisbon, Portugal
Projects

Contract

Designation Funders
2011/01/01 - 2013/12/31 Projecto Estratégico - UI 329 - 2011-2012
PEst-OE/BIA/UI0329/2011
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2008/03/15 - 2012/03/14 O papel das bactérias comensais na transmissão e propagação de genes de resistência a antibióticos
PTDC/BIA-BDE/66180/2006
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2008/08/15 - 2012/02/29 BIOCONTRACTO: Cooperação em mutualismos: contractos, mercados, espaço, e dispersão
TECH/0001/2007
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2005/01/01 - 2006/12/31 O papel da interacção social em bactérias na diversidade e evolução bacteriana
POCI/BIA-BDE/55758/2004
Fundação Calouste Gulbenkian, Portugal

Instituto Gulbenkian de Ciência, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Dionisio, Francisco. Corresponding author: Dionisio, Francisco. Uma Tampa para cada Tacho - Conflitos Genéticos e Evolução. Lisboa, Portugal: Editorial Bizâncio. 2011.
    Published
Book chapter
  1. Dionisio, Francisco; Nogueira, Teresa. "Mundo feito de mudanças. A variação textual é apenas uma das diferenças que caracterizam a vida humana". In Descubra as diferenças. Variação na literatura portuguesa desde a Idade Média até anteontem. Lisbon: CLUL, 2023.
    Published
  2. Borda-de-Água, Luís; Alirezazadeh, Saeid; Neves, Manuela; Hubbell, Stephen P.; Borges, Paulo A. V.; Cardoso, Pedro; Dionísio, Francisco; Pereira, Henrique M.. "Species Accumulation Curves and Extreme Value Theory". In The Species–Area Relationship, 211-226. Cambridge University Press, 2021.
    10.1017/9781108569422.014
  3. Dionísio, Francisco. "Symbiosis Between Non-Transferable Plasmids and Prokaryotic Cells". Switzerland, 2015.
    10.1007/978-3-319-16345-1_7
  4. Dionisio, Francisco; Nogueira, Teresa; Carvalho, Luís M.; Mendes-Soares, Helena; Mendonça, Sílvia C. M.; Domingues, Iolanda; Moreira, Bernardino; Reis, Ana M.. Corresponding author: Dionisio, Francisco. "What mantains plasmids among bacteria?". In Horizontal Gene Transfer in Microorganisms. United States: Caister Academic Press, U.K., 2012.
Conference paper
  1. Alirezazadeh, S.; Borda-De-Agua, L.; Borges, P.; Gabriel, R.; Dionísio, Francisco; Pereira, H.M.; Cardoso, P.. "Theoretical approach for how species abundance distributions change across scales*". 2018.
    10.1109/CONTROLO.2018.8514272
Conference poster
  1. Célia P. F. Domingues; João S. Rebelo; Dionisio, Francisco; Nogueira, Teresa. "Co-ocorrência de genes de resistência a antibióticos: localização em plasmídeos nos microorganismos patogénicos prioritários". Paper presented in Encontro Ciência 2024, 2024.
  2. Daniel G. Silva; Célia P. F. Domingues; João Figueiredo; Dionisio, Francisco; Ana Botelho; Nogueira, Teresa. "Potencial epidémico de aquaculturas portuguesas através de uma perspetiva Uma Só Saúde: análise metagenómica do resistoma". Paper presented in Encontro Ciência 2024, 2024.
  3. Daniel G. Silva; Celia P. F. Domingues; João F. Figueiredo; Dionisio, Francisco; Ana Botelho; Nogueira, Teresa. "Metagenomic study of bacterial resistance and its epidemic potential in estuarine farms in Portugal". Paper presented in Dare2Change, 2023.
  4. Silva, Daniel G.; Domingues, Célia P. F.; Figueiredo, João; Dionisio, Francisco; Botelho, Ana; Nogueira, Teresa. "Metagenomic analysis of the resistome of Portuguese aquacultures and its epidemic potential.". Paper presented in 2ndMicrobiome PT Summit, 2023.
  5. Daniel G. Silva; Celia P. F. Domingues; João F. Figueiredo; Dionisio, Francisco; Ana Rosa Botelho; Nogueira, Teresa. "Microbiome and resistome dynamics of Portuguese estuarine aquacultures". Paper presented in XVIII ENBE Annual Meeting of the Portuguese Association for Evolutionary Biology, 2022., 2022.
