Publications

Bacterial coaggregation in aquatic systems. Water Research

Afonso, A. C.; Gomes, I. B.; Saavedra, M. J.; Giaouris, E.; Simões, L. C.; Simões, M.,
Bacterial coaggregation in aquatic systems. Water Research, 196, 2021,
doi: 10.1016/j.watres.2021.117037

Biofilms in diabetic foot ulcers: Impact, risk factors and control strategies. International Journal of Molecular Sciences

Afonso, A. C.; Oliveira, D.; Saavedra, M. J.; Borges, A.; Simões, M.,
Biofilms in diabetic foot ulcers: Impact, risk factors and control strategies. International Journal of Molecular Sciences, 22 (15), 2021,
doi: 10.3390/ijms22158278

Interlaboratory study for the evaluation of three microtiter plate-based biofilm quantification methods

Allkja, J.; van Charante, F.; Aizawa, J.; Reigada, I.; Guarch-Pérez, C.; Vazquez-Rodriguez, J. A.; Cos, P.; Coenye, T.; Fallarero, A.; Zaat, S. A. J.; Felici, A.; Ferrari, L.; Azevedo, N. F.; Parker, A. E.; Goeres, D. M.,
Interlaboratory study for the evaluation of three microtiter plate-based biofilm quantification methods.
Scientific Reports, 11 (1), 2021, doi: 10.1038/s41598-021-93115-w

Biofilms vs. cities and humans vs. aliens – a tale of reproducibility in biofilms

Azevedo, N. F.; Allkja, J.; Goeres, D. M.,
Biofilms vs. cities and humans vs. aliens – a tale of reproducibility in biofilms.
Trends in Microbiology, 29 (12), 1062-1071, 2021,
doi: 10.1016/j.tim.2021.05.003

Bacterial coaggregation in aquatic systems. Water Research,

Afonso, A. C.; Gomes, I. B.; Saavedra, M. J.; Giaouris, E.; Simões, L. C.; Simões, M.,
Bacterial coaggregation in aquatic systems. Water Research, 196, 2021,
doi: 10.1016/j.watres.2021.117037

Biofilms in diabetic foot ulcers: Impact, risk factors and control strategies. International Journal of Molecular Sciences

Afonso, A. C.; Oliveira, D.; Saavedra, M. J.; Borges, A.; Simões, M.,
Biofilms in diabetic foot ulcers: Impact, risk factors and control strategies. International Journal of Molecular Sciences, 22 (15), 2021,
doi: 10.3390/ijms22158278

Interlaboratory study for the evaluation of three microtiter plate-based biofilm quantification methods.

Allkja, J.; van Charante, F.; Aizawa, J.; Reigada, I.; Guarch-Pérez, C.; Vazquez-Rodriguez, J. A.; Cos, P.; Coenye, T.; Fallarero, A.; Zaat, S. A. J.; Felici, A.; Ferrari, L.; Azevedo, N. F.; Parker, A. E.; Goeres, D. M.,
Interlaboratory study for the evaluation of three microtiter plate-based biofilm quantification methods.
Scientific Reports, 11 (1), 2021, doi: 10.1038/s41598-021-93115-w

Biofilms vs. cities and humans vs. aliens – a tale of reproducibility in biofilms.

Azevedo, N. F.; Allkja, J.; Goeres, D. M.,
Biofilms vs. cities and humans vs. aliens – a tale of reproducibility in biofilms.
Trends in Microbiology, 29 (12), 1062-1071, 2021,
doi: 10.1016/j.tim.2021.05.003

