Publications
Recent Publications
- Azevedo A.S., Sousa I.M., Fernandes R., Azevedo N.F. and C. Almeida (2019). 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.
- Sousa J.M., Rocha R., Cerqueira L., Almeida C., Azevedo N.F., Bastin B., Bird P., Benzinger M.J. Jr, Agin J. and D. Goins (2019).Validation of Biomode S.A. Probe4CronobacterTM for the Identification of Cronobacter spp. Journal of AOAC International, 102(3):855-864.
- Rosenberg M., Azevedo N.F. and A. Ivask (2019). “Propidium iodide staining underestimates viability of adherent bacterial cells”. Scientific Reports, 9(1):6483.
- Maia P., Pérez Rodríguez G., Pérez-Pérez M., Fdez-Riverola F., Lourenço A. and N.F. Azevedo (2019). “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.
- Rocha R., Sousa J.M., Cerqueira L., Vieira M.J., Almeida C. and N.F. Azevedo (2019). “Development and application of peptide nucleic acid fluorescence in situ hybridization for the specific detection of Listeria monocytogenes”. Food Microbiology, 80:1-8.
- Silva E.R., Ferreira O., Ramalho P.A., Azevedo N.F., Bayón R., Igartua A., Bordado J.C. and M.J. Calhorda (2019). “Eco-friendly non-biocide-release coatings for biofouling prevention”, Science of the Total Environment, 650:2499-2511.
2018
- Rocha, R., Sousa J.M., Cerqueira L., Vieira M.J., Almeida C. and N.F. Azevedo (2018). “Development and application of peptide nucleic acid fluorescence in situ hybridization for the specific detection of Listeria monocytogenes”. Food Microbiology, Accepted.
- Silva E.R., Ferreira O., Ramalho P.A., Azevedo N.F., Bayón R., Igartua A., Bordado J.C. and M.J. Calhorda (2018). “Eco-friendly non-biocide-release coatings for biofouling prevention”. STOTEN, Accepted.
- Müller V., Sousa J.M., Koydemir H.C., Veli M., Tseng D., Cerqueira L., Ozcan A., Azevedo N. F. and F. Westerlund (2018). “Identification of pathogenic bacteria in complex samples using a smartphone based fluorescence microscope”. RSC Advances,8(64):36493-36502.
- Santos R.S., Figueiredo C., Azevedo N.F., Braeckmans K. and S.C. De Smedt (2018). “Nanomaterials and molecular transporters to overcome the bacterial envelope barrier: towards advanced delivery of antibiotics”. Advanced Drug Delivery Reviews, 136-137:28-48.
- Lima J.F., Carvalho J., Ribeiro I.P., Almeida C., Wengel J., Cerqueira L., Figueiredo C., Oliveira C. and N.F. Azevedo (2018). “Targeting miR-9 in gastric cancer cells using Locked Nucleic Acid Oligonucleotides”. BMC Molecular Biology, 19(1):6.
- Lopes S.P., Azevedo N.F. and M.O. Pereira (2018). “Quantitative assessment of individual populations within polymicrobial biofilms”. Scientific Reports,8, Article number: 9494.
- Rocha, R., Almeida C. and N.F. Azevedo (2018). “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.
- Lima J., Cerqueira L., Figueiredo C., Oliveira C. and N.F. Azevedo (2018). “Anti-miRNA oligonucleotides: a comprehensive guide for design”. RNA Biology, 15(3):338-352.
- Pérez Rodríguez G., Dias S., Pérez-Pérez M., Fdez-Riverola F., Azevedo N.F. and A. Lourenço (2018). “Agent-based model of N-acyl homoserine lactones diffusion in a multicellular environment of Pseudomonas aeruginosaand Candida albicans”. Biofouling, 34(3):335-345.
- Adlhart C., Verran J., Azevedo N.F., Olmez H., Keinänen-Toivola M.N., Gouveia I., Melo L.F. and F. Crijns (2018). “Surface modifications for antimicrobial effects in the healthcare setting: a critical overview”. Journal of Hospital Infections, 99(3):239-249.
- Hidalgo B.M., López-Álvarez M., Azevedo A.S., Dorado J., Serra J., Azevedo N.F. and P. González (2018). “Pulsed laser deposition of copper and zinc dopedhydroxyapatite coatings for biomedical applications”. Surface and Coatings Technology, 333:168-177.