  6. Joao S. Rebelo; Celia P. F. Domingues; Monteiro, Francisca; Nogueira, Teresa; Dionisio, Francisco. "Human social interactions shape the distribution of pathogenicity and antibiotic- resistance genes". Paper presented in XVIII ENBE Annual Meeting of the Portuguese Association for Evolutionary Biology, 2022.
  7. Daniel Silva; João Figueiredo; Celia P. F. Domingues; Dionisio, Francisco; Maulvault, Ana Luísa; Soares, Florbela; Patricia Anacleto; Ana Rosa Botelho; Nogueira, Teresa. "Antibiotic resistance determinants in estuarine aquacultures in Portugal". Paper presented in IC2AR 2022 -5th International Caparica Congress in Antibiotic Resistance, 2022.
  8. Helena Silveira; Celia P. F. Domingues; João S. Rebelo; Ana Amaro; Dionisio, Francisco; Nogueira, Teresa. "Genomic dynamics of virulence and antibiotic resistance in bacterial genomes". Paper presented in XVII ENBE Annual Meeting of the Portuguese Association for Evolutionary Biology, 2021.
  9. Rebelo, J. S.; Célia P. F. Domingues; Monteiro, Francisca; Nogueira, Teresa; Dionisio, Francisco. "Plasmid transfer as a weapon against plasmid-free cells - a strategy that leads to plasmid maintenance". Paper presented in RECOMB 2021 - 25th International Conference on Research in Computational Molecular Biology, 2021.
  10. Domingues, C. P. F.; Rebelo, J. S.; Monteiro, Francisca; Nogueira, Teresa; Dionisio, Francisco. "Why is there a positive correlation between the diversity of virulence and antibiotic-resistance genes?". Paper presented in RECOMB 2021 - 25th International Conference on Research in Computational Molecular Biology, 2021.
  11. Domingues, Célia; Rebelo, João; Nogueira, Teresa; Pothier, Joel; Monteiro, Francisca; Dionisio, Francisco. "Ratio between contagion probability and resistance gene loss rate is key for the emergence of positive correlation between antibiotic resistance gene diversity and virulence gene diversity in human metagenomes". Paper presented in Ciências Research Day, 2020.
  12. Rebelo, João; Domingues, Célia; Monteiro, Francisca; Nogueira, Teresa; Dionisio, Francisco. "Long life of persister cells - faults and errors resulting in a power-law decay". Paper presented in Ciências Research Day, 2020.
  13. Domingues, C. P. F.; Rebelo, J. S.; Dionisio, F; Botelho, A.; Nogueira, T.. "The Distancing Imposed To Contain COVID-19 Can Affect Our Microbiome: a Double-Edged Sword in Human Health". Paper presented in 6th Annual Meeting 2020 Frontiers in E3, 2020.
  14. Silva, Rui F; Mendonça, Sílvia CM; Reis, Ana M; Gordo, Isabel; Trindade, Sandra; Dionisio, Francisco. "Additional Resistance Determinants Often Increase Bacterial Fitness - Sign Epistasis Involving Plasmids and Chromosomal Mutations". Paper presented in VI Encontro Nacional de Biologia Evolutiva, 2010.
  15. Trindade, Sandra; Sousa, Ana Margarida; Dionisio, Francisco; Gordo, Isabel. "Epistasis Between Antibiotic Resistance Mutations". Paper presented in European Society for Evolutionary Biology Congress, 2009.
  16. Trindade, Sandra; Sousa, Ana Margarida; Dionisio, Francisco; Gordo, Isabel. "Pervasive Epistasis in Antibiotic Resistance". Paper presented in MMES- The Evolution of Antibiotic Resistance Workshop, 2009.
  17. Trindade, Sandra; Dionisio, Francisco; Coutinho, António; Gordo, Isabel. "Pervasive Positive Epistasis Between Mutations Conferring Antibitic Resistance". Paper presented in III Encontro Nacional de Biologia Evolutiva, 2007.
Encyclopedia entry
  1. Dionisio, Francisco; Celia P. F. Domingues; João S. Rebelo; Francisca Monteiro; Nogueira, Teresa. "The Role of Commensal and other Non-Pathogenic Bacteria". In Scholarly Community Encyclopedia, 2023. https://encyclopedia.pub/entry/40892.