  1. Afonso, A. C.; Gomes, I. B.; Saavedra, M. J.; Giaouris, E.; Simões, L. C.; Simões, M., Bacterial coaggregation in aquatic systems. Water Research, 196, 2021, doi: 10.1016/j.watres.2021.117037
  2. Afonso, A. C.; Oliveira, D.; Saavedra, M. J.; Borges, A.; Simões, M., Biofilms in diabetic foot ulcers: Impact, risk factors and control strategies. International Journal of Molecular Sciences, 22 (15), 2021, doi: 10.3390/ijms22158278
  3. Allkja, J.; van Charante, F.; Aizawa, J.; Reigada, I.; Guarch-Pérez, C.; Vazquez-Rodriguez, J. A.; Cos, P.; Coenye, T.; Fallarero, A.; Zaat, S. A. J.; Felici, A.; Ferrari, L.; Azevedo, N. F.; Parker, A. E.; Goeres, D. M., Interlaboratory study for the evaluation of three microtiter plate-based biofilm quantification methods. Scientific Reports, 11 (1), 2021, doi: 10.1038/s41598-021-93115-w
  4. Azevedo, N. F.; Allkja, J.; Goeres, D. M., Biofilms vs. cities and humans vs. aliens – a tale of reproducibility in biofilms. Trends in Microbiology, 29 (12), 1062-1071, 2021, doi: 10.1016/j.tim.2021.05.003
  5. Barros, A. C.; Pereira, A.; Melo, L. F.; Sousa, J. P. S., New functionalized macroparticles for environmentally sustainable biofilm control in water systems. Antibiotics, 10 (4), 2021, doi: 10.3390/antibiotics10040399
  6. Carvalho, F. M.; Mergulhão, F. J. M.; Gomes, L. C., Using lactobacilli to fight escherichia coli and staphylococcus aureus biofilms on urinary tract devices. Antibiotics, 10 (12), 2021, doi: 10.3390/antibiotics10121525
  7. Carvalho, F. M.; Teixeira-Santos, R.; Mergulhão, F. J. M.; Gomes, L. C., Effect of lactobacillus plantarum biofilms on the adhesion of escherichia coli to urinary tract devices. Antibiotics, 10 (8), 2021, doi: 10.3390/antibiotics10080966
  8. Carvalho, F. M.; Teixeira-Santos, R.; Mergulhão, F. J. M.; Gomes, L. C., Targeting Biofilms in Medical Devices using Probiotic Cells: A Systematic. AIMS Materials Science, 8 (4), 501-523, 2021, doi: 10.3934/matersci.2021031
  9. Carvalho, F. M.; Teixeira-Santos, R.; Mergulhão, F. J. M.; Gomes, L. C., The use of probiotics to fight biofilms in medical devices: A systematic review and meta-analysis. Microorganisms, 9 (1), 1-26, 2021, doi: 10.3390/microorganisms9010027
  10. Esteves, G. M.; Pereira, J. A.; Azevedo, N. F.; Azevedo, A. S.; Mendes, L., Friends with benefits: An inside look of periodontal microbes’ interactions using fluorescence in situ hybridization—scoping review. Microorganisms, 9 (7), 2021, doi: 10.3390/microorganisms9071504
  11. Faria, S. I.; Gomes, L. C.; Teixeira-Santos, R.; Morais, J.; Vasconcelos, V.; Mergulhão, F. J. M., Developing new marine antifouling surfaces: Learning from single-strain laboratory tests. Coatings, 11 (1), 1-11, 2021, doi: 10.3390/coatings11010090
  12. Faria, S. I.; Teixeira-Santos, R.; Romeu, M. J.; Morais, J.; Jong, E.; Sjollema, J.; Vasconcelos, V.; Mergulhão, F. J., Unveiling the antifouling performance of different marine surfaces and their effect on the development and structure of cyanobacterial biofilms. Microorganisms, 9 (5), 2021, doi: 10.3390/microorganisms9051102
  13. Fernandes, S.; Gomes, I. B.; Simões, L. C.; Simões, M., Overview on the hydrodynamic conditions found in industrial systems and its impact in (bio)fouling formation. Chemical Engineering Journal, 418, 2021, doi: 10.1016/j.cej.2021.129348
  14. Ferreira, O.; Rijo, P.; Gomes, J.; Santos, R.; Monteiro, S.; Guedes, R.; Serralheiro, M. L.; Gomes, M.; Gomes, L. C.; Mergulhão, F. J.; Silva, E. R., Antimicrobial ceramic filters for water bio-decontamination. Coatings, 11 (3), 2021, doi: 10.3390/coatings11030323
  15. Gomes, I. B.; Lemos, M.; Fernandes, S.; Borges, A.; Simões, L. C.; Simões, M., The effects of chemical and mechanical stresses on bacillus cereus and pseudomonas fluorescens single-and dual-species biofilm removal. Microorganisms, 9 (6), 2021, doi: 10.3390/microorganisms9061174
  16. Gomes, L. C.; Faria, S. I.; Valcarcel, J.; Vázquez, J. A.; Cerqueira, M. A.; Pastrana, L.; Bourbon, A. I.; Mergulhão, F. J., The effect of molecular weight on the antimicrobial activity of chitosan from Loligo opalescens for food packaging applications. Marine Drugs, 19 (7), 2021, doi: 10.3390/md19070384
  17. Gomes, L. C.; Mergulhão, F. J. M., A selection of platforms to evaluate surface adhesion and biofilm formation in controlled hydrodynamic conditions. Microorganisms, 9 (9), 2021, doi: 10.3390/microorganisms9091993
  18. Gomes, M.; Gomes, L. C.; Teixeira-Santos, R.; Pereira, M. F. R.; Soares, O. S. G. P.; Mergulhão, F. J., Optimizing cnt loading in antimicrobial composites for urinary tract application. Applied Sciences (Switzerland), 11 (9), 2021, doi: 10.3390/app11094038
  19. Gonçalves, I. G.; Fernandes, H. S.; Melo, A.; Sousa, S. F.; Simões, L. C.; Simões, M., LegionellaDB – A Database on Legionella Outbreaks. Trends in Microbiology, 29 (10), 863-866, 2021, doi: 10.1016/j.tim.2021.01.015
  20. Gonçalves, I. G.; Simões, L. C.; Simões, M., Legionella pneumophila. Trends in Microbiology, 29 (9), 860-861, 2021, doi: 10.1016/j.tim.2021.04.005
  21. Lima, M.; Teixeira-Santos, R.; Gomes, L. C.; Faria, S. I.; Valcarcel, J.; Vázquez, J. A.; Cerqueira, M. A.; Pastrana, L.; Bourbon, A. I.; Mergulhão, F. J., Development of chitosan-based surfaces to prevent singleand dual-species biofilms of staphylococcus aureus and pseudomonas aeruginosa. Molecules, 26 (14), 2021, doi: 10.3390/molecules26144378
  22. Neves, S. F.; Ponmozhi, J.; Mergulhão, F. J.; Campos, J. B. L. M.; Miranda, J. M., Cell adhesion in microchannel multiple constrictions – Evidence of mass transport limitations. Colloids and Surfaces B: Biointerfaces, 198, 2021, doi: 10.1016/j.colsurfb.2020.111490
  23. Oliveira, D.; Borges, A.; Ruiz, R. M.; Negrín, Z. R.; Distinto, S.; Borges, F.; Simões, M., 2-(2-methyl-2-nitrovinyl)furan but not furvina interfere with staphylococcus aureus agr quorum-sensing system and potentiate the action of fusidic acid against biofilms. International Journal of Molecular Sciences, 22 (2), 1-15, 2021, doi: 10.3390/ijms22020613
  24. Oliveira, R.; Pinho, E.; Sousa, A. L.; DeStefano, J. J.; Azevedo, N. F.; Almeida, C., Improving aptamer performance with nucleic acid mimics: de novo and post-SELEX approaches. Trends in Biotechnology, 2021, doi: 10.1016/j.tibtech.2021.09.011
  25. Pereira, A.; Silva, A. R.; Melo, L. F., Legionella and biofilms—integrated surveillance to bridge science and real-field demands. Microorganisms, 9 (6), 2021, doi: 10.3390/microorganisms9061212
  26. Pinto, H.; Simões, M.; Borges, A., Prevalence and impact of biofilms on bloodstream and urinary tract infections: A systematic review and meta-analysis. Antibiotics, 10 (7), 2021, doi: 10.3390/antibiotics10070825
  27. Ribeiro, M.; Sousa, C. A.; Simões, M., Harnessing microbial iron chelators to develop innovative therapeutic agents. Journal of Advanced Research, 2021, doi: 10.1016/j.jare.2021.10.010
  28. Rita Pereira, A.; Gomes, I. B.; Simões, M., Choline-based ionic liquids for planktonic and biofilm growth control of Bacillus cereus and Pseudomonas fluorescens. Journal of Molecular Liquids, 2021, doi: 10.1016/j.molliq.2021.117077
  29. Romeu, M. J.; Domínguez-Pérez, D.; Almeida, D.; Morais, J.; Araújo, M. J.; Osório, H.; Campos, A.; Vasconcelos, V.; Mergulhão, F. J., Quantitative proteomic analysis of marine biofilms formed by filamentous cyanobacterium. Environmental Research, 201, 2021, doi: 10.1016/j.envres.2021.111566
  30. Silva, E. R.; Tulcidas, A. V.; Ferreira, O.; Bayón, R.; Igartua, A.; Mendoza, G.; Mergulhão, F. J. M.; Faria, S. I.; Gomes, L. C.; Carvalho, S.; Bordado, J. C. M., Assessment of the environmental compatibility and antifouling performance of an innovative biocidal and foul-release multifunctional marine coating. Environmental Research, 198, 2021, doi: 10.1016/j.envres.2021.111219
  31. Silva, L. M.; Correia, V. G.; Moreira, A. S. P.; Domingues, M. R. M.; Ferreira, R. M.; Figueiredo, C.; Azevedo, N. F.; Marcos-Pinto, R.; Carneiro, F.; Magalhães, A.; Reis, C. A.; Feizi, T.; Ferreira, J. A.; Coimbra, M. A.; Palma, A. S., Helicobacter pylori lipopolysaccharide structural domains and their recognition by immune proteins revealed with carbohydrate microarrays. Carbohydrate Polymers, 253, 2021, doi: 10.1016/j.carbpol.2020.117350
  32. Simões, M.; Pereira, A. R.; Simões, L. C.; Cagide, F.; Borges, F., Biofilm control by ionic liquids. Drug Discovery Today, 26 (6), 1340-1346, 2021, doi: 10.1016/j.drudis.2021.01.031
  33. Soares, A.; Gomes, L. C.; Monteiro, G. A.; Mergulhão, F. J., The influence of nutrient medium composition on escherichia coli biofilm development and heterologous protein expression. Applied Sciences (Switzerland), 11 (18), 2021, doi: 10.3390/app11188667
  34. Sousa, C. A.; Sousa, H.; Vale, F.; Simões, M., Microalgae-based bioremediation of wastewaters – Influencing parameters and mathematical growth modelling. Chemical Engineering Journal, 425, 2021, doi: 10.1016/j.cej.2021.131412
  35. Teixeira-Santos, R.; Gomes, M.; Gomes, L. C.; Mergulhão, F. J., Antimicrobial and anti-adhesive properties of carbon nanotube-based surfaces for medical applications: a systematic review. iScience, 24 (1), 2021, doi: 10.1016/j.isci.2020.102001
  36. Teixeira-Santos, R.; Lima, M.; Gomes, L. C.; Mergulhão, F. J., Antimicrobial coatings based on chitosan to prevent implant-associated infections: A systematic review. iScience, 24 (12), 2021, doi: 10.1016/j.isci.2021.103480
  1. Alves, P., Gomes, L.C., Rodríguez-Emmenegger, C., Mergulhão, F.J.
    Efficacy of a poly(Meoegma) brush on the prevention of escherichia coli biofilm formation and susceptibilituy
    Antibiotics, 9(5), 216, 2020, doi: 10.3390/antibiotics9050216
  2. Alves, P., Gomes, L.C., Vorobii, M., Rodriguez-Emmenegger, C., Mergulhão, F.J.
