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2023

  • Ribeiro I, Antunes JT, Alexandrino DAM, Tomasino MP, Almeida E, Hilário A, Urbatzka R, Leão PN, Mucha AP and Carvalho MF (2023) Actinobacteria from Arctic and Atlantic deep-sea sediments—Biodiversity and bioactive potential. Front. Microbiol. 14:1158441. doi: 10.3389/fmicb.2023.1158441
  • Coelho MC, Malcata FX, Silva CCG. Distinct Bacterial Communities in São Jorge Cheese with Protected Designation of Origin (PDO). Foods. 2023; 12(5):990. https://doi.org/10.3390/foods12050990
  • Paiva, Nuno M. L. and Ribeiro, Susana C. and Rosa, Henrique J. D. and Silva, Celia Costa Gomes, Comparative Study of the Bacterial Community of Organic and Conventional Milk. Available at SSRN: https://ssrn.com/abstract=4573793.
  • Duarte, S.; Vieira, P.E.; Leite, B.R.; Teixeira, M.A.L.; Neto, J.M.; Costa, F.O. Macrozoobenthos monitoring in Portuguese transitional waters in the scope of the water framework directive using morphology and DNA metabarcoding. Estuar. Coast. Shelf Sci. 2023, 281, 108207
  • Lavrador AS, Fontes JT, Vieira PE, Costa FO, Duarte S. Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. Diversity. 2023; 15(2):174. https://doi.org/10.3390/d15020174
  • Moutinho J, Carreira-Flores D, Gomes PT, Costa FO, Duarte S. Assessing the Seasonal and Spatial Dynamics of Zooplankton through DNA Metabarcoding in a Temperate Estuary. Animals. 2023; 13(24):3876. https://doi.org/10.3390/ani13243876
  • Leite BR, Duarte S, Troncoso JS, Costa FO. Artificial Seaweed Substrates Complement ARMS in DNA Metabarcoding-Based Monitoring of Temperate Coastal Macrozoobenthos. Diversity. 2023; 15(5):657. https://doi.org/10.3390/d15050657
  • Marques, J.; Ares, A.; Costa, J.; Marques, M.P.M.; de Carvalho, L.A.E.B.; Bessa, F. Plastisphere assemblages differ from the surrounding bacterial communities in transitional coastal environments. Sci. Total Environ. 2023, 869, 161703
  • Roxo, I., Amaral, A., Portugal, A. et al. A preliminary metabarcoding analysis of Portuguese raw honeys. Arch Microbiol 205, 386 (2023). https://doi.org/10.1007/s00203-023-03725-3
  • Esteves AR, Munoz-Pinto MF, Nunes-Costa D, Candeias E, Silva DF, Magalhães JD, Pereira-Santos AR, Ferreira IL, Alarico S, Tiago I, Empadinhas N, Cardoso SM. Footprints of a microbial toxin from the gut microbiome to mesencephalic mitochondria. Gut. 2023 Jan;72(1):73-89. doi: 10.1136/gutjnl-2021-326023. 
  • M.J.Ferreira, I.N., Sierra-Garcia, J. Cremades, C. António,  A.M. Rodrigues, D.C.G.A. Pinto, H. Silva, Â. Cunha. Biostimulation of Salicornia europaea L. crops with plant growth-promoting bacteria in laboratory and field conditions: effects on growth and metabolite profile. J. Appl. Microbiol., 134 (2023), doi:10.1093/jambio/lxad036
  • Bôto, M. L., Dias, S. M., Crespo, R. D., Mucha, A. P., & Almeida, C. M. R. (2023). Removing chemical and biological pollutants from swine wastewater through constructed wetlands aiming reclaimed water reuse. Journal of Environmental Management, 326, 116642. https://doi.org/10.1016/j.jenvman.2022.116642
  • Porras-Socias, Pau and Tomasino, Maria Paola and Fernandes, Joana P. and De Menezes, Alexandre B. and Fernández, Belén and Collins, Gavin and Alves, Maria João and Castro, Ricardo and Gomes, Carlos R. and Almeida, C. Marisa R. and Mucha, Ana Paula, Removal of Metals and Emergent Contaminants from Liquid Digestates in Constructed Wetlands for Agricultural Reuse. Available at SSRN: https://ssrn.com/abstract=4668623 or http://dx.doi.org/10.2139/ssrn.4668623
  • Ferreira MJ, Sierra-Garcia IN, Louvado A, Gomes NCM, Figueiredo S, Patinha C, Pinto DCGA, Cremades J, Silva H, Cunha A. 2023. Journal of Applied Microbiology, 134(8), lxad178,  https://doi.org/10.1093/jambio/lxad178
  • Usié, A., Serra, O., Barros, P.M. et al. An improved reference genome and first organelle genomes of Quercus suber. Tree Genetics & Genomes 19, 54 (2023). https://doi.org/10.1007/s11295-023-01624-8.
  • Albuquerque A, Garrido N, Charneca R, Egas C, Martin L, Ramos A, Costa F, Marmelo C, Martins JM. Influence of Sex and a High-Fiber Diet on the Gut Microbiome of Alentejano Pigs Raised to Heavy Weights. Veterinary Sciences. 2023; 10(11):641. https://doi.org/10.3390/vetsci10110641
  • Ordóñez, C.D., Mayoral-Campos, C., Egas, C., Redrejo-Rodríguez, M. A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences, NAR Genomics and Bioinformatics, Volume 5, Issue 3, September 2023, lqad073, https://doi.org/10.1093/nargab/lqad073