    Published
Journal article
  1. Bruno T. S. Luz; João S. Rebelo; Francisca Monteiro; Francisco Dionisio. "What Is the Impact of Antibiotic Resistance Determinants on the Bacterial Death Rate?". Antibiotics (2025): https://doi.org/10.3390/antibiotics14020201.
    10.3390/antibiotics14020201
  2. Fuertes, Marina; Faria, Anabela; Gonçalves, Joana L.; Antunes, Sandra; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Antibiotic Consumption, Illness, and Maternal Sensitivity in Infants with a Disorganized Attachment". Children (2023): https://doi.org/10.3390/children10071232.
    10.3390/children10071232
  3. Domingues, Célia P. F.; Rebelo, João S.; Dionisio, Francisco; Nogueira, Teresa. Corresponding author: Dionisio, Francisco. "Multi-Drug Resistance in Bacterial Genomes—A Comprehensive Bioinformatic Analysis". International Journal of Molecular Sciences (2023): https://doi.org/10.3390/ijms241411438.
    10.3390/ijms241411438
  4. Dionisio, Francisco; Fuertes, Marina. Corresponding author: Dionisio, Francisco. "Maternal emotions increase the desire for antibiotic use and pressure on health professionals to prescribe antibiotics to their infants". Evidence Based Nursing (2023): https://doi.org/10.1136/ebnurs-2022-103616.
    10.1136/ebnurs-2022-103616
  5. Dionisio, Francisco; Baquero, Fernando; Fuertes, Marina. Corresponding author: Dionisio, Francisco. "Psychological and cultural factors influencing antibiotic prescription". Trends in Microbiology 31 6 (2023): 559-570. http://dx.doi.org/10.1016/j.tim.2022.12.010.
    10.1016/j.tim.2022.12.010
  6. Rebelo, João S.; Domingues, Célia P. F.; Nogueira, Teresa; Dionisio, Francisco. "Plasmids Increase the Competitive Ability of Plasmid-Bearing Cells Even When Transconjugants Are Poor Donors, as Shown by Computer Simulations". Microorganisms 11 5 (2023): 1238. http://dx.doi.org/10.3390/microorganisms11051238.
    10.3390/microorganisms11051238
  7. Fuertes, Marina; Faria, Anabela; Gonçalves, Joana L.; Antunes, Sandra; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "The Association between Prematurity, Antibiotic Consumption, and Mother-Infant Attachment in the First Year of Life". Antibiotics 12 2 (2023): 309. http://dx.doi.org/10.3390/antibiotics12020309.
    10.3390/antibiotics12020309
  8. Dionisio, Francisco; Domingues, Célia P. F.; Rebelo, João S.; Monteiro, Francisca; Nogueira, Teresa. Corresponding author: Dionisio, Francisco. "The Impact of Non-Pathogenic Bacteria on the Spread of Virulence and Resistance Genes". International Journal of Molecular Sciences 24 3 (2023): 1967. http://dx.doi.org/10.3390/ijms24031967.
    10.3390/ijms24031967
  9. Silva, Daniel G.; Domingues, Célia P. F.; Figueiredo, João F.; Dionisio, Francisco; Botelho, Ana; Nogueira, Teresa. "Estuarine Aquacultures at the Crossroads of Animal Production and Antibacterial Resistance: A Metagenomic Approach to the Resistome". Biology (2022): https://doi.org/10.3390/biology11111681.
    10.3390/biology11111681
  10. Fuertes, Marina; Antunes, Sandra; Martelo, Inês; Dionisio, Francisco. "The impact of low birthweight in infant patterns of regulatory behavior, mother-infant quality of interaction, and attachment". Early Human Development 172 (2022): 105633. http://dx.doi.org/10.1016/j.earlhumdev.2022.105633.
    10.1016/j.earlhumdev.2022.105633
  11. Darmancier, Helena; Domingues, Célia P. F.; Rebelo, João S.; Amaro, Ana; Dionisio, Francisco; Pothier, Joel; Serra, Octavio; Nogueira, Teresa. "Are Virulence and Antibiotic Resistance Genes Linked? A Comprehensive Analysis of Bacterial Chromosomes and Plasmids". Antibiotics (2022): https://doi.org/10.3390/antibiotics11060706.
    10.3390/antibiotics11060706
  12. Domingues, Célia P. F.; Rebelo, João S.; Monteiro, Francisca; Nogueira, Teresa; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Harmful behaviour through plasmid transfer: a successful evolutionary strategy of bacteria harbouring conjugative plasmids". Philosophical Transactions of the Royal Society B: Biological Sciences (2022): https://doi.org/10.1098/rstb.2020.0473.