    The potential advantages of using a poly(HPMA) brush in urinary catheters: effects on biofilm cells and architecture
    Colloids and Surfaces B: Biointerfaces, 191, 110976, 2020, doi: 10.1016/j.colsurfb.2020.110976
  3. Alves, P., Moreira, J.M., Miranda, J.M., Mergulhão, F.J.
    Analysing the initial bacterial adhesion to evaluate the performance of antifouling surfaces
    Antibiotics, 9(7), 421, 1-11, 2020, doi: 10.3390/antibiotics9070421
  4. Alves, R., Kastora, S.L., Gomes-Gonçalves, A., Azevedo, N., Rodrigues, C.F., Silva, S., Demuyser, L., Van Dijck, P., Casal, M., Brown, A.J.P., Henriques, M., Paiva, S.
    Transcriptional responses of Candida glabrata biofilm cells to fluconazole are modulated by the carbon source npj Biofilms and Microbiomes, 6(1), 4, 2020, doi: 10.1038/s41522-020-0114-5
  5. Černáková, L., Rodrigues, C.F.
    Microbial interactions and immunity response in oral Candida species
    Future Microbiology, 15(17), 1653-1677, 2020, doi: 10.2217/fmb-2020-0113 Review
  6. Cerqueira, L., Moura, S., Almeida, C., Vieira, M.J., Azevedo, N.F.
    Establishment of a new pna-fish method for aspergillus fumigatus identification: First insights for future use in pulmonary samples
    Microorganisms, 8(12), 1950, 1-14, 2020, doi: 10.3390/microorganisms812195
  7. Cunha, P., Pereira, H., Costa, M., Pereira, J., Silva, J.T., Fernandes, N., Varela, J., Silva, J., Simões, M.
    Nannochloropsis oceanica cultivation in pilot-scale raceway ponds-from design to cultivation
    Applied Sciences (Switzerland), 10(5), 1725, 2020, doi: 10.3390/app10051725
  8. Dolid, A., Gomes, L.C., Mergulhão, F.J., Reches, M.
    Combining chemistry and topography to fight biofilm formation: Fabrication of micropatterned surfaces with a peptide-based coating
    Colloids and Surfaces B: Biointerfaces, 196, 111365, 2020, doi: 10.1016/j.colsurfb.2020.111365
  9. Faria, S.I., Teixeira-Santos, R., Gomes, L.C., Silva, E.R., Morais, J., Vasconcelos, V., Mergulhão, F.J.M.
    Experimental assessment of the performance of two marine coatings to curb biofilm formation of microfoulers
    Coatings, 10(9), 893, 2020, doi: 10.3390/COATINGS10090893
  10. Faria, S.I., Teixeira-Santos, R., Romeu, M.J., Morais, J., Vasconcelos, V., Mergulhão, F.J.
    The relative importance of shear forces and surface hydrophobicity on biofilm formation by coccoid cyanobacteria
    Polymers, 12(3), 653, 2020, doi: 10.3390/polym12030653
  11. Fernandes, S., Gomes, I.B., Simões, M.
    Antimicrobial activity of glycolic acid and glyoxal against Bacillus cereus and Pseudomonas fluorescens
    Food Research International, 136, 109346, 2020, doi: 10.1016/j.foodres.2020.109346
  12. Giaouris, E., Simoes, M., Dubois-Brissonnet, F.
    The role of biofilms in the development and dissemination of microbial resistance within the food industry
    Foods, 9(6), 816, 2020, doi: 10.3390/foods9060816 Review
  13. Gomes, I.B., Maillard, J.-Y., Simões, L.C., Simões, M.
    Emerging contaminants affect the microbiome of water systems—strategies for their mitigation
    npj Clean Water, 3(1), 39, 2020, doi: 10.1038/s41545-020-00086-y Review
  14. Gomes, I.B., Simões, M., Simões, L.C.
    Copper surfaces in biofilm control
    Nanomaterials, 10(12), 2491, 1-21, 2020, doi: 10.3390/nano10122491 Review
  15. Gomes, I.B., Simões, L.C., Simões, M.
    Influence of surface copper content on Stenotrophomonas maltophilia biofilm control using chlorine and mechanical stress
    Biofouling, 36(1), 1-13, 2020, doi: 10.1080/08927014.2019.1708334
  16. Gomes, L., Monteiro, G., Mergulhão, F.
    The impact of IPTG induction on plasmid stability and heterologous protein expression by escherichia coli biofilms
    International Journal of Molecular Sciences, 21(2), 576, 2020, doi: 10.3390/ijms21020576
  17. Leão, C., Borges, A., Simões, M.
    Nsaids as a drug repurposing strategy for biofilm control
    Antibiotics, 9(9), 591, 1-19, 2020, doi: 10.3390/antibiotics9090591
  18. Lima, J.F., Maia, P., T. Magalhães, B., Cerqueira, L., Azevedo, N.F.
    A comprehensive model for the diffusion and hybridization processes of nucleic acid probes in fluorescence in situ hybridization
    Biotechnology and Bioengineering, 117(10), 3212-3223, 2020, doi: 10.1002/bit.27462 Review
  19. Magalhães, R.P., Vieira, T.F., Fernandes, H.S., Melo, A., Simões, M., Sousa, S.F.
    The Biofilms Structural Database
    Trends in Biotechnology, 38(9), 937-940, 2020, doi: 10.1016/j.tibtech.2020.04.002
  20. Malheiro, J.F., Oliveira, C., Cagide, F., Borges, F., Simões, M., Maillard, J.-Y.
    Surface wiping test to study biocide-cinnamaldehyde combination to improve efficiency in surface disinfection
    International Journal of Molecular Sciences, 21(21), 7852, 1-14, 2020, doi: 10.3390/ijms21217852
  21. Melo, S.F., Neves, S.C., Pereira, A.T., Borges, I., Granja, P.L., Magalhães, F.D., Gonçalves, I.C.
    Incorporation of graphene oxide into poly(ɛ-caprolactone) 3D printed fibrous scaffolds improves their antimicrobial properties
    Materials Science and Engineering C, 109, 110537, 2020, doi: 10.1016/j.msec.2019.110537
  22. Olszewska, M.A., Gędas, A., Simões, M.
    Antimicrobial polyphenol-rich extracts: Applications and limitations in the food industry
    Food Research International, 134, 109214, 2020, doi: 10.1016/j.foodres.2020.109214 Review
  23. Olszewska, M.A., Gedas, A., Simões, M.
    The effects of eugenol, trans-cinnamaldehyde, citronellol, and terpineol on escherichia coli biofilm control as assessed by culture-dependent and -independent methods
    Molecules, 25(11), 2641, 2020, doi: 10.3390/molecules25112641
  24. Rodrigues, C.F., Černáková, L.
    Farnesol and tyrosol: Secondary metabolites with a crucial quorum-sensing role in candida biofilm development
    Genes, 11(4), 444, 2020, doi: 10.3390/genes11040444 Review
  25. Rodrigues, M.E., Gomes, F., Rodrigues, C.F.
    Candida spp./bacteria mixed biofilms
    Journal of Fungi, 6(1), 5, 2020, doi: 10.3390/jof6010005 Review
  26. Romeu, M.J.L., Domínguez-Pérez, D., Almeida, D., Morais, J., Campos, A., Vasconcelos, V., Mergulhão, F.J.M.
    Characterization of planktonic and biofilm cells from two filamentous cyanobacteria using a shotgun proteomic approach
    Biofouling, 36(6), 631-645, 2020, doi: 10.1080/08927014.2020.1795141
  27. Souza, J.N.M.D., Melo, L.F., Costa, A.L.H.
    Graph-based network modeling and simulation of condensers in once-through cooling water system under the effect of biofouling formation
    Applied Thermal Engineering, 165, 114577, 2020, doi: 10.1016/j.applthermaleng.2019.114577
  28. Vagos, M.R., Gomes, M., Moreira, J.M.R., Soares, O.S.G.P., Pereira, M.F.R., Mergulhão, F.J.
    Carbon nanotube/poly(Dimethylsiloxane) composite materials to reduce bacterial adhesion
    Antibiotics, 9(8), 434, 1-15, 2020, doi: 10.3390/antibiotics9080434
  1. Ramstedt, M., Ribeiro, I.A.C., Bujdakova, H., Mergulhão, F.J.M., Jordão, L., Thomsen, P., Alm, M., Burmølle, M., Vladkova, T., Can, F., Reches, M., Riool, M., Barros, A., Reis, R.L., Meaurio, E., Kikhney J., Moter, A., Zaat, S.A.J., Sjollema, J.
    Evaluating Efficacy of Antimicrobial and Antifouling Materials for Urinary Tract Medical Devices: Challenges and Recommendations
    Macromolecular Bioscience, 19(5), 1800384, 2019, doi: 10.1002/mabi.201800384
  2. Vagos, M.R., Moreira, J.M.R., Soares, O.S.G.P., Pereira, M.F.R., Mergulhão, F.J.
    Incorporation of carbon nanotubes in polydimethylsiloxane to control Escherichia coli adhesion
    Polymer Composites, 40(S2), E1697-E1704, 2019, doi: 10.1002/pc.25125
  3. Romeu, M.J., Alves, P., Morais, J., Miranda, J.M., de, Jong, E., Sjollema, J., Ramos, V., Vasconcelos, V. and Mergulhão, F.J.M.
    Biofilm formation behaviour of marine filamentous cyanobacterial strains in controlled hydrodynamic conditions.
    Environmental Microbiology, 21 (11), 4411-4424, 2019. doi: 10.1111/1462-2920.14807
  4. Soares A, Azevedo A, Gomes LC, Mergulhão FJ.
    Recombinant protein expression in biofilms.
    AIMS Microbiology, 5(3), 232-250, 2019. doi: 10.3934/microbiol.2019.3.232
  5. Baptista, J., Simões, M., Borges, A.
    Effect of plant-based catecholic molecules on the prevention and eradication of Escherichia coli biofilms: a structure activity relationship study
    International Biodeterioration & Biodegradation, 141, 101-113, 2019, doi: 10.1016/j.ibiod.2018.02.004
  6. Barros, A.C., Gonçalves, A.L., Simões, M.
    Microalgal/cyanobacterial biofilm formation on selected surfaces: the effects of surface physicochemical properties and culture media composition
    Journal of Applied Phycology, 31(1), 375-387, 2019, doi: 10.1007/s10811-018-1582-3
  7. Borges, A., Simões, M.
    Quorum sensing inhibition by marine bacteria
    Marine Drugs, 17(7), 427, 2019, doi: 10.3390/md17070427
  8. Canuto de Almeida e Silva, T., Fernandes Kettermann, V., Pereira, C., Simões, M., Wilhelm, M., Rezwan, K.
    Novel tape-cast SiOC-based porous ceramic electrode materials for potential application in bioelectrochemical systems
    Journal of Materials Science, 54(8), 6471-6487, 2019, doi: 10.1007/s10853-018-03309-3
  9. Dias, C., Ribeiro, M., Correia-Branco, A., Domínguez-Perles, R., Martel, F., Saavedra, M.J., Simões, M.
    Virulence, attachment and invasion of Caco-2 cells by multidrug-resistant bacteria isolated from wild animals
    Microbial Pathogenesis, 128, 230-235, 2019, doi: 10.1016/j.micpath.2019.01.011
  10. Fernandes S., Simões L.C., Lima N., Simões M.
    Adhesion of filamentous fungi isolated from drinking water under different process conditions
    Water Research, 164, 114951, 2019, doi: 10.1016/j.watres.2019.114951
  11. Gomes, I.B., Madureira, D., Simões, L.C., Simões, M.