  • Martins, D., Egas, C., Arrais, J.P. (2023). The Impact of Schizophrenia Misdiagnosis Rates on Machine Learning Models Performance. In: Rocha, M., Fdez-Riverola, F., Mohamad, M.S., Gil-González, A.B. (eds) Practical Applications of Computational Biology and Bioinformatics, 17th International Conference (PACBB 2023). PACBB 2023. Lecture Notes in Networks and Systems, vol 743. Springer, Cham. https://doi.org/10.1007/978-3-031-38079-2_1
  • Cardoso JMS, Esteves I, Egas C, Braga MEM, de Sousa HC, Abrantes I and Maleita C (2023) Transcriptome analysis reveals the high ribosomal inhibitory action of 1,4-naphthoquinone on Meloidogyne luci infective second-stage juveniles. Front. Plant Sci. 14:1191923. doi: 10.3389/fpls.2023.1191923
  • Pessoa J, Belew GD, Barroso C, Egas C, Jones JG. The Gut Microbiome Responds Progressively to Fat and/or Sugar-Rich Diets and Is Differentially Modified by Dietary Fat and Sugar. Nutrients. 2023; 15(9):2097. https://doi.org/10.3390/nu15092097
  • Sinninghe Damsté JS, Rijpstra WIC, Huber KJ, Albuquerque L, Egas C, Bale NJ (2023) Dominance of mixed ether/ester, intact polar membrane lipids in five species of the order Rubrobacterales: another group of bacteria not obeying the “lipid divide.” Syst Appl Microbiol 46(2):126404. https://doi.org/10.1016/j.syapm.2023.126404
  • Garcia-Pelaez, J., Barbosa-Matos, R., Lobo, S., Dias, A., Garrido, L., Castedo, S., Sousa, S., Pinheiro, H., Sousa, L., Monteiro, R., Maqueda, J.J., Fernandes, S., Carneiro, F., Pinto, N., Lemos, C., Pinto, C., Teixeira, M.R., Aretz, S., Bajalica-Lagercrantz, S., Balmaña, J., Blatnik, A., Benusiglio, P.R., Blanluet, M.,  Bours, V., Brems, H., Brunet, J., Calistri, D., Capellá, G., Carrera, S., Colas, C., Dahan, K., de Putter, R., Desseignés, C., Domínguez-Garrido, E., Egas, C., Evans, D.G., Feret, D., Fewings, E., Fitzgerald, R.C., Florence, C., Garcia-Barcina, M., Genuardi, M.,  Golmard, L., Hackmann, K., Hanson, H., Holinski-Feder, E., Hüneburg, R., Krajc, M., Lagerstedt-Robinson, R., Lázaro, C., Ligtenberg, M.J.L, Martínez-Bouzas, C., Merino, S., Michils, G., Novaković, S., Patiño-García, S., Ranzani, G.N., Schröck, E., Silva, I., Silveira, C., Soto, J.L., Spier, I., Steinke-Lange, V., Tedaldi, G., Tejada, M-I., Woodward, E.R., Tischkowitz, M., Hoogerbrugge, N., Oliveira, C. (2022). A genotype-first approach in carriers of CDH1 rare germline variants: a European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS) multicentre study. Lancet Oncology.
  • Almeida, J.F.; Marques, M.; Oliveira, V.; Egas, C.; Mil-Homens, D.; Viana, R.; Cleary, D.F.R.; Huang, Y.M.; Fialho, A.M.; Teixeira, M.C.; Gomes, N.C.M.; Costa, R.; Keller-Costa, T. Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human Pathogens. Mar. Drugs.
  • Beatriz M, Rodrigues RJ, Vilaça R, Egas C, Pinheiro PS, Daley GQ, Schlaeger TM, Raimundo N, Rego AC, Lopes C. Extracellular vesicles improve GABAergic transmission in Huntington's disease iPSC-derived neurons. Theranostics. 2023 Jun 26;13(11):3707-3724. doi: 10.7150/thno.81981.
  • Albuquerque L, and Egas C. Miltoncostaeales. In: Trujillo ME, Dedysh S, De Vos P, Hedlund B, Kämpfer P, Rainey, FA, Whitman WB (Eds), 2023. Bergey's Manual of Systematics of Archaea and Bacteria. Published by John Wiley & Sons, Inc., in association with Bergey's Manual Trust.
  • Albuquerque L, and Egas C. Gaiellaceae. In: Trujillo ME, Dedysh S, De Vos P, Hedlund B, Kämpfer P, Rainey, FA, Whitman WB (Eds), 2023, Bergey's Manual of Systematics of Archaea and Bacteria. Published by John Wiley & Sons, Inc., in association with Bergey's Manual Trust.
  • Albuquerque L, and Egas C. Miltoncostaea. In: Trujillo ME, Dedysh S, De Vos P, Hedlund B, Kämpfer P, Rainey, FA, Whitman WB (Eds), 2023, Bergey's Manual of Systematics of Archaea and Bacteria. Published by John Wiley & Sons, Inc., in association with Bergey's Manual Trust.
  • Albuquerque L, and Egas C. Gaiellales. In: Trujillo ME, Dedysh S, De Vos P, Hedlund B, Kämpfer P, Rainey, FA, Whitman WB (Eds), 2023, Bergey's Manual of Systematics of Archaea and Bacteria. Published by John Wiley & Sons, Inc., in association with Bergey's Manual Trust.
  • Albuquerque L, and Egas C. Calidithermus. In: Trujillo ME, Dedysh S, De Vos P, Hedlund B, Kämpfer P, Rainey, FA, Whitman WB (Eds), 2023, Bergey's Manual of Systematics of Archaea and Bacteria. Published by John Wiley & Sons, Inc., in association with Bergey's Manual Trust.
  • Albuquerque L, and Egas C. Miltoncostaeaceae. In: Trujillo ME, Dedysh S, De Vos P, Hedlund B, Kämpfer P, Rainey, FA, Whitman WB (Eds), 2023, Bergey's Manual of Systematics of Archaea and Bacteria. Published by John Wiley & Sons, Inc., in association with Bergey's Manual Trust.