2017
- Lopes S.P., Azevedo N.F. and M.O. Pereira (2017). “Developing a model for cystic fibrosis sociomicrobiology based on antibiotic and environmental stress”. International Journal of Medical Microbiology, 307(8):460-470.
- Fernandes R.M., Silva H., Almeida C., Azevedo N.F. and M.J. Vieira (2017). “Morphological transition of Helicobacter pylori adapted to water”. Future Microbiology, 12(13):1167-1179.
- Costa A.M., Mergulhão F.J., Briandet R. and N.F. Azevedo (2017). “It’s all about location: how to pinpoint microorganisms in multispecies biofilms”. Future Microbiology, 12(11):987-999.
- Bogas D., Nyberg L., Pacheco R., Azevedo N.F., Beech J.P., Gomila M., Lalucat J., Manaia C.M., Nunes O.C., Tegenfeldt J.O. and F. Westerlund (2017). “Applications of optical DNA mapping in microbiology”. Biotechniques, 62(6):255–267.
- Santos R.S., Dakwar G.R., Zagato E., Brans T., Figueiredo C., Raemdonck K., Azevedo N.F., De Smedt S.C., and K. Braeckmans (2017). “Intracellular delivery of oligonucleotides in Helicobacter pylori by fusogenic liposomes in the presence of gastric mucus”. Biomaterials, 138:1-12.
- Azevedo A.S., Almeida C., Melo L.F. and N.F. Azevedo (2017). “Impact of polymicrobial biofilms in catheter-associated urinary tract infections”. Critical Reviews in Microbiology, 43(4):423-439.
- Santos R.S, Lima C.C., Carvalho D., Meireles F., Guimarães N. and N.F. Azevedo (2017). “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.
- Ferreira A.M., Cruz-Moreira D., Cerqueira L., Miranda J.M. and N.F. Azevedo (2017). “Yeasts identification in microfluidic devices using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH)”. Biomedical Microdevices, 19(1):art11.
- Rodrigues E., Lopes S.P., Pereira C.R., Azevedo N.F., Lourenço A., Henriques M. and M.O. Pereira (2017). “Polymicrobial ventilator-associated pneumonia: fighting in vitro Candida albicans-Pseudomonas aeruginosa biofilms with antifungal-antibacterial combination therapy”. PLoS One, 12 (1):e0170433.
- Azeredo J., Azevedo N.F., Briandet R., Cerca N., Coenye T., Costa A.R., Desvaux M., Di Bonaventura G., Hébraud M., Jaglič Z., Kačániová M., Knøchel S., Lourenço A., Mergulhão F., Meyer R.L., Nychas G., Simões M., Tresse O. and C. Sternberg (2017). “Critical review on biofilm methods”. Critical Reviews in Microbiology, 43(3):313-351.
- Azevedo A.S., Almeida C., Gomes L.C., Ferreira C., Mergulhão F.J., Melo L.F. and N.F. Azevedo (2017). “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.
- Lopes S.P., Carvalho D.T., Pereira M.O. and N.F. Azevedo (2017). “Discriminating typical and atypical cystic fibrosis-related bacteria by multiplex PNA FISH”. Biotechnology and Bioengineering, 114(2):355-367. Selected as a Spotlight for the Journal.
2016
- Mendes L., Rocha R., Azevedo A.S., Ferreira C., Henriques M., Pinto M.G. and N.F. Azevedo (2016). “Novel strategy to detect and locate periodontal pathogens: the PNA-FISH technique”. Microbiological Research, 192:185-191.
- Fontenete S., Carvalho D., Lourenço A., Guimarães N., Madureira P., Figueiredo C., Wengel J. and N.F. Azevedo (2016). “FISHji: new ImageJ macros for the quantification of fluorescence in epifluorescence images”. Biochemical Engineering Journal, 112:61-69.
- Pérez Rodríguez G., Gameiro D., Pérez-Pérez M., Lourenço A. and N.F. Azevedo (2016). “Single Molecule Simulation of Diffusion and Enzyme Kinetics”. The Journal of Physical Chemistry B, 120(16):3809-20.