    The effects of pharmaceutical and personal care products on the behavior of Burkholderia cepacia isolated from drinking water
    International Biodeterioration & Biodegradation, 141, 87-93, 2019, DOI: 10.1016/j.ibiod.2018.03.018
  12. Gomes, I.B., Querido, M.M., Teixeira, J.P., Pereira, C.C., Simões, L.C., Simões, M.
    Prolonged exposure of Stenotrophomonas maltophilia biofilms to trace levels of clofibric acid alters antimicrobial tolerance and virulence
    Chemosphere, 235, 327-335, 2019, doi: 10.1016/j.chemosphere.2019.06.184
  13. Gomes, I.B., Simões, L.C., Simões, M.
    The role of surface copper content on biofilm formation by drinking water bacteria
    RSC Advances, 9(55), 32184-32196, 2019, doi: 10.1039/c9ra05880j
  14. Gonçalves, A.C., Bento, C., Silva, B., Simões, M., Silva, L.R.
    Nutrients, bioactive compounds and bioactivity: The health benefits of sweet cherries (prunus avium L.)
    Current Nutrition and Food Science, 15(3), 208-227, 2019, doi: 10.2174/1573401313666170925154707
  15. Malheiro, J., Mayllard, J.Y., Borges, F., Simões, M.
    Evaluation of cinnamaldehyde and cinnamic acid derivatives in microbial growth control
    International Biodeterioration & Biodegradation, 141, 71-78, 2019, DOI: 10.1016/j.ibiod.2018.06.003
  16. Meireles, A., Faia, S., Giaouris, E., Simões, M.
    Antimicrobial susceptibility and sessile behaviour of bacteria isolated from a minimally processed vegetables plant
    Biofouling, 34(10), 1150-1160, 2018, doi: 10.1080/08927014.2018.1554742
  17. Oliveira, I.M., Borges, A., Borges, F., Simões, M.
    Repurposing ibuprofen to control Staphylococcus aureus biofilms
    European Journal of Medicinal Chemistry, 166, 197-205, 2019, doi: 10.1016/j.ejmech.2019.01.046
  18. Pereira, J., Simões, M., Silva, J.L.
    Microalgal assimilation of vitamin B12 toward the production of a superfood
    Journal of Food Biochemistry, 43(8), e12911, 2019, doi: 10.1111/jfbc.12911
  19. Quelhas, P.M., Trovão, M., Silva, J.T., Machado, A., Santos, T., Pereira, H., Varela, J., Simões, M., Silva, J.L.
    Industrial production of Phaeodactylum tricornutum for CO2 mitigation: biomass productivity and photosynthetic efficiency using photobioreactors of different volumes
    Journal of Applied Phycology, 31(4), 2187-2196, 2019, doi: 10.1007/s10811-019-1750-0
  20. Silva A.F., dos Santos A.R., Trevisan D.A.C., Bonin E., Freitas C.F., Batista A.F.P., Hioka N., Simões M., Graton Mikcha J.M.
    Xanthene Dyes and Green LED for the Inactivation of Foodborne Pathogens in Planktonic and Biofilm States
    Photochemistry and Photobiology, 95(5), 1230-1238, 2019, doi: 10.1111/php.13104
  21. Silva, A. F., Borges, A., Giaouris, E., Mikcha, J. M. G., Simões, M.
    Photodynamic inactivation as an emergent strategy against foodborne pathogenic bacteria in planktonic and sessile states
    Critical Reviews in Microbiology, 44(6), 667-684, 2018. doi: 10.1080/1040841X.2018.1491528
  22. Vale, J., Ribeiro, M., Abreu, A.C., Soares-Silva, I., Simões, M.
    The use of selected phytochemicals with EDTA against Escherichia coli and Staphylococcus epidermidis single- and dual-species biofilms
    Letters in Applied Microbiology, 68(4), 313-320, 2019, doi: 10.1111/lam.13137
  23. Vilas Boas, J., Oliveira, V.B., Marcon, L.R.C., Simões, M., Pinto, A.M.F.R.
    Optimization of a single chamber microbial fuel cell using Lactobacillus pentosus: Influence of design and operating parameters
    Science of the Total Environment, 648, 263-270, 2019, doi: 10.1016/j.scitotenv.2018.08.061
  24. Azevedo, A.S., Sousa, I.M., Fernandes, R.M., Azevedo, N.F., Almeida, C.
    Optimizing locked nucleic acid/2′-O-methyl-RNA fluorescence in situ hybridization (LNA/2′OMe-FISH) procedure for bacterial detection
    PLoS ONE, 14(5), e0217689, 2019, doi: 10.1371/journal.pone.0217689
  25. Maia, P., Pérez-Rodríguez, G., Pérez-Pérez, M., Fdez-Riverola, F., Lourenço, A., Azevedo, N.F.
    Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli
    Computers in Biology and Medicine, 107, 218-226, 2019, doi : 10.1016/j.compbiomed.2019.02.020
  26. Müller, V., Sousa, J.M., Ceylan Koydemir, H., Veli, M., Tseng, D., Cerqueira, L., Ozcan, A., Azevedo, N.F., Westerlund, F.
    Identification of pathogenic bacteria in complex samples using a smartphone based fluorescence microscope
    RSC Advances, 8(64), 36493-36502, 2018, doi: 10.1039/c8ra06473c
  27. Rocha, R., Sousa, J.M., Cerqueira, L., Vieira, M.J., Almeida, C., Azevedo, N.F.
    Development and application of Peptide Nucleic Acid Fluorescence in situ Hybridization for the specific detection of Listeria monocytogenes
    Food Microbiology, 80, 1-8, 2019, doi: 10.1016/j.fm.2018.12.009
  28. Rosenberg, M., Azevedo, N.F., Ivask, A.
    Propidium iodide staining underestimates viability of adherent bacterial cells
    Scientific Reports, 9(1), 6483, 2019, doi: 10.1038/s41598-019-42906-3
  29. Silva, E.R., Ferreira, O., Ramalho, P.A., Azevedo, N.F., Bayón, R., Igartua, A., Bordado, J.C., Calhorda, M.J.
    Eco-friendly non-biocide-release coatings for marine biofouling prevention
    Science of the Total Environment, 650, 2499-2511, 2019, doi: 10.1016/j.scitotenv.2018.10.010
  30. Salehi, B; Lopez, MD; Martínez, M; Victoriano, M; Sharifi-Rad, J; Martorell, M; Rodrigues, CF; Martins, N.
    Stevia rebaudiana Bertoni bioactive effects: From in vivo to clinical trials towards future therapeutic approaches.
    Phytotherapy research, 33 (11), 2904-2917, 2019. doi: 10.1002/ptr.6478
  31. Tabarzad, M; Iorigooini, Z; Hosseinabadi, T; Salehi, B; Sharifi-Rad, J; Rodrigues, CF; Martins, N.
    Silymarin antiproliferative and apoptotic effects: Insights into its clinical impact in various types of cancer
    Phytotherapy research, 33 (11), 2849-2861, 2019. doi: 10.1002/ptr.6470
  32. Salehi, B; Fokou, PVT; Yamthe, PRT; Tali, BT; Oluwaseun, AC; Rahavian, A; Mudau, FN; Martorell, M; Setzer, WN; Rodrigues, CF; Martins, N; Cho, WC; Sharifi-Rad, J.
    Phytochemicals in Prostate Cancer: From Bioactive Molecules to Upcoming Therapeutic Agents
    Nutrients, 11 (7), 1483, 2019. Doi: 10.3390/nu11071483
  33. Salehi, B; Capanoglu, E; Adrar, N; Catalkaya, G; Shaheen, S; Jaffer, M; Giri, L; Suyal, R; Jugran, AK; Calina, D; Docea, AO; Kamiloglu, S; Kregiel, D; Antolak, H; Pawlikowska, E; Sem, S; Acharya, K; Selamoglu, Z; Sharifi-Rad, J; Martorell, M; Rodrigues, CF.; Sharopov, F; Martins, N; Capasso, R.
    Cucurbits Plants: A Key Emphasis to Its Pharmacological Potential
    Molecules, 24 (10), 1854, 2019. Doi: 3390/molecules24101854
  34. Franco-Duarte, R; Černáková, L; Kadam, S; Salehi, K; Salehi, B; Bevilacqua, A; Corbo, MR; Antolak, H; Dybka-Stępień, K; Leszczewicz, M; Tintino, RS; Souza, VCA; Coutinho, HDM; Sharifi-Rad, J; Martins, N; Rodrigues, CF
    Advances in Chemical and Biological Methods to Identify Microorganisms—From Past to Present
    Microorganisms, 7(5), 130, 2019. Doi: 10.3390/microorganisms7050130
  35. Salehi, B; Jornet, PL; Lopez, EPF; Calina, D; Sharifi-Rad, M; Ramirez-Alarcon, K; Forman, K; Fernandez, M; Martorell, M; Setzer, WN; Martins, N; Rodrigues, CF; Sharifi-Rad, J
    Plant-Derived Bioactives in Oral Mucosal Lesions: A Key Emphasis to Curcumin, Lycopene, Chamomile, Aloe vera, Green Tea and Coffee Properties.
    Biomolecules, 9(3), 106, 2019. Doi:10.3390/biom9030106
  36. Rashid, A; Javed, I; Rasco, B; Sablani, S; Ayaz, M; Ali, MA; Abdullah, M; Imran, M; Gondal, TA; Afzal, MI; Atif, M; Salehi, B; ,Rodrigues, CF; Sharifi-Rad, J; Martins, N.
    Measurement of Off-Flavoring Volatile Compounds and Microbial Load as a Probable Marker for Keeping Quality of Pasteurized Milk.
    Applied Sciences, 9 (5), 959, 2019. Doi: 10.3390/app9050959
  37. Rodrigues, CF; Costa, AC; Vilanova, M; Henriques, M.
    Inflammatory cell recruitment in Candida glabrata biofilm cells-infected mice receiving antifungal chemotherapy
    Journal of Clinical Medicine, 8 (2), 142, 2019. DOI: 10.3390/jcm8020142
  38. Rodrigues, CF; Rodrigues, ME; Henriques, M.
    Candida spp. Infections in patients with diabetes mellitus
    Journal of Clinical Medicine, 8 (1), 76, 2019. Doi: 10.3390/jcm8010076
  1. Alves, P., Nir, S., Reches, M., Mergulhão, F.
    The effects of fluid composition and shear conditions on bacterial adhesion to an antifouling peptide-coated surface
    MRS Communications, 8(3), 938-946, 2018, doi: :10.1557/mrc.2018.160
  2. Gomes, L.C., Deschamps, J., Briandet, R., Mergulhão, F.J.
    Impact of modified diamond-like carbon coatings on the spatial organization and disinfection of mixed-biofilms composed of Escherichia coli and Pantoea agglomerans industrial isolates
    International Journal of Food Microbiology, 277, 74-82, 2018, doi: 10.1016/j.ijfoodmicro.2018.04.017
  3. Lopez-Mila, B., Alves, P., Riedel, T., Dittrich, B., Mergulhão, F., Rodriguez-Emmenegger, C.
    Effect of shear stress on the reduction of bacterial adhesion to antifouling polymers
    Bioinspiration & Biomimetics, 13, Number 6, 2018, doi: 1088/1748-3190/aadcc2
  4. Soares, A., Gomes, L.C., Mergulhão, F.J.
    Comparing the Recombinant Protein Production Potential of Planktonic and Biofilm Cells
    Microorganisms, 6, 48, 2018, doi: 10.3390/microorganisms6020048
  5. Adlhart, C., Verranb, J., Azevedo, N.F., Olmez, H., Keinänen-Toivola, M.M., Gouveia, I., Melo, L.M., Crijns, F.
    Surface modifications for antimicrobial effects in the healthcare setting: a critical overview
    Journal of Hospital Infection, 99(3), 239-249, 2018, doi: 10.1016/j.jhin.2018.01.018
  6. Sousa-Silva, M., Simões, M., Melo, L., Machado, I.
    Pseudomonas fluorescens tolerance to benzyldimethyldodecyl ammonium chloride: altered phenotype and cross-resistance