 

2022

  • Adrião A, Santana I, Ribeiro C, Cancela ML, Conceição N, Grazina M. Identification of a novel mutation in MEF2C gene in an atypical patient with frontotemporal lobar degeneration. Neurol Sci. 2022;43(1):319-326. doi:10.1007/S10072-021-05269-0/FIGURES/5
  • Almeida JF, Marques M, Oliveira V, et al. Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human Pathogens. Mar Drugs. 2022;21(1):34. doi:10.3390/MD21010034/S1
  • Bastos Almeida D, Semedo M, Magalhães C, Blanquet I, Mucha AP. The network of nitrifying and pathogenic prokaryotic interactions in a recirculating aquaculture system of a sole (Solea senegalensis) hatchery. Front Mar Sci. 2022;9:2445. doi:10.3389/FMARS.2022.1038196/BIBTEX
  • Beatriz M, Rodrigues R, Vilaça R, et al. Extracellular vesicles improve GABAergic transmission in Huntington’s disease iPSC-derived neurons. bioRxiv. December 2022:2022.12.18.520919. doi:10.1101/2022.12.18.520919
  • Cardoso H, Campos C, Grzebelus D, Egas C, Peixe A. Understanding the Role of PIN Auxin Carrier Genes under Biotic and Abiotic Stresses in Olea europaea L. Biol 2022, Vol 11, Page 1040. 2022;11(7):1040. doi:10.3390/BIOLOGY11071040
  • Castro J, Costa D, Tavares RM, Baptista P, Lino-Neto T. Olive Fungal Epiphytic Communities Are Affected by Their Maturation Stage. Microorg 2022, Vol 10, Page 376. 2022;10(2):376. doi:10.3390/MICROORGANISMS10020376
  • Costa D, Tavares RM, Baptista P, Lino-Neto T. The influence of bioclimate on soil microbial communities of cork oak. BMC Microbiol. 2022;22(1):1-17. doi:10.1186/S12866-022-02574-2/FIGURES/7
  • Costa J, Sierra-Garcia IN, Cunha A. A Culture-Independent Comparison of Microbial Communities of Two Maturating Craft Beers Styles. Microbiol Biotechnol Lett. 2022;50(3):404-413. doi:10.48022/mbl.2204.04002
  • de Figueiredo DR, Lopes AR, Pereira MJ, et al. Bacterioplankton Community Shifts during a Spring Bloom of Aphanizomenon gracile and Sphaerospermopsis aphanizomenoides at a Temperate Shallow Lake. Hydrobiology. 2022;1(4):499-517. doi:10.3390/hydrobiology1040030
  • Guerra V, Tiago I, Aires A, et al. The gastrointestinal microbiome of browsing goats (Capra hircus). PLoS One. 2022;17(10):e0276262. doi:10.1371/journal.pone.0276262
  • Hageskal G, Heggeset TMB, Nguyen GS, et al. Flow-based method for biofilm microbiota enrichment and exploration of metagenomes. AMB Express. 2022;12(1):1-11. doi:10.1186/S13568-022-01377-Y/FIGURES/5
  • Lopes AR, Bunin E, Viana AT, et al. In silico prediction of the enzymes involved in the degradation of the herbicide molinate by Gulosibacter molinativorax ON4T. Sci Rep. 2022;12(1):15502. doi:10.1038/s41598-022-18732-5
  • Paiva DS, Fernandes L, Trovão J, Mesquita N, Tiago I, Portugal A. Uncovering the Fungal Diversity Colonizing Limestone Walls of a Forgotten Monument in the Central Region of Portugal by High-Throughput Sequencing and Culture-Based Methods. Appl Sci. 2022;12(20):10650. doi:10.3390/APP122010650/S1
  • Ribeirinho-Soares S, Moreira NFF, Graça C, Pereira MFR, Silva AMT, Nunes OC. Overgrowth control of potentially hazardous bacteria during storage of ozone treated wastewater through natural competition. Water Res. 2022;209:117932. doi:10.1016/J.WATRES.2021.117932
  • Ribeiro H, Wijaya IMW, Soares-Santos V, et al. Microbial community composition, dynamics, and biogeochemistry during the start-up of a partial nitritation-anammox pathway in an upflow reactor. Sustain Environ Res. 2022;32(1):1-11. doi:10.1186/S42834-022-00130-1/FIGURES/4
  • Sanches-Fernandes GMM, Califano G, Castanho S, et al. Effects of live feed manipulation with algal-derived antimicrobial metabolites on fish larvae microbiome assembly: A molecular-based assessment. Aquac Res. 2022;53(3):1062-1083. doi:10.1111/ARE.15648
  • Serra D, Henriques JF, Sousa FJ, et al. Attenuation of Autism-like Behaviors by an Anthocyanin-Rich Extract from Portuguese Blueberries via Microbiota–Gut–Brain Axis Modulation in a Valproic Acid Mouse Model. Int J Mol Sci 2022, Vol 23, Page 9259. 2022;23(16):9259. doi:10.3390/IJMS23169259
  • Silva NC, Madureira AR, Pintado M, Moreira PR. Biocontamination and diversity of epilithic bacteria and fungi colonising outdoor stone and mortar sculptures. Appl Microbiol Biotechnol. 2022;106(9-10):3811-3828. doi:10.1007/S00253-022-11957-4/FIGURES/7
  • Soares F, Trovão J, Portugal A. Phototrophic and fungal communities inhabiting the Roman cryptoporticus of the national museum Machado de Castro (UNESCO site, Coimbra, Portugal). World J Microbiol Biotechnol. 2022;38(9):157. doi:10.1007/s11274-022-03345-x