    10.1098/rstb.2020.0473
  13. Rebelo, João; Célia P. F. Domingues; Monteiro, Francisca; Nogueira, Teresa; Dionisio, Francisco; Domingues, Célia P. F.; Nogueira, Teresa; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Bacterial persistence is essential for susceptible cell survival in indirect resistance, mainly for lower cell densities". PLOS ONE (2021): https://doi.org/10.1371/journal.pone.0246500.
    10.1371/journal.pone.0246500
  14. Rebelo, João S.; Domingues, Célia P. F.; Dionisio, Francisco; Gomes, Manuel C.; Botelho, Ana; Nogueira, Teresa. "COVID-19 Lockdowns May Reduce Resistance Genes Diversity in the Human Microbiome and the Need for Antibiotics". International Journal of Molecular Sciences (2021): https://doi.org/10.3390/ijms22136891.
    10.3390/ijms22136891
  15. Domingues, Célia P. F.; Rebelo, João S.; Pothier, Joël; Monteiro, Francisca; Nogueira, Teresa; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "The Perfect Condition for the Rising of Superbugs: Person-to-Person Contact and Antibiotic Use Are the Key Factors Responsible for the Positive Correlation between Antibiotic Resistance Gene Diversity and Virulence Gene Diversity in Human Metagenomes". Antibiotics 10 5 (2021): 605. http://dx.doi.org/10.3390/antibiotics10050605.
    10.3390/antibiotics10050605
  16. Domingues, Célia P. F.; Rebelo, João S.; Dionisio, Francisco; Botelho, Ana; Nogueira, Teresa. "The Social Distancing Imposed To Contain COVID-19 Can Affect Our Microbiome: a Double-Edged Sword in Human Health". mSphere 5 5 (2020): http://dx.doi.org/10.1128/msphere.00716-20.
    10.1128/msphere.00716-20
  17. Gama, João Alves; Fredheim, Elizabeth G. Aarag; Cléon, François; Reis, Ana Maria; Zilhão, Rita; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Dominance Between Plasmids Determines the Extent of Biofilm Formation". Frontiers in Microbiology 11 (2020): http://dx.doi.org/10.3389/fmicb.2020.02070.
    10.3389/fmicb.2020.02070
  18. Gama, João Alves; Zilhão, Rita; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Plasmid Interactions Can Improve Plasmid Persistence in Bacterial Populations". Frontiers in Microbiology 11 (2020): http://dx.doi.org/10.3389/fmicb.2020.02033.
    10.3389/fmicb.2020.02033
  19. Fuertes, Marina; Gonçalves, Joana L; Faria, Anabela; Lopes-dos-Santos, Pedro; Conceição, Inês C; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Maternal sensitivity and mother-infant attachment are associated with antibiotic uptake in infancy". Journal of Health Psychology 27 9 (2020): 2197-2210. http://dx.doi.org/10.1177/1359105320941245.
    10.1177/1359105320941245
  20. Escudeiro, Pedro; Pothier, Joël; Dionisio, Francisco; Nogueira, Teresa. "Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes". mSphere (2019): https://doi.org/10.1128/mSphere.00135-19.
    10.1128/mSphere.00135-19
  21. Dionisio, Francisco; Zilhão, Rita; Gama, João Alves. "Interactions between plasmids and other mobile genetic elements affect their transmission and persistence". Plasmid 102 (2019): 29-36. http://dx.doi.org/10.1016/j.plasmid.2019.01.003.
    10.1016/j.plasmid.2019.01.003
  22. Gama, João Alves; Zilhão, Rita; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance". Plasmid 99 (2018): 82-88. http://dx.doi.org/10.1016/j.plasmid.2018.09.009.
    10.1016/j.plasmid.2018.09.009
  23. Gama, João Alves; Zilhão, Rita; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Conjugation efficiency depends on intra and intercellular interactions between distinct plasmids: Plasmids promote the immigration of other plasmids but repress co-colonizing plasmids". Plasmid 93 (2017): 6-16. http://dx.doi.org/10.1016/j.plasmid.2017.08.003.
    Published • 10.1016/j.plasmid.2017.08.003
  24. Gama, João A.; Zilhão, Rita; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Co-resident plasmids travel together". Plasmid (2017): https://doi.org/10.1016%2Fj.plasmid.2017.08.004.