    Journal of Global Antimicrobial Resistance, 15, 188-195, 2018, doi: 10.1016/j.jgar.2018.07.004
  7. Borges, A., Simões, M., Todorović, T.R., Filipović, N.R., Alfonso, T.G.-S.
    Cobalt complex with thiazole-based ligand as new pseudomonas aeruginosa quorum quencher, biofilm inhibitor and virulence attenuator
    Molecules, 23(6), 1385, 2018, doi: 10.3390/molecules23061385
  8. Dias, C., Borges, A., Oliveira, D., Martinez-Murcia, A., Saavedra, M.J., Simões, M.
    Biofilms and antibiotic susceptibility of multidrug-resistant bacteria from wild animals
    PeerJ, 6, e4974, 2018, doi: 10.7717/peerj.4974
  9. Dias, C., Borges, A., Saavedra, M.J., Simões, M.
    Biofilm formation and multidrug-resistant Aeromonas spp. from wild animals
    Journal of Global Antimicrobial Resistance, 12, 227-234, 2018, doi: 10.1016/j.jgar.2017.09.010
  10. Gomes, I.B., Lemos, M., Mathieu, L., Simões, M., Simões, L.C.
    The action of chemical and mechanical stresses on single and dual species biofilm removal of drinking water bacteria
    Science of the Total Environment, 631-632, 987-993, 2018, doi: 10.1016/j.scitotenv.2018.03.042
  11. Gomes, I.B., Simões, L.C., Simões, M.
    The effects of emerging environmental contaminants on Stenotrophomonas maltophilia isolated from drinking water in planktonic and sessile states
    Science of the Total Environment, 643, 1348-1356, 2018, doi: 10.1016/j.scitotenv.2018.06.263
  12. Iliadis, I., Daskalopoulou, A., Simões, M., Giaouris, E.
    Integrated combined effects of temperature, pH and sodium chloride concentration on biofilm formation by Salmonella enterica ser. Enteritidis and Typhimurium under low nutrient food-related conditions
    Food Research International, 107, 10-18, 2018, doi: 10.1016/j.foodres.2018.02.015
  13. Oliveira, D., Borges, A., Simões, M.
    Staphylococcus aureus toxins and their molecular activity in infectious diseases.
    Toxins, 10(6), 252, 2018, doi: 10.3390/toxins10060252
  14. Ribeiro, M., Malheiro, J., Grenho, L., Fernandes, M.H., Simões, M.
    Cytotoxicity and antimicrobial action of selected phytochemicals against planktonic and sessile Streptococcus mutans
    PeerJ, 2018 (6), e4872, 2018, doi: 10.7717/peerj.4872
  15. Silva, A. F., Borges, A., Freitas, C. F., Hioka, N., Mikcha, J. M. G., Simões, M.
    Antimicrobial photodynamic inactivation mediated by rose bengal and erythrosine is effective in the control of food-related bacteria in planktonic and biofilm states.
    Molecules, 23(9), 2288, 2018, doi: 10.3390/molecules23092288
  16. Hidalgo-Robatto, B.M., López-Álvarez, M., Azevedo, A.S., Dorado, J., Serra, J., Azevedo, N.F., González, P.
    Pulsed laser deposition of copper and zinc doped hydroxyapatite coatings for biomedical applications
    Surface and Coatings Technology, 333, 168-177, 2018, doi: 10.1016/j.surfcoat.2017.11.006
  17. Lima, J.F., Carvalho, J., Pinto-Ribeiro, I., Almeida, C., Wengel, J., Cerqueira, L., Figueiredo, C., Oliveira, C., Azevedo, N.F.
    Targeting miR-9 in gastric cancer cells using locked nucleic acid oligonucleotides
    BMC Molecular Biology, 19(1), 6, 2018, doi: 10.1186/s12867-018-0107-6
  18. Lima, J.F., Cerqueira, L., Figueiredo, C., Oliveira, C., Azevedo, N.F.
    Anti-miRNA oligonucleotides: A comprehensive guide for design
    RNA Biology, 15(3), 338-352, 2018, doi: 10.1080/15476286.2018.1445959
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    Quantitative assessment of individual populations within polymicrobial biofilms
    Scientific Reports, 8(1), 9494, 2018, doi: 10.1038/s41598-018-27497-9
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    Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of Pseudomonas aeruginosa and Candida albicans
    Biofouling, 34(3), 335-345, 2018, doi: 10.1080/08927014.2018.1440392
  21. Rocha, R., Almeida, C., Azevedo, N.F.
    Influence of the fixation/permeabilization step on peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria
    PLoS ONE, 13(5), e0196522, 2018, doi: 10.1371/journal.pone.0196522
  1. Gomes, L.C., Mergulhão, F.J.,Effect of heterologous protein expression on Escherichia coli biofilm formation and biocide susceptibility
    Aims Microbiology, 2(4), 434-446, 2016, doi: 10.3934/microbiol.2016.4.434
  2. Celaya, L.S., Viturro, C.I., Silva, L.R., Moreno, S.
    Natural antioxidants isolated from Schinus areira leaves by ultrasound-assisted extraction
    International Journal of Food Studies, 5(2), 167-179, 2016, doi: 10.7455/ijfs/5.2.2016.a5
  3. Gomes, L.C., Carvalho, D., Briandet, R., Mergulhão, F.J.
    Temporal variation of recombinant protein expression in Escherichia coli biofilms analysed at single-cell level
    Process Biochemistry, 51(9), 1155-1161, 2016, doi: 10.1016/j.procbio.2016.05.016
  4. Moreira, J.M.R., Fulgêncio, R., Alves, P., Machado, I., Bialuch, I., Melo, L.F., Simões, M., Mergulhão, F.J.
    Evaluation of SICAN performance for biofouling mitigation in the food industry
    Food Control, 62, 201-207, 2016, doi: 10.1016/j.foodcont.2015.10.023
  5. Moreira, J.M.R., Fulgêncio, R., Oliveira, F., Machado, I., Bialuch, I., Melo, L.F., Simões, M., Mergulhão, F.J.
    Evaluation of SICON® surfaces for biofouling mitigation in critical process areas
    Food and Bioproducts Processing, 98, 173-180, 2016, doi: 10.1016/j.fbp.2016.01.009
  6. Azevedo, A.S., Almeida, C., Pereira, B., Melo, L.F., Azevedo, N.F.
    Impact of Delftia tsuruhatensis and Achromobacter xylosoxidans on Escherichia coli dual-species biofilms treated with antibiotic agents
    Biofouling, 32(3), 227-241, 2016, doi: 10.1080/08927014.2015.1124096
  7. Fontenete, S., Carvalho, D., Guimarães, N., Madureira, P., Figueiredo, C., Wengel, J., Azevedo, N.F.
    Application of locked nucleic acid-based probes in fluorescence in situ hybridization
    Applied Microbiology and Biotechnology, 100(13), 5897-5906, 2016, doi: 10.1007/s00253-016-7429-4
  8. Fontenete, S., Carvalho, D., Lourenço, A., Guimarães, N., Madureira, P., Figueiredo, C., Azevedo, N.F.
    FISHji: New ImageJ macros for the quantification of fluorescence in epifluorescence images
    Biochemical Engineering Journal, 112, 61-69, 2016, doi: 10.1016/j.bej.2016.04.001
  9. Fontenete, S., Guimarães, N., Wengel, J., Azevedo, N.F.
    Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models
    Critical Reviews in Biotechnology, 36(3), 566-577, 2016, doi: 10.3109/07388551.2014.993589
  10. Fontenete, S., Leite, M., Cappoen, D., Santos, R., Van Ginneken, C., Figueiredo, C., Wengel, J., Cos, P., Azevedo, N.F.
    Fluorescence in vivo hybridization (FIVH) for detection of helicobacter pylori infection in a C57BL/6 mouse model
    PLoS ONE, 11(2), 2016, doi: 10.1371/journal.pone.0148353
  11. Gameiro, D., Pérez-Pérez, M., Pérez Rodríguez, G., Monteiro, G., Azevedo, N.F., Lourenço, A.
    Computational resources and strategies to construct single-molecule metabolic models of microbial cells
    Briefings in Bioinformatics, 17(5), 863-876, 2016, DOI: 10.1093/bib/bbv096
  12. Machado, I., Meireles, A., Fulgêncio, R., Mergulhão, F., Simões, M., Melo, L.F.
    Disinfection with neutral electrolyzed oxidizing water to reduce microbial load and to prevent biofilm regrowth in the processing of fresh-cut vegetables
    Food and Bioproducts Processing, 98, 333-340, 2016, doi: 10.1016/j.fbp.2016.02.008
  13. Mendes, L., Rocha, R., Azevedo, A.S., Ferreira, C., Henriques, M., Pinto, M.G., Azevedo, N.F.
    Novel strategy to detect and locate periodontal pathogens: The PNA-FISH technique
    Microbiological Research, 192, 185-191, 2016, doi: 10.1016/j.micres.2016.07.002
  14. Pérez-Rodríguez, G., Gameiro, D., Pérez-Pérez, M., Lourenço, A., Azevedo, N.F.
    Single Molecule Simulation of Diffusion and Enzyme Kinetics
    Journal of Physical Chemistry B, 120(16), 3809-3820, 2016, doi: 10.1021/acs.jpcb.5b12544
  15. Rocha, R., Santos, R.S., Madureira, P., Almeida, C., Azevedo, N.F.
    Optimization of peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria: The effect of pH, dextran sulfate and probe concentration
    Journal of Biotechnology, 226, 1-7, 2016, doi: 10.1016/j.jbiotec.2016.03.047
  16. Sampaio, J., Machado, D., Marta Gomes, A., Machado, I., Santos, C., Lima, N., Carvalho, M.J., Cabrita, A., Rodrigues, A., Martins, M.
    Deciphering the contribution of biofilm to the pathogenesis of peritoneal dialysis infections: Characterization and microbial behaviour on dialysis fluids
    PLoS ONE, 11(6), 2016, doi: 10.1371/journal.pone.0157870
  17. Vilas Boas, D., Almeida, C., Sillankorva, S., Nicolau, A., Azeredo, J., Azevedo, N.F.
    Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH)
    Biofouling, 32(2), 179-190, 2016, doi: 10.1080/08927014.2015.1131821
  18. Abreu, A.C., Paulet, D., Coqueiro, A., Malheiro, J., Borges, A., Saavedra, M.J., Choi, Y.H., Simões, M.
    Antibiotic adjuvants from: Buxus sempervirens to promote effective treatment of drug-resistant Staphylococcus aureus biofilms
    RSC Advances, 6(97), 95000-95009, 2016, doi: 10.1039/c6ra21137b
  19. Abreu, A.C., Saavedra, M.J., Simões, L.C., Simões, M.
    Combinatorial approaches with selected phytochemicals to increase antibiotic efficacy against Staphylococcus aureus biofilms
    Biofouling, 32(9), 1103-1114, 2016, doi: 10.1080/08927014.2016.1232402
  20. Araújo, P.A., Malheiro, J., MacHado, I., Mergulhão, F., Melo, L., Simões, M.
    Influence of flow velocity on the characteristics of pseudomonas fluorescens biofilms
    Journal of Environmental Engineering (United States), 142(7), 2016, doi: 10.1061/(ASCE)EE.1943-7870.0001068
  21. Borges, A., Abreu, A.C., Dias, C., Saavedra, M.J., Borges, F., Simões, M.
    New perspectives on the use of phytochemicals as an emergent strategy to control bacterial infections including biofilms