2021

  • Adrião A, Santana I, Ribeiro C, Cancela ML, Conceição N, Grazina M. Identification of a novel mutation in MEF2C gene in an atypical patient with frontotemporal lobar degeneration. Neurol Sci. 2021:1-8. doi:10.1007/s10072-021-05269-0
  • Albuquerque L, Egas C. Ampullimonas. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2021:1-7. doi:10.1002/9781118960608.gbm01905
  • Albuquerque L, Egas C. Raineya. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2021:1-8. doi:10.1002/9781118960608.gbm01902
  • Albuquerque L, Egas C. Tepidimonas. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2021:1-18. doi:10.1002/9781118960608.gbm00959.pub2
  • Alexandrino, D. A. M., Mucha, A. P., Tomasino, M. P., Almeida, C. M. R., & Carvalho, M. F. (2021). Combining Culture-Dependent and Independent Approaches for the Optimization of Epoxiconazole and Fludioxonil-Degrading Bacterial Consortia. Microorganisms 2021, Vol. 9, Page 2109, 9(10), 2109. doi:10.3390/MICROORGANISMS9102109
  • Almeida DB, Magalhães C, Sousa Z, et al. Microbial community dynamics in a hatchery recirculating aquaculture system (RAS) of sole (Solea senegalensis). Aquaculture. 2021;539:736592. doi:10.1016/J.AQUACULTURE.2021.736592
  • Ares A, Costa J, Joaquim C, et al. Effect of Low-Input Organic and Conventional Farming Systems on Maize Rhizosphere in Two Portuguese Open-Pollinated Varieties (OPV), “Pigarro” (Improved Landrace) and “SinPre” (a Composite Cross Population). Front Microbiol. 2021;0:173. doi:10.3389/FMICB.2021.636009
  • Bellisario B, Fais M, Duarte S, Vieira PE, Canchaya C, Costa FO. The spatial network structure of intertidal meiofaunal communities derived from environmental DNA metabarcoding surveys in Northwest Iberia. bioRxiv. 2021:2021.03.16.435605. doi:10.1101/2021.03.16.435605
  • Bôto ML, Magalhães C, Perdigão R, et al. Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast. Front Microbiol. 2021;0:879. doi:10.3389/FMICB.2021.633659
  • Esteves, A Raquel, Mário F Munoz-Pinto, Daniela Nunes-Costa, Emanuel Candeias, Diana F Silva, João D Magalhães, A Raquel Pereira-Santos, et al. 2021. “Footprints of a Microbial Toxin from the Gut Microbiome to Mesencephalic Mitochondria.” Gut 0 (November): gutjnl-2021-326023. doi:10.1136/GUTJNL-2021-326023.
  • Leal C, Fontaine F, Aziz A, Egas C, Clément C, Trotel-Aziz P. Genome sequence analysis of the beneficial Bacillus subtilis PTA-271 isolated from a Vitis vinifera (cv. Chardonnay) rhizospheric soil: assets for sustainable biocontrol. Environ Microbiomes. 2021;16(1):1-14. doi:10.1186/s40793-021-00372-3
  • Miguel-Ruano V, Rivera I, Rajkovic J, et al. Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family. Comput Struct Biotechnol J. 2021;19:1214-1232. doi:10.1016/J.CSBJ.2021.01.047
  • Montenegro IPFM, Mucha AP, Tomasino MP, Gomes CR, Almeida CMR. Alkylphenols and Chlorophenols Remediation in Vertical Flow Constructed Wetlands: Removal Efficiency and Microbial Community Response. Water 2021, Vol 13, Page 715. 2021;13(5):715. doi:10.3390/W13050715
  • Moreira NFF, Ribeirinho-Soares S, Viana AT, et al. Rethinking water treatment targets: Bacteria regrowth under unprovable conditions. Water Res. 2021;201. doi:10.1016/j.watres.2021.117374
  • Nones, Stefano, Fernanda Simões, Cândida Sofia Trindade, José Matos, and Edmundo Sousa. 2021. “Microbiome Associated with the Mycangia of Female and Male Adults of the Ambrosia Beetle Platypus Cylindrus Fab. (Coleoptera: Curculionidae).” Insects 2021, Vol. 12, Page 881 12 (10): 881. doi:10.3390/INSECTS12100881.
  • Oliveira, Jacinta M.M., Isabel Henriques, Daniel S. Read, Hyun S. Gweon, Rui G. Morgado, Sara Peixoto, António Correia, Amadeu M.V.M. Soares, and Susana Loureiro. 2021. “Gut and Faecal Bacterial Community of the Terrestrial Isopod Porcellionides Pruinosus: Potential Use for Monitoring Exposure Scenarios.” Ecotoxicology 2021 30:10 30 (10): 2096–2108. doi:10.1007/S10646-021-02477-4.
  • Picó C, Reis F, Egas C, Mathias P, Matafome P. Lactation as a Programming Window for Metabolic Syndrome. Blackwell Publishing Ltd; 2021:13482. doi:10.1111/eci.13482
  • Rocha, Rui, Manuela Vaz Velho, Joana Santos, and Paulo Fernandes. 2021. “Serra Da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing.” Microorganisms 2021, Vol. 9, Page 2007 9 (10): 2007doi:10.3390/MICROORGANISMS9102007.
  • Semedo M, Lopes E, Baptista MS, et al. Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific. Front Microbiol. February 2021:319. doi:10.3389/FMICB.2021.624071
  • Tomasino, Maria Paola, Mariana Aparício, Inês Ribeiro, Filipa Santos, Miguel Caetano, C. Marisa R. Almeida, Maria de Fátima Carvalho, and Ana P. Mucha. 2021. “Diversity and Hydrocarbon-Degrading Potential of Deep-Sea Microbial Community from the Mid-Atlantic Ridge, South of the Azores (North Atlantic Ocean).” Microorganisms 2021, Vol. 9, Page 2389 9 (11): 2389. doi:10.3390/MICROORGANISMS9112389.