    10.1016/j.plasmid.2017.08.004
  25. Gama, J.A.; Zilhão, Rita; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Multiple plasmid interference - Pledging allegiance to my enemy's enemy". Plasmid (2017): https://doi.org/10.1016%2Fj.plasmid.2017.08.002.
    10.1016/j.plasmid.2017.08.002
  26. Gaivão, Maria; Dionisio, Francisco; Gjini, Erida. Corresponding author: Gjini, Erida. "Transmission Fitness in Co-colonization and the Persistence of Bacterial Pathogens". Bulletin of Mathematical Biology 79 9 (2017): 2068-2087. https://doi.org/10.1007%2Fs11538-017-0320-3.
    10.1007/s11538-017-0320-3
  27. Domingues, I L; Gama, J A; Carvalho, L M; Dionisio, F. Corresponding author: Dionisio, F. "Social behaviour involving drug resistance: the role of initial density, initial frequency and population structure in shaping the effect of antibiotic resistance as a public good". Heredity 119 5 (2017): 295-301. http://dx.doi.org/10.1038/hdy.2017.33.
    10.1038/hdy.2017.33
  28. Özkaya, Özhan; Xavier, Karina Bivar; Dionisio, Francisco; Balbontín, Roberto; Xavier, Karina B.. "Maintenance of Microbial Cooperation Mediated by Public Goods in Single- and Multiple-Trait Scenarios". Journal of Bacteriology 199 22 (2017): http://hdl.handle.net/10400.7/950.
    Published • 10.1128/JB.00297-17
  29. Miranda, António; Carvalho, Luís M.; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Lower Within-Community Variance of Negative Density Dependence Increases Forest Diversity". PLOS ONE 10 5 (2015): e0127260. http://dx.doi.org/10.1371/journal.pone.0127260.
    10.1371/journal.pone.0127260
  30. Gama, J. A.; Reis, A. M.; Domingues, I.; Mendes-Soares, H.; Matos, A. M.; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Temperate Bacterial Viruses as Double-Edged Swords in Bacterial Warfare". PLoS ONE 8 3 (2013): https://doi.org/10.1371/journal.pone.0059043.
    10.1371/journal.pone.0059043
  31. Gama, J.A.; Abby, S.S.; Vieira-Silva, S.; Dionísio, Francisco; Rocha, E.P.C.. "Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens". PLoS Pathogens 8 2 (2012): https://doi.org/10.1371/journal.ppat.1002503.
    10.1371/journal.ppat.1002503
  32. Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "The Importance of Mathematics to Biology". Journal of Ecosystem & Ecography (2012): http://www.omicsonline.org/the-importance-of-mathematics-to-biology-2157-7625.1000e112.php?aid=8646.
    10.4172/2157-7625.1000e112
  33. Silva, R. F.; Mendonça, S. C. M.; Carvalho, L. M.; Reis, A.M.; Gordo, Isabel; Trindade, S.; Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Pervasive sign epistasis between conjugative plasmids and Drug-Resistance chromosomal mutations". PLoS Genetics 7 7 (2011): https://doi.org/10.1371/journal.pgen.1002181.
    10.1371/journal.pgen.1002181
  34. Trindade, S.; Sousa, A.; Xavier, K.B.; Dionisio, F.; Ferreira, M.G.; Gordo, I.. "Positive epistasis drives the acquisition of multidrug resistance". PLoS Genetics 5 7 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-68249108837&partnerID=MN8TOARS.
    10.1371/journal.pgen.1000578
  35. Combadão, J.; Campos, P.R.A.; Dionisio, Francisco; Gordo, Isabel; Dionisio, F.; Gordo, I.. "Small-world networks decrease the speed of Muller's ratchet". Genetical Research 89 01 (2007): 7-7. https://doi.org/10.1017%2Fs0016672307008658.
    10.1017/s0016672307008658
  36. Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Selfish and spiteful behaviour through parasites and pathogens". Evolutionary Ecology Research 9 7 (2007): 1199-1210. https://www.evolutionary-ecology.com/issues/v09n07/kkar2176.pdf.
    Published
  37. Dionisio, Francisco; Gordo, I.. Corresponding author: Dionisio, Francisco. "Controlling excludability in the evolution of cooperation". Evolutionary Ecology Research 9 2 (2007): 365-373. http://www.evolutionary-ecology.com/issues/v09n02/mmar2106.pdf.