- Fontenete S., Leite M., Cappoen D., Santos R., Figueiredo C., Wengel J., Cos P. and N.F. Azevedo (2016). “Fluorescence in vivo hybridization (FIVH) for detection of Helicobacter pylori infection in a C57BL/6 mouse model”. PLoS ONE, 11(2):e0148353.
- Rocha, R., Santos R.S., Madureira P., Almeida C. and N.F. Azevedo (2016). “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.
- Fontenete S., Carvalho D., Guimarães N., Madureira P., Figueiredo C., Wengel J. and N.F. Azevedo (2016). “Application of locked nucleic acid-based probes in fluorescence in situ hybridization”. Applied Microbiology and Biotechnology, 100(13):5897-906.
- Magalhães A.P., Azevedo N.F., Pereira M.O. and S.P. Lopes (2016). “The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy”. Applied Microbiology and Biotechnology, 100(3):1163-81.
- Azevedo A.S., Almeida C., Melo L.F. and N.F. Azevedo (2016). “Impact of Delftia tsuruhatensis and Achromobacter xylosoxidans on coli dual-species biofilms treated with antibiotic agents”. Biofouling, 32(3):227-41.
- Vilas-Boas D., Almeida C., Sillankorva S., Nicolau A., Azeredo J. and N.F. Azevedo (2016). “Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH)”. Biofouling, 32(2):179-90.
- Fontenete S., Guimarães N., Wengel J. and N.F. Azevedo (2016). “Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models”. Critical Reviews in Biotechnology, 36(3):566-77.
- Gameiro D., Pérez-Pérez M., Pérez Rodríguez G., Monteiro G., Azevedo N.F. and A. Lourenço (2016). “Computational resources and strategies to construct single-molecule metabolic models of microbial cells” Briefings in Bioinformatics, 17(5): 863-876.
2015
- 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. and N.F. Azevedo (2015). “Effect of native gastric mucus on in vivo hybridization therapies directed at Helicobacter pylori”. Molecular Therapy – Nucleic acids, 4:e269.
- Azevedo, A.S., Almeida, C., Melo, L.F. and N.F. Azevedo (2015). “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.
- Fontenete S., Leite M., Guimarães N., Madureira P., Ferreira R.M., Figueiredo C., Wengel J. and N.F. Azevedo (2015). “Towards fluorescence in vivo hybridization (FIVH) detection of H. pylori in gastric mucosa using advanced LNA probes”. PLoS One, 10(4):e0125494.
- Pérez-Rodríguez G., Glez-Peña D., Azevedo N.F., Pereira M.O., Fdez-Riverola F. and A. Lourenço (2015). “Enabling systematic, harmonised and large-scale biofilms data computation: the Biofilms Experiment Workbench”. Computer Methods and Programs in Biomedicine, 118(3):309-321.
- Fontenete S., Barros J., Madureira P., Figueiredo C., Wengel J. and N.F. Azevedo (2015). “Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids”. Applied Microbiology and Biotechnology, 99(9): 3961-3969.
- Mendes L., Azevedo N. F., Felino A. and M.G. Pinto (2015). “Relationship between invasion of the periodontium by periodontal pathogens and periodontal disease: a systematic review”. Virulence, 6(3):208-15.
- Lopes S.P., Azevedo N.F. and M.O. Pereira (2015). “Microbial diversity in cystic fibrosis: shaping polymicrobial interactions for advances in CF therapy”. Critical Reviews in Microbiology, 41(3):353-365.
- Pérez-Rodríguez G., Pérez-Pérez M., Glez-Peña D., Fdez-Riverola F., Azevedo N.F. and A. Lourenço (2015). “Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework”. Biomed Research International, ID 769471.
2014
- Almeida C., Constante D., Ferreira A., Cerqueira L., Vieira M.J. and N.F. Azevedo (2014). “A new colorimetric PNA-based assay for the specific detection of bacteria”. Future Microbiology, 9(10):1131–1142.
- Sousa A.M., Pereira M. O., Azevedo N.F. and A. Lourenço (2014). “A harmonised vocabulary for communicating and interchanging biofilms experimental results”. Journal of Integrative Bioinformatics, 11(3):249.
- Azevedo, A.S., Almeida, C., Melo, L.F. and N.F. Azevedo (2014). “Interaction between atypical microorganisms and coli in catheter-associated urinary tract biofilms”. Biofouling, 30(8):893-902.