2020

  • Albuquerque L, Castelhano N, Raposo P, et al. Comparative genome sequence analysis of several species in the genus tepidimonas and the description of a novel species tepidimonas charontis sp. Nov. Int J Syst Evol Microbiol. 2020;70(3):1596-1604. doi:10.1099/ijsem.0.003942
  • Albuquerque L, Egas C, Costa MS. Schleiferia. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2020:1-6. doi:10.1002/9781118960608.gbm01901
  • Albuquerque L, Egas C, Costa MS. Schleiferiaceae. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2020:1-2. doi:10.1002/9781118960608.fbm00369
  • Albuquerque L, Egas C, Froufe HJC, Costa MS. Hydrotalea. In: Kämpfer P, ed. Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2020:1-8. doi:10.1002/9781118960608.gbm01442
  • Albuquerque L, Egas C. Cavicella. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2020:1-6. doi:10.1002/9781118960608.gbm01904
  • Albuquerque L, Egas C. Heliimonas. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2020:1-6. doi:10.1002/9781118960608.gbm01903
  • Albuquerque L, Egas C. Oceanicella. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2020:1-8. doi:10.1002/9781118960608.gbm01899
  • Albuquerque L, Egas C. Raineyaceae. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2020:1-1. doi:10.1002/9781118960608.fbm00370
  • Almeida PM, MJ Simoes, J Sa, J Pereira, C Ribeiro, H Froufe, C Egas, S Pinto, C Correia, JM Saraiva, F Ramos 2020. A new case with a splicing PIEZO2 mutation causing distal arthrogryposis with distal muscle weakness, scoliosis and proprioception defects. MEDICINE 99 (9).
  • Ferreira LL, Cervantes M, Froufe HJC, et al. Doxorubicin persistently rewires cardiac circadian homeostasis in mice. Arch Toxicol. 2020. doi:10.1007/s00204-019-02626-z
  • Garcia-Pelaez J, AR Monteiro, L Sousa, H Pinheiro, S Castedo, L Garrido, M Teixeira, G Michils, V Bours, R de Putter, L Golmard, M Blanluet, C Colas, P Benusiglio, S Aretz, I Spier, R Hueneburg, L Gieldon, E Schroeck, E Holinski-Feder, V Steinke, D Calistri, G Tedaldi, GN Ranzani, M Genuardi, C Silveira, I Silva, M Krajc, AB, S Novakovic, A Patino-Garcia, JL Soto, C Lazaro, G Capella, J Brunet-Vidal, J Balmana, E Dominguez-Garrido, M Ligtenberg, E Fewings, RC Fitzgerald, ER Woodward, G Evans, H Hanson, K Lagerstedt-Robinson, S Bajalica-Lagercrantz, C Egas, MI Tejada, C Martinez-Bouzas, S Merino, S Carrera, M Garcia-Bercina, K Dahan, D Feret, N Hoogerbrugge, M Tischkowitz, C Oliveira. 2020. The first genotype-phenotype study of European carriers of CDH1 germline mutations. MEDICINE 99 (9).
  • Pinho D, Barroso C, Froufe H, et al. Linking Tree Health, Rhizosphere Physicochemical Properties, and Microbiome in Acute Oak Decline. 2020;11(11):1153. https://www.mdpi.com/1999-4907/11/11/1153. Accessed April 5, 2021.
  • Ribeiro C, SB Sousa, MC Macario, L Diogo, J Mendes, MJ Simoes, H Froufe, C Egas, S Pinto, C Correia, HC Silva, JM Saraiva, M Venancio. 2020. The mildest known phenotype in a patient with GFM1 biallelic variant: case report and literature review. MEDICINE 99 (9).
  • Rosas CS, B Campos-Xavier, J de Sa, MJ Simoes, H Froufe, C Egas, S Pinto, C Correia, J Pereira, L Ramos, JM Saraiva, AL Carvalho. 2020. Novel POGZ gene truncating variant: a case report of syndromic intellectual disability. MEDICINE 99 (9).
  • Salgado JR, J Pereira, M McEntagart, S Mansour, P Daubney, R Power, C Hall, B Campos-Xavier, C Egas, H Froufe, MJose Simoes, C Gomes, JM Saraiva, SB Sousa. 2020. Cardiospondylocarpofacial syndrome as a distinct hereditary connective tissue disorder: novel missense variant in MAP3K7 in two unrelated patients. MEDICINE 99 (9)
  • Simoes MJ, C Barroso, AL Carvalho, S Ribeiro, JM Saraiva, C Egas. 2020. CYP1B1 mutational screening in a Portuguese cohort of congenital glaucoma patients. MEDICINE 99 (9).
  • Simoes MJ, PM Almeida, H Froufe, S Magalhaes, D Martins, S Pinto, C Correia, J Pereira, A Oliveira, SB Sousa, C Egas. 2020. A novel splicing FOXP1variant found in a patient with syndromic intellectual disability through the GenoinVar end-to-end solution. MEDICINE 99 (9).
  • Varandas R, Egas C, Conceição IL. Potato cyst nematodes: New solutions to an old problem. Crop Prot. 2020;137. doi:10.1016/j.cropro.2020.105303
  • Young TL, Whisenhunt KN, Jin J, et al. SVEP1 as a genetic modifier of TEK-Related primary congenital glaucoma. Investig Ophthalmol Vis Sci. 2020;61(12):6-6. doi:10.1167/IOVS.61.12.6

2019

  • Albuquerque L, Egas C, Costa MS. Rubritepida. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2019:1-7. doi:10.1002/9781118960608.gbm01457
  • Albuquerque L, Rainey FA, Egas C, et al. Cecembia. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2019:1-12. doi:10.1002/9781118960608.gbm01443
  • Almeida AR, Alves M, Domingues I, Henriques I. The impact of antibiotic exposure in water and zebrafish gut microbiomes: A 16S rRNA gene-based metagenomic analysis. Ecotoxicol Environ Saf. 2019;186:109771. doi:10.1016/J.ECOENV.2019.109771
  • Almeida D, Sousa Z, Magalhães C, Silva E, Blanquet I, Mucha A P. Water microbiota in a recirculating aquaculture system for environmental sustainability and fish welfare. :2019-00633. doi:10.1093/nar/gks1219
  • Bragança I, Mucha AP, Tomasino MP, et al. Deltamethrin impact in a cabbage planted soil: Degradation and effect on microbial community structure. Chemosphere. 2019;220:1179-1186. doi:10.1016/J.CHEMOSPHERE.2019.01.004
  • Costa MS, Albuquerque L, Rainey FA, et al. Elioraea. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley; 2019:1-6. doi:10.1002/9781118960608.gbm01458
  • Fernandes T, Vaz-Moreira I, Manaia CM. Neighbor urban wastewater treatment plants display distinct profiles of bacterial community and antibiotic resistance genes. Environ Sci Pollut Res 2019 2611. 2019;26(11):11269-11278. doi:10.1007/S11356-019-04546-Y
  • Grehs BWN, Lopes AR, Moreira NFF, et al. Removal of microorganisms and antibiotic resistance genes from treated urban wastewater: A comparison between aluminium sulphate and tannin coagulants. Water Res. 2019;166:115056. doi:10.1016/J.WATRES.2019.115056
  • Mahmoudi N, Cruz C, Mahdhi M, Mars M, Caeiro MF. Arbuscular mycorrhizal fungi in soil, roots and rhizosphere of Medicago truncatula: Diversity and heterogeneity under semi-arid conditions. PeerJ. 2019;2019(3). doi:10.7717/PEERJ.6401
  • Paiva de Carvalho H, Sequeira SO, Pinho D, et al. Combining an innovative non-invasive sampling method and high-throughput sequencing to characterize fungal communities on a canvas painting. Int Biodeterior Biodegrad. 2019;145. doi:10.1016/j.ibiod.2019.104816
  • Pereira R, Barbosa T, Gales L, et al. Clinical and Genetic Analysis of Children with Kartagener Syndrome. Cells 2019, Vol 8, Page 900. 2019;8(8):900. doi:10.3390/CELLS8080900
  • Raposo P, Viver T, Albuquerque L, et al. Transfer of meiothermus chliarophilus (Tenreiro et al.1995) Nobre et al. 1996, meiothermus Roseus Ming et al. 2016, meiothermus terrae Yu et al. 2014 and meiothermus timidus Pires et al. 2005, to calidithermus gen. nov., as calidithermus chliarophilus com. Int J Syst Evol Microbiol. 2019. doi:10.1099/ijsem.0.003270
  • Reis AC, Kolvenbach BA, Chami M, et al. Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader “Candidatus Leucobacter sulfamidivorax” strain GP. BMC Genomics. 2019;20(1). doi:10.1186/s12864-019-6206-z
  • Severino R, Froufe HJC, Barroso C, et al. High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum Actinobacteria. Microbiologyopen. 2019;8(9). doi:10.1002/mbo3.840
  • Trovão J, Tiago I, Soares F, et al. High-Quality Draft Genome Sequence of the Microcolonial Black Fungus Aeminium ludgeri DSM 106916. 2019. doi:10.1128/MRA.00202-19