  38. Campos, P.R.; Combadão, J.; Dionisio, F.; Gordo, I.; Campos, P.R.A.. "Muller's ratchet in random graphs and scale-free networks.". Physical review. E, Statistical, nonlinear, and soft matter physics 74 4 Pt 1 (2006): http://www.scopus.com/inward/record.url?eid=2-s2.0-35148876208&partnerID=MN8TOARS.
    10.1103/PhysRevE.74.042901
  39. Dionisio, Francisco; Gordo, I.. Corresponding author: Dionisio, Francisco. "The tragedy of the commons, the public goods dilemma, and the meaning of rivalry and excludability in evolutionary biology". Evolutionary Ecology Research 8 2 (2006): 321-332. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645865566&partnerID=MN8TOARS.
  40. Isabel Gordo; Francisco Dionisio; Gordo, I.; Dionisio, F.. "Nonequilibrium model for estimating parameters of deleterious mutations". Physical Review E 71 3 (2005): https://doi.org/10.1103%2Fphysreve.71.031907.
    10.1103/physreve.71.031907
  41. Dionisio, Francisco. Corresponding author: Dionisio, Francisco. "Plasmids survive despite their cost and male-specific phages due to heterogeneity of bacterial populations". Evolutionary Ecology Research 7 8 (2005): 1089-1107. http://www.scopus.com/inward/record.url?eid=2-s2.0-31044435748&partnerID=MN8TOARS.
  42. Dionisio, F.; Conceição, I.C.; Marques, A.C.R.; Fernandes, L.; Gordo, I.. "The evolution of a conjugative plasmid and its ability to increase bacterial fitness". Biology Letters 1 2 (2005): 250-252. http://www.scopus.com/inward/record.url?eid=2-s2.0-25444496227&partnerID=MN8TOARS.
    10.1098/rsbl.2004.0275
  43. Dionisio, Francisco; Matic, I.; Radman, M.; Rodrigues, O.R.; Taddei, F.. Corresponding author: Dionisio, Francisco. "Plasmids spread very fast in heterogeneous bacterial communities". Genetics 162 4 (2002): 1525-1532. https://doi.org/10.1093/genetics/162.4.1525.
  44. Vulic, M.; Dionisio, Francisco; Taddei, F.; Radman, M.. "Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria". Proceedings of the National Academy of Sciences of the United States of America 94 18 (1997): 9763-9767. https://doi.org/10.1073/pnas.94.18.9763.
    10.1073/pnas.94.18.9763
Report
  1. Borda-de-Água, Luís; Cardoso, Pedro; Dionísio, Francisco; Pereira, Henrique M.; Borges, PAV; Gabriel, Rosalina; Alirezazadeh, Saheid. 2019. Relatório Final do Projecto FCT- PTDC/BIA-BIC/5558/2014– “MOMENTOS - Spatial scaling of species diversity” (2016-2019).
  2. Matos, Ana Marta. 2011. Bactérias comensais na transmissão de genes de resistência a antibióticos. http://hdl.handle.net/10451/4782.
Website
  1. Fuertes, Marina; Dionisio, Francisco. Qual a relação entre a vinculação do bebé, o stress materno e a toma de antibiótico?. 2022. https://primeirosanos.iscte-iul.pt/2023/02/22/vinculacao-e-antibiotico/..

Other

Other output
  1. The power of dying slowly - persistence as unintentional dormancy. 2021. João S. Rebelo; Célia P. F. Domingues; Francisca Monteiro; Teresa Nogueira; Francisco Dionisio; Rebelo, João S.; Domingues, Célia P. F.; et al. https://doi.org/10.1101/2021.01.20.427471.
    10.1101/2021.01.20.427471
  2. Gene transmission and antibiotic usage are the key factors responsible for the positive correlation between antibiotic resistance gene diversity and virulence gene diversity in human metagenomes. 2020. Célia P. F. Domingues; João S. Rebelo; Teresa Nogueira; Joel Pothier; Francisca Monteiro; Francisco Dionisio. https://doi.org/10.1101/2020.04.25.061853.
    10.1101/2020.04.25.061853
  3. The diversity of antibiotic resistance and virulence genes are correlated in human gut and environmental microbiomes. 2018. Pedro Escudeiro; Joël Pothier; Francisco Dionisio; Teresa Nogueira. https://doi.org/10.1101/298190.