- Santos R.S., Guimarães N., Madureira P. and N.F. Azevedo (2014). “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.
- Guimarães N., Azevedo N. F., Vieira M.J. and C. Figueiredo (2014). “Water-induced modulation of pylori virulence properties”. Memórias do Instituto Oswaldo Cruz, 109(4):414-419.
- Lopes S. P., Azevedo N. F. and M. O. Pereira (2014). “Emergent bacteria in cystic fibrosis: in vitro biofilm formation and resilience under variable oxygen conditions”. Biomed Research International, ID67830
- Danko A.S., Fontenete S.J., Leite D.A., Leitão P.O., Almeida C., Schaefer C., Vainberg S., Steffan R.J. and N.F. Azevedo (2014). “Detection of Dehalococcoides by peptide nucleic acid fluorescent in situ hybridization”. Journal of Molecular Microbiology and Biotechnology, 24: 142-149.
- 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. and N.F. Azevedo (2014). “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.
2013
- Fontenete S., Guimarães N., Leite M., Figueiredo C., Wengel J. and N.F. Azevedo (2013). “Hybridization-based detection of Helicobacter pylori at human body temperature using advanced locked nucleic acid (LNA) probes”. PLoS ONE, 8(11):e81230.
- Almeida C., Sousa J., Rocha R., Cerqueira L., Fanning S., Azevedo N. F. and M. J. Vieira (2013). “Detection of Escherichia coli O157 using PNA-FISH: comparison to a standard culture method”. Applied and Environmental Microbiology, 79(20):6293-6300.
- Cerqueira L., Oliveira J. A., Nicolau A., Azevedo N. F. and M. J. Vieira (2013). “Biofilm formation with mixed cultures of Pseudomonas aeruginosa / Escherichia coli on silicone using artificial urine to mimic urinary catheters”. Biofouling, 29(7):829-840.
- 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. and N. F. Azevedo (2013). “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.
- Machado A., Almeida C., Salgueiro D., Henriques A., Vaneechoutte M., Haesebrouck F., Vieira M.J., Rodrigues L., Azevedo N.F. and N. Cerca (2013). “Fluorescence in situ hybridization method using peptide nucleic acid probes for rapid detection of Lactobacillus and Gardnerella spp”. BMC Microbiology, 13:82.
- Almeida C., Azevedo N. F., Bento J. C., Cerca N., Ramos H., Vieira M. J. and C. W. Keevil (2013). “Rapid detection of urinary tract infections caused by Proteus using PNA-FISH”. European Journal of Clinical Microbiology & Infectious Diseases, 32(6):781-786.
- Machado A., Almeida C., Carvalho A., Boyen F., Haesebrouck F., Rodrigues L., Cerca N. and N. F. Azevedo (2013). “Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Lactobacillus in milk samples”. International Journal of Food Microbiology, 162(1):64-70.
- Almeida C., Cerqueira L., Azevedo N. F. and M. J. Vieira (2013). 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.
2012
- Bessa L. J., Correia D. M., Cellini L., Azevedo F. and I. Rocha (2012). “Optimization and 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.
- Azevedo N. F., Bragança S. M., Simões L. C., Cerqueira L., Almeida C., Keevil C. W. and M. J. Vieira (2012). “Proposal for a method to estimate nutrient shock effects in bacteria”. BMC Research Notes 5(1):422.
- Sousa A. M., Ferreira A., Azevedo N., Pereira M. O. and A. Lourenço (2012). “Computational approaches to standard-compliant biofilm data for reliable analysis and integration”. Journal of Integrative Bioinformatics 9(3):203.
- Lourenço A., Ferreira A., Veiga N., Machado I., Pereira, M. O. and N. F. Azevedo (2012). “BiofOmics: a web platform for the systematic and standardized collection of high-throughput biofilm data”. PLoS ONE 7(6):e39960.
- Barreiros L., Peres J., Azevedo N. F., Manaia C. M. and O. C. Nunes (2012). “Environmental factors influencing molinate biodegradation by a two-member mixed culture in rice paddy field floodwater”. International Biodeterioration & Biodegradation 72:52-58.