    Molecules, 21(7), 2016, doi: 10.3390/molecules21070877
  22. Gomes, I.B., Malheiro, J., Mergulhão, F., Maillard, J.Y., Simões, M.
    Comparison of the efficacy of natural-based and synthetic biocides to disinfect silicone and stainless steel surfaces
    Pathogens and Disease, 74(4), ftw014-ftw014, 2016, doi: 10.1093/femspd/ftw014
  23. Gomes, I.B., Simões, M., Simões, L.C.
    The effects of sodium hypochlorite against selected drinking water-isolated bacteria in planktonic and sessile states
    Science of the Total Environment, 565, 40-48, 2016, doi: 10.1016/j.scitotenv.2016.04.136
  24. Gonçalves, A.L., Abreu, A.C., Coqueiro, A., Gaspar, A., Borges, F., Choi, Y.H., Pires, J.C.M., Simões, M.
    Co-cultivation of Synechocystis salina and Pseudokirchneriella subcapitata under varying phosphorus concentrations evidences an allelopathic competition scenario
    RSC Advances, 6(61), 56091-56100, 2016, doi: 10.1039/c6ra07771d
  25. Gonçalves, A.L., Alvim-Ferraz, M.C.M., Martins, F.G., Simões, M., Pires, J.C.M.
    Integration of microalgae-based bioenergy production into a petrochemical complex: Techno-economic assessment
    Energies, 9, Article Number 224, 2016, doi: 10.3390/en9040224
  26. Gonçalves, A.L., Pires, J.C.M., Simões, M.
    Biotechnological potential of Synechocystis salina co-cultures with selected microalgae and cyanobacteria: Nutrients removal, biomass and lipid production
    Bioresource Technology, 200, 279-286, 2016, doi: 10.1016/j.biortech.2015.10.023
  27. Gonçalves, A.L., Pires, J.C.M., Simões, M.
    The effects of light and temperature on microalgal growth and nutrient removal: An experimental and mathematical approach
    RSC Advances, 6(27), 22896-22907, 2016, doi: 10.1039/c5ra26117a
  28. Gonçalves, A.L., Pires, J.C.M., Simões, M.
    Wastewater polishing by consortia of Chlorella vulgaris and activated sludge native bacteria
    Journal of Cleaner Production, 133, 348-357, 2016, doi: 10.1016/j.jclepro.2016.05.109
  29. Gonçalves, A.L., Rodrigues, C.M., Pires, J.C.M., Simões, M.
    The effect of increasing CO2 concentrations on its capture, biomass production and wastewater bioremediation by microalgae and cyanobacteria
    Algal Research, 14, 127-136, 2016, doi: 10.1016/j.algal.2016.01.008
  30. Lemos, M., Wang, S., Ali, A., Simões, M., Wilson, D. I.
    A fluid dynamic gauging device for measuring biofilm thickness on cylindrical surfaces
    Biochemical Engineering Journal, 106, 48-60, 2016, doi: 10.1016/j.bej.2015.11.006
  31. Malheiro, J., Araújo, P., Machado, I., Lemos, M., Mergulhão, F., Melo, L., Simões, M.
    The Effects of Selected Brominated and Chlorinated Chemicals on Pseudomonas fluorescens Planktonic Cells and Flow-Generated Biofilms
    Journal of Food Processing and Preservation, 40(2), 316-328, 2016, doi: 10.1111/jfpp.12609
  32. Malheiro, J., Gomes, I., Borges, A., Bastos, M.M.S.M., Maillard, J.Y., Borges, F., Simões, M.
    Phytochemical profiling as a solution to palliate disinfectant limitations
    Biofouling, 32(9), 1007-1016, 2016, doi: 10.1080/08927014.2016.1220550
  33. Meireles, A., Borges, A., Giaouris, E., Simões, M.
    The current knowledge on the application of anti-biofilm enzymes in the food industry
    Food Research International, 86, 140-146, 2016, doi: 10.1016/j.foodres.2016.06.006
  34. Meireles, A., Giaouris, E., Simões, M.
    Alternative disinfection methods to chlorine for use in the fresh-cut industry
    Food Research International, 82, 71-85, 2016, doi: 10.1016/j.foodres.2016.01.021
  35. Oliveira, V., Carvalho, T., Melo, L., Pinto, A., Simões, M.
    Effects of hydrodynamic stress and feed rate on the performance of a microbial fuel cell
    Environmental Engineering and Management Journal, 15(11), 2497-2504, 2016
  1. Gomes, L.C., Silva, L.N., Simões, M., Melo, L.F., Mergulhão, F.J.
    Escherichia coli adhesion, biofilm development and antibiotic susceptibility on biomedical materials
    Journal of Biomedical Materials Research – Part A, 103(4), 1414-1423, 2015, doi: 10.1002/jbm.a.35277
  2. Moreira, J.R., Simões, M., Melo, L.F., Mergulhão, F.
    Escherichia coli adhesion to surfaces–a thermodynamic assessment
    Colloid and Polymer Science, 293(1), 177-185, 2015, doi: 10.1007/s00396-014-3390-x
  3. Moreira, J.M.R., Ponmozhi, J., Campos, J.B.L.M., Miranda, J.M., Mergulhão, F.J.
    Micro- and macro-flow systems to study Escherichia coli adhesion to biomedical materials
    Chemical Engineering Science, 126, 440-445, 2015, doi: 10.1016/j.ces.2014.12.054
  4. Moreira, J.M.R., Gomes, L.C., Simões, M., Melo, L.F., Mergulhão, F.J.
    The impact of material properties, nutrient load and shear stress on biofouling in food industries
    Food and Bioproducts Processing, 95, 228-236, 2015, doi: 10.1016/j.fbp.2015.05.011
  5. Pogiatzis, T.A., Vassiliadis, V.S., Mergulhão, F.J., Wilson, D.I.
    Choosing When to Clean and How to Clean Biofilms in Heat Exchangers
    Heat Transfer Engineering, 36(7-8), 676-684, 2015, doi: 10.1080/01457632.2015.954940
  6. Moreira, J.M.R., Simões, M., Melo, L.F., Mergulhão, F.J.
    The combined effects of shear stress and mass transfer on the balance between biofilm and suspended cell dynamics
    Desalination and Water Treatment, 53(12), 3348-3354, 2015, doi: 10.1080/19443994.2014.933625
  7. Fontenete, S., Barros, J., Madureira, P., Figueiredo, C., Wengel, J., Azevedo, N.F.
    Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids
    Applied Microbiology and Biotechnology, 99(9), 3961-3969, 2015, doi: 10.1007/s00253-015-6568-3
  8. Azevedo, A.S., Almeida, C., Pereira, B., Madureira, P., Wengel, J., Azevedo, N.F.
    Detection and discrimination of biofilm populations using locked nucleic acid/2′-O-methyl-RNA fluorescence in situ hybridization (LNA/2’OMe-FISH)
    Biochemical Engineering Journal, 104, 64-73, 2015, doi: 10.1016/j.bej.2015.04.024
  9. Pérez-Rodríguez, G., Glez-Peña, D., Azevedo, N.F., Pereira, M.O., Fdez-Riverola, F., Lourenço, A.
    Enabling systematic, harmonised and large-scale biofilms data computation: The Biofilms Experiment Workbench
    Computer Methods and Programs in Biomedicine, 118(3), 309-321, 2015, doi: 10.1016/j.cmpb.2014.12.005
  10. Santos, R.S., Dakwar, G.R., Xiong, R., Forier, K., Remaut, K., Stremersch, S., Guimarães, N., Fontenete, S., Wengel, J., Leite, M., Figueiredo, C.,
    De Smedt, S.C., Braeckmans, K., Azevedo, N.F.
    Effect of Native Gastric Mucus on in vivo Hybridization Therapies Directed at Helicobacter pylori
    Molecular Therapy – Nucleic Acids, 4(12), 2015, doi: 10.1038/mtna.2015.46
  11. Pérez-Rodríguez, G., Pérez-Pérez, M., Glez-Peña, D., Fernandez-Riverola, F., Azevedo, N.F., Lourenço, A.
    Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework
    BioMed Research International, 2015, 2015, doi: 10.1155/2015/769471
  12. Fontenete, S., Leite, M., Guimarães, N., Madureira, P., Ferreira, R.M., Figueiredo, C., Wengel, J., Azevedo, N.F.
    Towards fluorescence in vivo hybridization (FIVH) detection of H. pylori in gastric mucosa using advanced LNA probes
    PLoS ONE, 10(4), 2015, doi: 10.1371/journal.pone.0125494
  13. Lopes, S.P., Azevedo, N.F., Pereira, M.O.
    Microbiome in cystic fibrosis: Shaping polymicrobial interactions for advances in antibiotic therapy
    Critical Reviews in Microbiology, 41(3), 353-365, 2015, doi: 10.3109/1040841X.2013.847898
  14. Mendes, L., Azevedo, N. F., Felino, A., Pinto, M. G.
    Relationship between invasion of the periodontium by periodontal pathogens and periodontal disease: a systematic review
    Virulence, 6(3), 208-215, 2015, doi: 10.4161/21505594.2014.984566
  15. Simões, L.C., Simões, M., Lima, N.
    Kinetics of biofilm formation by drinking water isolated Penicillium expansum
    Biofouling, 31(4), 349-362, 2015, doi: 10.1080/08927014.2015.1042873
  16. Borges, A., Abreu, A.C., Ferreira, C., Saavedra, M.J., Simões, L.C., Simões, M.
    Antibacterial activity and mode of action of selected glucosinolate hydrolysis products against bacterial pathogens
    Journal of Food Science and Technology, 52(8), 4737-4748, 2015, doi: 10.1007/s13197-014-1533-1
  17. Meireles, A., Machado, I., Fulgêncio, R., Mergulhão, F., Melo, L., Simões, M.
    Efficacy of antimicrobial combinations to reduce the use of sodium hypochlorite in the control of planktonic and sessile Escherichia coli
    Journal of Biochemical Engineering, 104, 115-122, 2015, doi: 10.1016/j.bej.2015.02.035
  18. Vilas Boas, J., Oliveira, V.B., Marcon, L.R.C., Pinto, D.P., Simões, M., Pinto, A.M.F.R.
    Effect of operating and design parameters on the performance of a microbial fuel cell with Lactobacillus pentosus
    Biochemical Engineering Journal, 104, 34-40, 2015, doi: 10.1016/j.bej.2015.05.009
  19. Lemos, M., Gomes, I., Mergulhão, F., Melo, L., Simões, M.
    The effects of surface type on the removal of Bacillus cereus and Pseudomonas fluorescens single and dual species biofilms
    Food and Bioproducts Processing, 93, 234-241, 2015, doi: 10.1016/j.fbp.2014.08.009
  20. Lemos, M., Mergulhão, F., Melo, L., Simões, M.
    The effect of shear stress on the formation and removal of Bacillus cereus biofilms
    Food and Bioproducts Processing, 93, 242-248, 2015, doi: 10.1016/j.fbp.2014.09.005
  21. Barros, A.I., Gonçalves, A.L., Simões, M., Pires, J.C.M.
    Harvesting techniques applied to microalgae: A review
    Renewable and Sustainable Energy Reviews, 41, 1489-1500, 2015, doi: 10.1016/j.rser.2014.09.037
  22. Andrade, M., Benfeito, S., Soares, P., Magalhães e Silva, D., Loureiro, J., Borges, A., Borges, F., Simões, M.
    Fine-tuning of the hydrophobicity of caffeic acid: studies on the antimicrobial activity against Staphylococcus aureus and Escherichia coli