    10.1101/298190
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023 - 2023 Comparative resistome, virulome and mobilome analysis of metagenomes from wild and farm animals
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Unravelling the factors that influence the ability of antiviral peptide-porphyrin conjugates to translocate the blood-brain barrier
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Impact of molecular changes in centrosome function and Barrett’s esophagus progression
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Resistome and mobilome of Portuguese aquacultures: metagenomic characterization
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Helicobacter pylori prophages – distribution, diversity and contribution to bacterial fitness and pathogenicity
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 Sex differences in SARS-CoV-2 infection
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 Impact of SARS-CoV-2 infection in human pregnancy
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 Deletion of sdaB reduces the susceptibility to vancomycin in Clostridioides difficile
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Virulência cooperativa em Salmonela - Simulação num ambiente estruturado
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Significance of mycobacterial peptidoglycan amidation in host immune recognition and antibiotic resistance
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 The Role of Exosomes in Cellular Communication
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Role of the Candida glabrata Mediator complex subunit Pgd1 in azole drug resistance and susceptibility: a transcriptomics approach
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Characterization of Resistance Mechanisms to Critically Important Antibiotics in Multidrug Escherichia coli Isolated from Food-Producing Animals
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Assessing optimal treatments for intracellular infection: host immunity, heterogeneity, and the antibiotic resistance challenge
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Virulence genes and antibiotic resistance genes in microbiomes of human populations - a network perspective
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Modelling phenotypic resistance to ampicillin in a Petri dish
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Metabolic remodeling of endothelial cells upon hypoxia and β-blockers as anti-angiogenic drugs
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2018 Macrophages in M1/M2 states and exposed to amyloid-beta: a RNA-seq analysis in human cells
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2018 SimulATe: a simulator of antibiotic therapy effects on the dynamics of bacterial populations
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2017 Genomes of Helicobacter pylory prophages
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2017 Genomic deletions in Escherichia coli K-12 MG1655 for plasmid DNA production
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 A discrete, logical modelling framework to study tissue patterning and morphogenesis
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 Metagenomic mining of pathogenicity and antibiotic resistance traits across human populations worlwide
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 "Trimethoprim-sulfamethoxazole resistance in Staphylococcus aureus in Africa: distribution of resistance genes and evaluation of the sucess of major mrsa clones"
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 A stochastic model of centriole assembly
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 Metabolic-derived functions during adaptation of E. coli to the mammalian gut
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 A look into the 3D world of a cell: how 3D simulations can shed lights on morphogenesis
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Mathematical modelling of co-colonization and within-host abundance ratios in multi-type pathogen dynamics
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Insights on contact-dependent communication in bacteria
Supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 Genotypic analysis of the Leishmania infantum resistance to conventional drugs and new chemically synthesized compounds
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 Screening and isolation of compounds with antimicrobial activity produced by multi-resistant bacteria
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 Tropism based analysis of Chlamydia trachomatis chromosome
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 Caracterização genetica de Staphylococcus e Lactobacillus isolados de produtos cárneos fermentados com capacidades tecnológicas e protetoras
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 Evolution of Escherichia coli in the mouse gut
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 The impact of the phytopathogen Pectobacterium carotovorum in Drosophila melanogaster development
Co-supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2013 Influência da densidade bacteriana na epistasia
Supervisor
 Biologia Evolutiva e do Desenvolvimento (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2013 Nephrotic syndrome in childhood: genotype-phenotype association studies and screening for novel mutations
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2013 The reciprocal influence of malaria and sleeping sickness co-infections
Co-supervisor
 Biologia Molecular e Genética (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2013 " On Plasmids: studies of plasmid-host and plasmid- plasmid interactions"
Supervisor
 Biologia (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2012 - 2012 "Cooperative and Harmful Behaviour in the Bacterial World"
Supervisor
 Biologia (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2010 - 2010 Harming and Spiteful Behaviour Mediated by Parasites and Pathogens
Supervisor
 Biologia (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2008 - 2008 Rich Dynamics in Multi-strain Models: Non Linear Dynamics and Deterministic Chaos in Dengue Fever Epidemiology
Co-supervisor
 Biologia (PhD)
Universidade de Lisboa, Portugal
2007 - 2007 Searching without information: A quantitative analysis of Caenorhabditis elegans locomotion
Co-supervisor
 Biologia (PhD)
Universidade de Lisboa, Portugal