2018

  • Albuquerque L, Froufe H, Egas C, Rainey FA, Costa MS. Albidovulum. In: Bergey’s Manual of Systematics of Archaea and Bacteria. Chichester, UK: John Wiley & Sons, Ltd; 2018:1-8. doi:10.1002/9781118960608.gbm01456
  • Albuquerque L, Polónia ARM, Barroso C, et al. Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum bacteroidetes and the description of raineyaceae fam. nov. Int J Syst Evol Microbiol. 2018;68(4):982-989. doi:10.1099/ijsem.0.002556
  • Amorim CL, Alves M, Castro PML, Henriques I. Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals. Ecotoxicol Environ Saf. 2018;147:905-912. doi:10.1016/J.ECOENV.2017.09.060
  • Barros I, Froufe H, Marnellos G, et al. Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure. AIMS Microbiol. 2018;4(2):240-260. doi:10.3934/microbiol.2018.2.240
  • Bettencourt, R; Barros, I; Martins, E; Martins, I; Cerqueira, T; Colaco, A; Costa, V; Rosa, D; Froufe, H; Egas, C; Stefanni, S; Dando, PR; Santos R. An Insightful Model to Study Innate Immunity and Stress Response in Deep‐Sea Vent Animals: Profiling the Mussel Bathymodiolus azoricus. In: Ray S, ed. Organismal and Molecular Malacology. Rijek:  Intech; 2017:141-187. http://plymsea.ac.uk/7500/.
  • Cardoso JMS, Fonseca L, Egas C, Abrantes I. Cysteine proteases secreted by the pinewood nematode, Bursaphelenchus xylophilus: In silico analysis. Comput Biol Chem. 2018;77:291-296. doi:10.1016/j.compbiolchem.2018.10.011
  • Cerqueira T, Barroso C, Froufe H, Egas C, Bettencourt R. Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields. Microb Ecol. 2018;76(2):387-403. doi:10.1007/s00248-018-1144-x
  • Dias L, Rosado T, Coelho A, et al. Natural limestone discolouration triggered by microbial activity—a contribution. AIMS Microbiol. 2018;4(4):594. doi:10.3934/MICROBIOL.2018.4.594
  • Gonçalves MTP, Benito MJ, Córdoba M de G, et al. Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis. J Food Sci. 2018;83(5):1333-1341. doi:10.1111/1750-3841.14141
  • Margesin R, Albuquerque L, Zhang D-C, et al. Solimicrobium silvestre gen. nov., sp. nov., isolated from alpine forest soil. Int J Syst Evol Microbiol. June 2018. doi:10.1099/ijsem.0.002861
  • Margesin R, Zhang D-C, Albuquerque L, Froufe HJC, Egas C, da Costa MS. Lysobacter silvestris sp. nov., isolated from alpine forest soil, and reclassification of Luteimonas tolerans as Lysobacter tolerans comb. nov. Int J Syst Evol Microbiol. 2018;68(5):1571-1577. doi:10.1099/ijsem.0.002710
  • Moreira NFF, Narciso-da-Rocha C, Polo-López MI, et al. Solar treatment (H2O2, TiO2-P25 and GO-TiO2 photocatalysis, photo-Fenton) of organic micropollutants, human pathogen indicators, antibiotic resistant bacteria and related genes in urban wastewater. Water Res. 2018;135:195-206. doi:10.1016/J.WATRES.2018.01.064
  • Narciso-da-Rocha C, Rocha J, Vaz-Moreira I, et al. Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant. Environ Int. 2018;118:179-188. doi:10.1016/J.ENVINT.2018.05.040
  • Pinto C, Sousa S, Froufe H, et al. Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain Fito-F321, an endophyte microorganism from Vitis vinifera with biocontrol potential. Stand Genomic Sci. 2018;13(1). doi:10.1186/s40793-018-0327-x
  • Ramos AM, Usié A, Barbosa P, et al. The draft genome sequence of cork oak. Sci Data. 2018;5:180069. doi:10.1038/sdata.2018.69
  • Ribeiro T, Cardoso V, Ferreira LMA, et al. Xylo-oligosaccharides display a prebiotic activity when used to supplement wheat or corn-based diets for broilers. Poult Sci. 2018;97(12):4330-4341. doi:10.3382/PS/PEY336