    RSC Advances, 5(66), 53915-53925, 2015, doi: 10.1039/c5ra05840f
  23. Abreu, A.C., Serra, S.C., Borges, A., Saavedra, M.J., McBain, A.J., Salgado, A.J., Simões, M.
    Combinatorial activity of flavonoids with antibiotics against drug-resistant staphylococcus aureus
    Microbial Drug Resistance, 21(6), 600-609, 2015, doi: 10.1089/mdr.2014.0252
  24. Lopez-Romero, J.C., González-Ríos, H., Borges, A., Simões, M.
    Antibacterial Effects and Mode of Action of Selected Essential Oils Components against Escherichia coli and Staphylococcus aureus Evidence-based
    Complementary and Alternative Medicine, 2015(2015), doi: 10.1155/2015/795435
  25. Borges, A., Saavedra, M.J., Simões, M.
    Insights on antimicrobial resistance, biofilms and the use of phytochemicals as new antimicrobial agents
    Current Medicinal Chemistry, 22(21), 2590-2614, 2015, doi: 10.2174/0929867322666150530210522
  26. Giaouris, E., Heir, E., Desvaux, M., Hébraud, M., Møretrø, T., Langsrud, S., Doulgeraki, A., Nychas, G.J., Kacániová, M., Czaczyk, K., Ölmez, H., Simões, M.
    Intra- and inter-species interactions within biofilms of important foodborne bacterial pathogens
    Frontiers in Microbiology, 6, 2015, doi: 10.3389/fmicb.2015.00841
  27. Hassanein, H.D., Elsayed, W.M., Abreu, A.C., Simões, M., Abdelmohsen, M.M.
    Polyphenolic constituents and antimicrobial activity of Rhapis excels (Arecaceae, Coryphoideae)
    Research Journal of Pharmaceutical, Biological and Chemical Sciences, 6(1), 1714-1722, 2015
  1. Gomes, L.C., Mergulhão, F.J. Effects of antibiotic concentration and nutrient medium composition on Escherichia coli biofilm formation and green fluorescent protein expression
    FEMS Microbiology Letters, 5, 2017, doi: 10.1093/femsle/fnx042
  2. Gomes, L.C., Mergulhão, F.J. Heterologous protein production in Escherichia coli biofilms: A non-conventional form of high cell density cultivation
    Process Biochemistry, 57, 1-8, 2017, doi: 10.1016/j.procbio.2017.03.018
  3. Gomes, L.C., Mergulhão, F.J.
    SEM Analysis of Surface Impact on Biofilm Antibiotic Treatment
    Scanning, 2017, 2017, doi: 10.1155/2017/2960194
  4. Gomes, L.C., Moreira, J.M.R., Araújo, J.D.P., Mergulhão, F.J.
    Surface conditioning with Escherichia coli cell wall components can reduce biofilm formation by decreasing initial adhesion
    AIMS Microbiology, 3, 613-628, 2017, doi: 10.3934/microbiol.2017.3.613
  5. Gomes, L.C., Piard, J.C., Briandet, R., Mergulhão, F.J.
    Pseudomonas grimontii biofilm protects food contact surfaces from Escherichia coli colonization
    LWT – Food Science and Technology, 43(9), 2017, doi: 10.1016/j.lwt.2017.03.005
  6. Gonçalves, A.C., Bento, C., Silva, B.M., Silva, L.R.
    Sweet cherries from Fundão possess antidiabetic potential and protect human erythrocytes against oxidative damage
    Food Research International, 95, 91-100, 2017, doi: 10.1016/j.foodres.2017.02.023
  7. Moreira, J.M.R., Gomes, L.C., Whitehead, K.A., Lynch, S., Tetlow, L.A., Mergulhão, F.J.
    Effect of surface conditioning with cellular extracts on Escherichia coli adhesion and initial biofilm formation
    Food and Bioproducts Processing, 104, 1-12, 2017, doi: 10.1016/j.fbp.2017.03.008
  8. Azevedo, A. S., Almeida, C., Melo, L. F., Azevedo, N. F.
    Impact of polymicrobial biofilms in catheter-associated urinary tract infections
    Critical Reviews in Microbiology, 43(4), 423-439, 2017, doi: 10.1080/1040841X.2016.1240656
  9. Azevedo, A.S., Almeida, C., Gomes, L.C., Ferreira, C., Mergulhão, F.J., Melo, L.F., Azevedo, N.F.
    An in vitro model of catheter-associated urinary tract infections to investigate the role of uncommon bacteria on the Escherichia coli microbial consortium
    Biochemical Engineering Journal, 118, 64-69, 2017, doi: 10.1016/j.bej.2016.11.013
  10. Barros, J., Grenho, L., Fontenente, S., Manuel, C.M., Nunes, O.C., Melo, L.F., Monteiro, F.J., Ferraz, M.P. 2017. Staphylococcus aureus and Escherichia coli dual-species biofilms on nanohydroxyapatite loaded with CHX or ZnO nanoparticles. J Biomed Mater Res Part A 105(2): 491-497.
  11. Costa, A.M., Mergulhão, F.J., Briandet, R., Azevedo, N.F.
    It is all about location: How to pinpoint microorganisms and their functions in multispecies biofilms
    Future Microbiology, 12(11), 987-999, 2017, doi: 10.2217/fmb-2017-0053
  12. Fernandes, R.M., Silva, H., Oliveira, R., Almeida, C., Azevedo, N.F., Vieira, M.J.
    Morphological transition of Helicobacter pylori adapted to water
    Future Microbiology, 12(13), 1167-1179, 2017, doi: 10.2217/fmb-2016-0174
  13. Ferreira, A.M., Cruz-Moreira, D., Cerqueira, L., Miranda, J.M., Azevedo, N.F.
    Yeasts identification in microfluidic devices using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH)
    Biomedical Microdevices, 19(1), 2017, doi: 10.1007/s10544-017-0150-y
  14. Lopes, S.P., Azevedo, N.F., Pereira, M.O.
    Developing a model for cystic fibrosis sociomicrobiology based on antibiotic and environmental stress
    International Journal of Medical Microbiology, 307(8), 460-470, 2017, doi: 10.1016/j.ijmm.2017.09.018
  15. Lopes, S.P., Carvalho, D.T., Pereira, M.O., Azevedo, N.F.
    Discriminating typical and atypical cystic fibrosis-related bacteria by multiplex PNA-FISH
    Biotechnology and Bioengineering, 114(2), 355-367, 2017, doi: 10.1002/bit.26085
  16. Rodrigues, M.E., Lopes, S.P., Pereira, C.R., Azevedo, N.F., Lourenço, A., Henriques, M., Pereira, M.O.
    Polymicrobial ventilator-associated pneumonia: Fighting in vitro Candida albicans-pseudomonas aeruginosa biofilms with antifungal-antibacterial combination therapy
    PLoS ONE, 12(1), 2017, doi: 10.1371/journal.pone.0170433
  17. Santos, R.S., Dakwar, G.R., Zagato, E., Brans, T., Figueiredo, C., Raemdonck, K., Azevedo, N.F., De Smedt, S.C., Braeckmans, K., Intracellular delivery of oligonucleotides in Helicobacter pylori by fusogenic liposomes in the presence of gastric mucus, Biomaterials, 138, 1-12, 2017, doi: 10.1016/j.biomaterials.2017.05.029
  18. Santos, R.S., Lima, C.C., Carvalho, D., Meireles, F., Guimarães, N., Azevedo, N.F.
    Response surface methodology to optimize peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) in Saccharomyces cerevisiae
    LWT – Food Science and Technology, 80, 27-31, 2017, doi: 10.1016/j.lwt.2017.01.077
  19. Abreu, A.C., Coqueiro, A., Sultan, A.R., Lemmens, N., Kim, H.K., Verpoorte, R., Van Wamel, W.J.B., Simões, M., Choi, Y.H.
    Looking to nature for a new concept in antimicrobial treatments: Isoflavonoids from Cytisus striatus as antibiotic adjuvants against MRSA
    Scientific Reports, 7(1), 2017, doi: 10.1038/s41598-017-03716-7
  20. Araújo, P.A., Machado, I., Meireles, A., Leiknes, T., Mergulhão, F., Melo, L.F., Simões, M.
    Combination of selected enzymes with cetyltrimethylammonium bromide in biofilm inactivation, removal and regrowth
    Food Research International, 95, 101-107, 2017, doi: 10.1016/j.foodres.2017.02.016
  21. Azeredo, J., Azevedo, N.F., Briandet, R., Cerca, N., Coenye, T., Costa, A.R., Desvaux, M., Di Bonaventura, G., Hébraud, M., Jaglic, Z., Kačániová, M., Knøchel, S., Lourenço, A., Mergulhão, F., Meyer, R.L., Nychas, G., Simões, M., Tresse, O., Sternberg, C.
    Critical review on biofilm methods
    Critical Reviews in Microbiology, 43(3), 313-351, 2017, doi: 10.1080/1040841X.2016.1208146
  22. Barros, A., Guerra, L.T., Simões, M., Santos, E., Fonseca, D., Silva, J., Costa, L., Navalho, J.
    Mass balance analysis of carbon and nitrogen in industrial scale mixotrophic microalgae cultures
    Algal Research, 21, 35-41, 2017, doi: 10.1016/j.algal.2016.10.014
  23. Borges, A., Lopez-Romero, J.C., Oliveira, D., Giaouris, E., Simões, M.
    Prevention, removal and inactivation of Escherichia coli and Staphylococcus aureus biofilms using selected monoterpenes of essential oils
    Journal of Applied Microbiology, 123(1), 104-115, 2017, doi: 10.1111/jam.13490
  24. Borges, A., Sousa, P., Gaspar, A., Vilar, S., Borges, F., Simões, M.
    Furvina inhibits the 3-oxo-C12-HSL-based quorum sensing system of Pseudomonas aeruginosa and QS-dependent phenotypes
    Biofouling, 33(2), 156-168, 2017, doi: 10.1080/08927014.2017.1280732
  25. Celaya, L., Viturro, C., Silva, L.R.
    Chemical Composition and Biological Prospects of Essential Oils and Extracts of Aphyllocladus spartioides Growing in Northwest Argentina
    Chemistry and Biodiversity, 14(4), 2017, doi: 10.1002/cbdv.201600227
  26. Gomes, I. B., Meireles, A., Gonçalves, A. L., Goeres, D. M., Sjollema, J., Simões, L. C., Simões, M.
    Standardized reactors for the study of medical biofilms: a review of the principles and latest modifications
    Critical Reviews in Biotechnology, 1-14, 2017, doi: 10.1080/07388551.2017.1380601 – in Press
  27. Gonçalves, A.L., Pires, J.C.M., Simões, M.
    A review on the use of microalgal consortia for wastewater treatment
    Algal Research, 24, Part B, 403-415, 2017, doi: 10.1016/j.algal.2016.11.008
  28. Gonçalves, A.L., Simões, M.
    Metabolic engineering of Escherichia coli for higher alcohols production: An environmentally friendly alternative to fossil fuels
    Renewable and Sustainable Energy Reviews, 77, 580-589, 2017, doi: 10.1016/j.rser.2017.04.047
  29. Meireles, A., Ferreira, C., Melo, L., Simões, M.
    Comparative stability and efficacy of selected chlorine-based biocides against Escherichia coli in planktonic and biofilm states
    Food Research International, 2017, doi: 10.1016/j.foodres.2017.09.033 – in Press
  30. Meireles, A., Fulgêncio, R., Machado, I., Mergulhão, F., Melo, L., Simões, M. Characterization of the heterotrophic bacteria from a minimally processed vegetables plant
    LWT – Food Science and Technology, 2017, doi: 10.1016/j.lwt.2017.01.038