- Lopes S. P., Ceri H., Azevedo N. F. and M. O. Pereira (2012). “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.
2011
- Azevedo N. F., Jardim T., Almeida C., Cerqueira L., Almeida A. J., Rodrigues F., Keevil C. W. and M. J. Vieira (2011). “Application of flow cytometry for the identification of Staphylococcus epidermidis labelled by peptide nucleic acid fluorescence in situ hybridization (PNA FISH) in blood samples”. Antonie van Leeuwenhoek 100(3):463-470.
- Cerqueira L., Fernandes R. M., Ferreira R. M., Carneiro F., Dinis-Ribeiro M., Figueiredo C., Keevil C. W., Azevedo N. F. and M. J. Vieira (2011). “PNA-FISH as a new diagnostic method for the determination of clarithromycin resistance of Helicobacter pylori”. BMC Microbiology 11:101.
- Almeida C., Azevedo N. F., Santos S., Keevil C. W. and M. J. Vieira. (2011). “Discriminating multi-species populations in biofilms with peptide nucleic acid fluorescence in situ hybridization (PNA FISH)”. PLoS ONE 6(3):e14786.
- Gião M. S., Azevedo N. F., Wilks S. A., Vieira M. J. and C. W. Keevil. (2011). “Interaction of Legionella pneumophila and Helicobacter pylori with bacterial species isolated from drinking water biofilms”. BMC Microbiology 11-57.
2010
- Almeida C., Azevedo N. F., Fernandes R. M., Keevil C. W. and M. J. Vieira. (2010). “Fluorescence in situ hybridization method using a peptide nucleic acid probe for the identification of Salmonella in a broad spectrum of samples”. Applied and Environmental Microbiology 76(13):4476-4485.
- Ferreira J. A., Azevedo N. F., Vieira M. J., Figueiredo C., Goodfellow B. J., Vitorino R., Monteiro A. and M. A. Coimbra. (2010). “Identification of cell-surface mannans in a virulent Helicobacter pylori strain”. Carbohydrate Research 345(6):715-860.
- Gião M. S., Azevedo N. F., Wilks S. A., Vieira M. J. and C. W. Keevil. (2010). “Effect of chlorine on the incorporation of Helicobacter pylori into drinking water biofilms”. Applied and Environmental Microbiology 76(5):1669-73.
2009
- Ferreira J. A., Pires C., Paulo M., Azevedo N. F., Domingues M. R., Vieira M. J., Monteiro A. and M. A. Coimbra. (2009). “Bioaccumulation of amylose-like glycans by Helicobacter pylori”. Helicobacter 14(6):559-570.
- Azevedo N. F., Huntington J. and K. Goodman. (2009). “The epidemiology of Helicobacter pylori and public health implications”. Helicobacter 14(Suppl 1):1-7. (Invited Review)
- Gião M. S., Wilks S. A., Azevedo N. F., Vieira M. J. and C. W. Keevil. (2009). “Validation of SYTO 9/Propidium Iodide uptake for rapid detection of viable but non-cultivable Legionella pneumophila”. Microbial Ecology 58(1):56-62.
- Almeida C., Azevedo N. F., Iversen C., Fanning S., Keevil C. W. and M. J. Vieira. (2009). “Development and application of a novel peptide nucleic acid probe for the specific detection of Cronobacter genomospecies (Enterobacter sakazakii) in powdered infant formula”. Applied and Environmental Microbiology 75(9):2925-2930.
- Gião M. S., Wilks S. A., Azevedo N. F., Vieira M. J. and C. W. Keevil. (2009). “Comparison between standard culture and peptide nucleic acid 16S rRNA hybridization quantification to study the influence of physico-chemical parameters on Legionella pneumophila survival in drinking water biofilms”. Biofouling 25(4):343-351.
- Gião M. S., Wilks S. A., Azevedo N. F., Vieira M. J. and C. W. Keevil. (2009). “Incorporation of natural uncultivable Legionella pneumophila into potable water biofilms provides a protective niche against chlorination stress”. Biofouling 25(4):335-41.
- Azevedo N. F., Lopes S. P., Keevil C. W., Pereira M. O. and M. J. Vieira. (2009). “Time to “go large” on biofilm research: advantages of an omics approach”. Biotechnology letters 31:477–485.