2017

  • Almeida CMR, Oliveira T, Reis I, Gomes CR, Mucha AP. Bacterial community dynamic associated with autochthonous bioaugmentation for enhanced Cu phytoremediation of salt-marsh sediments. Mar Environ Res. 2017;132:68-78. doi:10.1016/J.MARENVRES.2017.10.007
  • Antweiler K, Schreiter S, Keilwagen J, et al. Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils. Microb Biotechnol. 2017;10(2):434-449. doi:10.1111/1751-7915.12595
  • Becerra-Castro C, Lopes AR, Teixeira S, et al. Characterization of bacterial communities from Masseiras, a unique Portuguese greenhouse agricultural system. Antonie Van Leeuwenhoek. 2017;110(5):665-676. doi:10.1007/s10482-017-0833-7
  • Bettencourt R, Barros I, Martins E, et al. An Insightful Model to Study Innate Immunity and Stress Response in Deep‐Sea Vent Animals: Profiling the Mussel Bathymodiolus azoricus. In: Organismal and Molecular Malacology. InTech; 2017. doi:10.5772/68034
  • Califano G, Castanho S, Soares F, et al. Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery. Front Microbiol. 2017;8:204. doi:10.3389/fmicb.2017.00204
  • Carmona S, da Luz Freitas M, Froufe H, et al. Novel de novo FOXC1 nonsense mutation in an Axenfeld-Rieger syndrome patient. Am J Med Genet Part A. 2017;173(6):1607-1610. doi:10.1002/ajmg.a.38234
  • Cerqueira T, Pinho D, Froufe H, Santos RS, Bettencourt R, Egas C. Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores. Microb Ecol. 2017;74(2):332-349. doi:10.1007/s00248-017-0943-9
  • Cleary DFR, Coelho FJRC, Oliveira V, Gomes NCM, Polónia ARM. Sediment depth and habitat as predictors of the diversity and composition of sediment bacterial communities in an inter-tidal estuarine environment. Mar Ecol. March 2017. doi:10.1111/maec.12411
  • Duarte A, Maleita C, Egas C, Abrantes I, Curtis R. Significant effects of RNAi silencing of the venom allergen-like protein ( Mhi-vap-1 ) of the root-knot nematode Meloidogyne hispanica in the early events of infection. Plant Pathol. February 2017. doi:10.1111/ppa.12673
  • Engelen AH, Costa J, Bermejo R, Marba N, Duarte CM, Serrão EA. A population genetics toolbox for the threatened canopy-forming brown seaweeds Cystoseira tamariscifolia and C. amentacea (Fucales, Sargassaceae). J Appl Phycol. 2017;29(1):627-629. doi:10.1007/s10811-016-0964-7
  • Gaspar D, Trindade C, Usié A, et al. Expression Profiling in Pinus pinaster in Response to Infection with the Pine Wood Nematode Bursaphelenchus xylophilus. Forests. 2017;8(8):279. doi:10.3390/f8080279
  • Gonçalves Dos Santos MTP, Benito MJ, Córdoba M de G, Alvarenga N, Ruiz-Moyano Seco de Herrera S. Yeast community in traditional Portuguese Serpa cheese by culture-dependent and -independent DNA approaches. Int J Food Microbiol. 2017;262:63-70. doi:10.1016/J.IJFOODMICRO.2017.09.013
  • Hollatz C, Leite BR, Lobo J, Froufe H, Egas C, Costa FO. Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities. Chain F, ed. Genome. 2017;60(3):260-271. doi:10.1139/gen-2015-0220
  • Leite BR, Hollatz C, Lobo J, Froufe H, Egas C, Costa FO. Impact of sequencing platform, target amplicon, and OTU-clustering on DNA metabarcoding of mock communities of marine macrobenthos. Genome. 2017;60(11):961-963.
  • Martins I, Goulart J, Martins E, et al. Physiological impacts of acute Cu exposure on deep-sea vent mussel Bathymodiolus azoricus under a deep-sea mining activity scenario. Aquat Toxicol. 2017;193:40-49. doi:10.1016/J.AQUATOX.2017.10.004
  • Monteiro M, Séneca J, Torgo L, et al. Environmental controls on estuarine nitrifying communities along a salinity gradient. Aquat Microb Ecol. 2017;80(2):167-180. doi:10.3354/ame01847
  • Narciso-da-Rocha C, Manaia CM. The influence of the autochthonous wastewater microbiota and gene host on the fate of invasive antibiotic resistance genes. Sci Total Environ. 2017;575:932-940. doi:10.1016/j.scitotenv.2016.09.157
  • Neiva J, Serrão EA, Anderson L, et al. Cryptic diversity, geographical endemism and allopolyploidy in NE Pacific seaweeds. BMC Evol Biol. 2017;17(1):30. doi:10.1186/s12862-017-0878-2
  • Pimentel T, Marcelino J, Ricardo F, Soares AMVM, Calado R. Bacterial communities 16S rDNA fingerprinting as a potential tracing tool for cultured seabass Dicentrarchus labrax. Sci Rep. 2017;7(1):11862. doi:10.1038/s41598-017-11552-y
  • Pinheiro AM, Carreira A, Prescott TAK, Ferreira RB, Monteiro SA. Bridging the Gap to Non-toxic Fungal Control: Lupinus-Derived Blad-Containing Oligomer as a Novel Candidate to Combat Human Pathogenic Fungi. Front Microbiol. 2017;8:1182. doi:10.3389/fmicb.2017.01182
  • Ramos VMC, Castelo-Branco R, Leão PN, et al. Cyanobacterial Diversity in Microbial Mats from the Hypersaline Lagoon System of Araruama, Brazil: An In-depth Polyphasic Study. Front Microbiol. 2017;8:1233. doi:10.3389/fmicb.2017.01233
  • Reis F, Pereira E, Tavares R, Baptista P, Lino-Neto T. Fungal community in chestnut orchards with different Hypholoma fasciculare aboveground abundance: potential implications for sustainable production. Rev Ciências Agrárias. 2017;40(1):124-132. doi:10.19084/RCA15153
  • Simões MJ, Carmona S, Roberts R, et al. CYP1B1 mutational screening in a Portuguese cohort of primary congenital glaucoma patients. Ophthalmic Genet. 2017;38(2):197-199. doi:10.1080/13816810.2016.1188121