Xiong, Y., Hozic, D., Goncalves, A.L., Simões, M., Hong, P.-Y.
Increasing tetracycline concentrations on the performance and communities of mixed microalgae-bacteria photo-bioreactors
(2018) Algal Research, 29, pp. 249-256.

  1. Gomes L., Moreira J., Miranda J.M., Simões M., Melo L., Mergulhão F., “Macroscale versus microscale methods for physiological analysis of biofilms formed in 96-well microtiter plates”, Journal of Microbiological Methods, 95 (3), 342-349, 2013.
  2. Moreira J., Gomes L., Araújo J., Miranda J.M., Simões M., Melo L., Mergulhão F., “The effect of glucose concentration and shaking conditions on Escherichia coli biofilm formation in microtiter plates”, Chemical Engineering Science, 94, 192-199, 2013.
  3. Moreira J., Teodósio J., Silva F., Simões M., Melo L., Mergulhão F., “Influence of flow rate variation on the development of Escherichia coli biofilms”, Bioprocess and Biosystems Engineering, 36 (11), 1787-1796, 2013.
  4. Teodósio J., Silva F., Moreira J., Simões M., Melo L., Alves M., Mergulhão F., “Flow cells as quasi-ideal systems for biofouling simulation of industrial piping systems”, Biofouling, 29 (8), 953-966, 2013.
  5. Almeida C., Azevedo N.F., Bento J.C., Cerca N., Ramos H., Vieira M.J., Keevil C.W., “Rapid detection of urinary tract infections caused by Proteus spp. using PNA-FISH”. European Journal of Clinical Microbiology & Infectious Diseases, 32 (6), 781-786, 2013.
  6. Almeida C., Cerqueira L., Azevedo N.F., Vieira M.J., “Detection of Salmonella enterica serovar Enteritidis using real time PCR, immunocapture assay, PNA FISH and standard culture methods in different types of food samples”, International Journal of Food Microbiology 161 (1), 16-22, 2013.
  7. Almeida C., Sousa J., Rocha R., Cerqueira L., Fanning S., Azevedo N.F., Vieira M.J., “Detection of Escherichia coli O157 using PNA-FISH: comparison to a standard culture method”, Applied and Environmental Microbiology, 79 (20), 6293-300, 2013.
  8. Cerqueira L., Fernandes R.M., Ferreira R.M., Oleastro M., Carneiro F., Brandão C., Pimentel-Nunes P., Dinis-Ribeiro M., Figueiredo C., Keevil C.W., Vieira M.J., Azevedo N.F., “Validation of a PNA-FISH method for the detection of Helicobacter pylori clarithromycin resistance in gastric biopsies”, Journal of Clinical Microbiology, 51 (6), 1887-1893, 2013.
  9. Cerqueira L., Oliveira J.A., Nicolau A., Azevedo N.F., Vieira M.J., “Biofilm formation with mixed cultures of Pseudomonas aeruginosa / Escherichia coli on silicone using artificial urine to mimic urinary catheters”, Biofouling, 29 (7), 829-40, 2013.
  10. Ferreira C., Pereira A.M., Pereira M.C., Simões M., Melo L.F., “Biofilm Control with new Microparticleswith Immobilized Biocide”, Heat Transfer Engineering, 34 (8-9), 712-718, 2013.
  11. Fontenete S., Guimarães N., Leite M., Figueiredo C., Wengel J., Azevedo N.F., “Hybridization-based detection of Helicobacter pylori at human body temperature using advanced locked nucleic acid (LNA) probes”, PLoS ONE, 8 (11), e81230, 2013.
  12. Fontenete S., Guimarães N., Leite M., Figueiredo C., Wengel J., Azevedo N.F., “Hybridization-based detection of Helicobacter pylori at human body temperature using advanced locked nucleic acid (LNA) probes”, PLoS ONE, 8 (11):e81230, 2013.
  13. Machado A., Almeida C., Carvalho A., Boyen F., Haesebrouck F., Rodrigues L., Cerca N., Azevedo N.F., “Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Lactobacillus spp. in milk samples”, International Journal of Food Microbiology, 162 (1), 64-70, 2013.
  14. Machado A., Almeida C., Salgueiro D., Henriques A., Vaneechoutte M., Haesebrouck F., Vieira M.J., Rodrigues L., Azevedo N.F., Cerca N., “Fluorescence in situ hybridization method using peptide nucleic acid probes for rapid detection of Lactobacillus and Gardnerella spp”, BMC Microbiology, 13, 82, 2013.
  15. Oliveira V., Simões M., Melo L., Pinto A.R., “A 1D mathematical model for a microbial fuel cell”, Energy, 61, 467-471, 2013.
  16. Oliveira V.B., Simões M., Melo L.F., Pinto A.M.F.R., “Overview on the development of microbial fuel cells”, Biochemical Engineering Journal, 73, 53-64, 2013.
  17. Rodrigues A., Nogueira R., Melo L.F., Brito A.G., “Effect of low concentrations of synthetic surfactants on polycyclic aromatic hydrocarbons (PAH) biodegradation”, International Biodeterioration & Biodegradation, 83, 48-55, 2013.
  18. Abreu A.C., Borges A., Simões L.C., Saavedra M.J., Simões M., “Antimicrobial activity of phenyl isothiocyanate on Escherichia coli and Staphylococcus aureus.”, Medicinal Chemistry, 9, 756-761, 2013.
  19. Abreu A.C., Tavares R.R., Borges A., Mergulhão F.J., Simões M., “Current and emergent strategies for disinfection of hospital environments”, Journal of Antimicrobial Chemotherapy, 68, 2718-2732, 2013.
  20. Borges A., Ferreira C., Saavedra M.J., Simões M., “Antibacterial activity and mode of action of ferulic and gallic acids against pathogenic bacteria”, Microbial Drug Resistance, 19, 256-265, 2013.
  21. Gonçalves A.L., Pires J.C., Simões M., “Green fuel production: processes applied to microalgae”, Environmental Chemistry Letters, 11, 315-324, 2013.
  22. Pires J.C., Alvim-Ferraz M.C., Martins F.G., Simões M., “Wastewater treatment to enhance the economic viability of microalgae culture”, Environmental Science and Polution Research, 20 (8), 5096-5105, 2013.
  23. Simões L.C., Simões M., “Biofilms in drinking water: Problems and solutions”, RSC Advances, 3, 2520-2533, 2013.
  1. Gomes, L.C., Moreira, J.M.R., Teodósio, J.S., Araújo, J.D.P., Miranda, J.M., Simões, M., Melo, L.F.,Mergulhão, F.J. 96-well microtiter plates for biofouling simulation in biomedical settings Biofouling, 30(5), 535-546, 2014, doi: 10.1080/08927014.2014.890713
  2. Moreira J.M.R., Araujo J.D.P., Miranda J.M., Simões M., Melo L.F., Mergulhão F.J., “The effects of surface properties on Escherichia coli adhesion are modulated by shear stress”, Colloids and Surfaces B: Biointerfaces, 123, 1-7, 2014.
  3. Azevedo, A.S., Almeida, C., Melo, L.F.,Azevedo, N.F. Interaction between atypical microorganisms andE. coliin catheter-associated urinary tract biofilms Biofouling, 30(8), 893-902, 2014, doi: 10.1080/08927014.2014.944173
  4. Lopes, S.P., Azevedo, N.F.,Pereira, M.O. Emergent Bacteria in Cystic Fibrosis:In VitroBiofilm Formation and Resilience under Variable Oxygen Conditions BioMed Research International, 2014, 1-7, 2014, doi: 10.1155/2014/678301
  5. Fernández, I., Bravo, J.I., Mosquera-Corral, A., Pereira, A., Campos, J.L., Méndez, R.,Melo, L.F. Influence of the shear stress and salinity on Anammox biofilms formation: modelling results Bioprocess and Biosystems Engineering, 37(10), 1955-1961, 2014, doi: 10.1007/s00449-014-1171-z
  6. Almeida C., Constante D., Ferreira A., Cerqueira L., Vieira M.J., Azevedo N.F., “A new colorimetric PNA-based assay for the specific detection of bacteria”. Future Microbiology, 9 (10), 1131–1142, 2014.
  7. Teixeira R., Pereira A., Mendes J., Melo L.F., “Identifying the nature of fouling layers by online Monitoring of the propagation of vibrations along the deposition surface”, Heat Transfer Engineering, 35(3), 251-257, 2014.
  8. Santos R.S., Guimarães N., Madureira P., Azevedo N.F., “Optimization of a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method for the detection of bacteria and disclosure of a formamide effect”, Journal of Biotechnology, 187, 16-24, 2014.
  9. Sousa A.M., Pereira M. O., Azevedo N.F., Lourenço A., “An harmonised vocabulary for communicating and interchanging biofilms experimental results”, Journal of Integrative Bioinformatics, 11 (3), 249, 2014.
  10. Danko A.S., Fontenete S.J., Leite D.A., Leitão P.O., Almeida C., Schaefer C., Vainberg S., Steffan R.J., Azevedo N.F., “Detection of Dehalococcoides spp. by peptide nucleic acid fluorescent in situ hybridization”, Journal of Molecular Microbiology and Biotechnology, 24, 142-149, 2014.
  11. Lourenço A., Coenye T., Goeres D., Donelli G., Azevedo A.S., Ceri H., Coelho F.L., Flemming H.-C., Juhna T., Lopes S.P., Oliveira R., Oliver A., Shirtliff M.E., Sousa A.M., Stoodley P., Pereira M.O., Azevedo N.F., “Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces”, Pathogens and Disease, 70 (3), 250-256, 2014.
  12. Araújo, P.A., Mergulhão, F., Melo, L.,Simões, M. The ability of an antimicrobial agent to penetrate a biofilm is not correlated with its killing or removal efficiency Biofouling, 30(6), 675-683, 2014, doi: 10.1080/08927014.2014.904294
  13. Borges, A., Serra, S., Cristina Abreu, A., Saavedra, M.J., Salgado, A.,Simões, M. Evaluation of the effects of selected phytochemicals on quorum sensing inhibition andin vitrocytotoxicity Biofouling, 30(2), 183-195, 2014, doi: 10.1080/08927014.2013.852542
  14. Meireles A.C., Simões M., “Metabolic control analysis: theoretical aspects and practical applications”, Current Bioinformatics, 9 (5), 490 – 498, 2014.
  15. Abreu A.C., Serra S., Borges A., Saavedra M.J., Salgado A., Simões M., “Evaluation of the best method to assess antibiotic potentiation by phytochemicals against Staphylococcus aureus”, Diagnostic Microbiology & Infectious Disease, 179, 125-134, 2014.
  16. Pimenta F., Abreu A.C., Simões L.C, Simões M., “What should be considered in the treatment of bacterial infections by multi-drug therapies: a mathematical perspective?”, Drug Resistance Updates 17, 51-63, 2014.
  17. Gonçalves A.L., Simões M., Pires J.C., “The effect of light supply on microalgal growth, CO2 uptake and nutrient removal from wastewater”, Energy Conversion and Management 85, 530-536, 2014.
  18. Abreu A.C., Borges A., Mergulhão F., Simoes M., “Use of phenyl isothiocyanate for biofilm prevention and control”, International Biodeterioration and Biodegradation, 86, 34-41, 2014.
  19. Borges A., Simões L.C., Saavedra M.J., Simões M., “The action of selected isothiocyanates on bacterial biofilm prevention and control”, International Biodeterioration & Biodegradation 86, 25-33, 2014.
  20. Lemos M., Borges A., Teodósio J., Araújo P., Mergulhão F.J., Melo L.F., Simões M., “The effects of ferulic and salycilic acids on Bacillus cereus and Pseudomonas fluorescens single- and dual-species biofilms”, International Biodeterioration and Biodegradation, 86, 42-51, 2014.
  21. Pires J.C.M., Gonçalves A.L., Martins F.G., Alvim-Ferraz M.C.M., Simões M., “Effect of light supply on CO2 capture from atmosphere by Chlorella vulgaris and Pseudokirchneriella subcapitata”, Mitigation and Adaptation of Strategies for Global Change, 19, 1109-1117, 2014.
  22. Dias C., Serra C.R., Simões L.C., Simões M., Martinez-Murcia A., Saavedra M.J., “Extended-spectrum beta-lactamase and carbapenemase-producing Aeromonas 1 spp. in wild animals from Portugal”, The Veterinary Record, 174, 532, 2014.
  23. Gomes I.B., Simões M., Simões L.C., “An overview on the reactors to study drinking water biofilms”, Water Research 62, 63-87, 2014.
  1. Teodósio J.S., Simões M., Alves M.A., Melo L.F., Mergulhão F.J., “Setup and validation of flow cell systems for biofouling simulation in industrial settings”, The Scientific World Journal, art. no. 361496, 2012.
  2. Teodósio J.S., Simões M., Mergulhão F.J., “The influence of nonconjugative Escherichia coli plasmids on biofilm formation and resistance”, Journal of Applied Microbiology, 113, 2, 373-382, 2012.
  3. Azevedo N. F., Bragança S. M., Simões L.C., Cerqueira L., Almeida C., Keevil C. W., Vieira M. J., “Proposal for a method to estimate nutrient shock effects in bacteria”, BMC Research Notes, 5, 1, 422, 2012.
  4. Bessa L.J., Correia D.M., Cellini L., Azevedo N.F., Rocha I., “Optimization of culture conditions to improve Helicobacter pylori growth in Ham’s F-12 by response surface methodology”, International Journal of Immunopathology and Pharmacology, 25 (4), 901-909, 2012
  5. Lopes S. P., Ceri H., Azevedo N. F., Pereira M. O., “Antibiotic resistance of mixed biofilms in cystic fibrosis: the impact of emerging microorganisms on infection treatment”, International Journal of Antimicrobial Agents, 40, 3, 260-263, 2012.
  6. Lourenço A., Ferreira A., Veiga N., Machado I., Pereira M.O., Azevedo N.F., “Biofomics: A web platform for the systematic and standardized collection of high-throughput biofilm data”, PLoS ONE, 7, 6, Article numbere39960, 2012.
  7. Sousa A. M., Ferreira A., Azevedo N., Pereira M. O., Lourenço A., “Computational approaches to standard-compliant biofilm data for reliable analysis and integration”, Journal of Integrative Bioinformatics, 9, 3, 203, 2012.
  8. Borges A., Saavedra M.J., Simões M., “The activity of ferulic and gallic acids on biofilm prevention and control of pathogenic bactéria”, Biofouling, 28, 755-767, 2012.
  9. Gomes L., Simões M., “13C metabolic flux analysis: from the principle to recent applications”, Current Bioinformatics 7, 1, 77-86, 2012.
  10. Pires J.C.M., Alvim-Ferraz M.C.M., Martins F.G., Simões M., “Carbon dioxide capture from flue gases using microalgae: Engineering aspects and biorefinery concept”, Renewable and Sustainable Energy Reviews, 16 (5), 3043-3053, 2012.
  11. Simões L.C., Simões M., Vieira M.J., “A comparative study on drinking water biofilm monitoring with flow cell and PropellaTM bioreactors”, Water Science and Technology: Water Supply, 12 (3), 334-342, 2012.