  • Teixeira RT, Fortes AM, Bai H, Pinheiro C, Pereira H. Transcriptional profiling of cork oak phellogenic cells isolated by laser microdissection. Planta. 2018;247(2):317-338. doi:10.1007/s00425-017-2786-5
 2016
  • Aires T, Serrão EA, Engelen AH. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis). Front Microbiol. 2016;7:559. doi:10.3389/fmicb.2016.00559.
  • Alves M, Pereira A, Matos P, et al. Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus. Sci Rep. 2016;6:23908. doi:10.1038/srep23908.
  • Barros I, Mendes S, Rosa D. Vibrio diabolicus Immunomodulatory Effects on Bathymodiolus azoricus During Long-term Acclimatization at Atmospheric Pressure. J Aquac Res Dev. 2016;7(12). doi:10.4172/2155-9546.1000464.
  • Becerra-Castro C, Macedo G, Silva AMT, Manaia CM, Nunes OC. Proteobacteria become predominant during regrowth after water disinfection. Sci Total Environ. 2016;573:313-323. doi:10.1016/j.scitotenv.2016.08.054.
  • Cardoso JMS, Anjo SI, Fonseca L, Egas C, Manadas B, Abrantes I. Bursaphelenchus xylophilus and B. mucronatus secretomes: a comparative proteomic analysis. Sci Rep. 2016;6:39007. doi:10.1038/srep39007.
  • Cleary DFR, Becking LE, De Voogd NJ, et al. Variation in the diversity and composition of benthic taxa as a function of distance offshore, depth and exposure in the Spermonde Archipelago, Indonesia. Estuar Coast Shelf Sci. 2005;65(3):557-570. doi:10.1016/j.ecss.2005.06.025.
  • Cleary DFR, Becking LE, Polónia ARM, Freitas RM, Gomes NCM. Jellyfish-associated bacterial communities and bacterioplankton in Indonesian Marine lakes. FEMS Microbiol Ecol. March 2016:fiw064. doi:10.1093/femsec/fiw064.
  • Cleary DFR, Polónia ARM, Sousa AI, Lillebø AI, Queiroga H, Gomes NCM. Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima. Plant Biol (Stuttg). April 2016. doi:10.1111/plb.12459.
  • Coelho FJRC, Cleary DFR, Costa R, et al. Multi-taxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution. Mol Ecol. August 2016. doi:10.1111/mec.13779.
  • Domingos S, Fino J, Cardoso V, et al. Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L. BMC Plant Biol. 2016;16(1):38. doi:10.1186/s12870-016-0722-7.
  • Domingos S, Fino J, Paulo OS, Oliveira CM, Goulao LF. Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles. Plant Sci. 2016;244:40-56. doi:10.1016/j.plantsci.2015.12.009.
  • Duarte S, Cássio F, Ferreira V, Canhoto C, Pascoal C. Seasonal Variability May Affect Microbial Decomposers and Leaf Decomposition More Than Warming in Streams. Microb Ecol. May 2016. doi:10.1007/s00248-016-0780-2.
  • Eberlein C, Heuer H, Vidal S, Westphal A. Microbial Communities in Globodera pallida Females Raised in Potato Monoculture Soil. Phytopathology. 2016;106(6):581-590. doi:10.1094/PHYTO-07-15-0180-R.
  • Engelen AH, Costa J, Bermejo R, Marba N, Duarte CM, Serrão EA. A population genetics toolbox for the threatened canopy-forming brown seaweeds Cystoseira tamariscifolia and C. amentacea (Fucales, Sargassaceae). J Appl Phycol. September 2016:1-3. doi:10.1007/s10811-016-0964-7.
  • Jones-Dias D, Clemente L, Egas C, et al. Salmonella Enteritidis Isolate Harboring Multiple Efflux Pumps and Pathogenicity Factors, Shows Absence of O Antigen Polymerase Gene. Front Microbiol. 2016;7:1130. doi:10.3389/fmicb.2016.01130.
  • Martins I, Romão C V., Goulart J, Cerqueira T, Santos RS, Bettencourt R. Activity of antioxidant enzymes in response to atmospheric pressure induced physiological stress in deep-sea hydrothermal vent mussel Bathymodiolus azoricus. Mar Environ Res. 2016;114:65-73. doi:10.1016/j.marenvres.2016.01.003.
  • Paulino C, Neiva J, Coelho NC, et al. Characterization of 12 polymorphic microsatellite markers in the sugar kelp Saccharina latissima. J Appl Phycol. February 2016. doi:10.1007/s10811-016-0811-x.
  • Polónia ARM, Cleary DFR, Freitas R, Coelho FJR da C, de Voogd NJ, Gomes NCM. Comparison of archaeal and bacterial communities in two sponge species and seawater from an Indonesian coral reef environment. Mar Genomics. 2016;29:69-80. doi:10.1016/j.margen.2016.04.014.
  • Silva MEF, Lopes AR, Cunha-Queda AC, Nunes OC. Comparison of the bacterial composition of two commercial composts with different physicochemical, stability and maturity properties. Waste Manag. 2016;50:20-30. doi:10.1016/j.wasman.2016.02.023.
  • Simões MJ, Carmona S, Roberts R, et al. CYP1B1 mutational screening in a Portuguese cohort of primary congenital glaucoma patients. Ophthalmic Genet. 2016;7:1-3. doi:10.1080/13816810.2016.1188121.
  • Vaz-Moreira I, Varela AR, Pereira T V., Fochat RC, Manaia CM. Multidrug Resistance in Quinolone-Resistant Gram-Negative Bacteria Isolated from Hospital Effluent and the Municipal Wastewater Treatment Plant. Microb Drug Resist. 2016;22(2):155-163. doi:10.1089/mdr.2015.0118.
  • Wolters B, Ding G-C, Kreuzig R, Smalla K. Full-scale mesophilic biogas plants using manure as C-source: bacterial community shifts along the process cause changes in the abundance of resistance genes and mobile genetic elements. FEMS Microbiol Ecol. 2016;92(2). doi:10.1093/femsec/fiv163.

 2015 

  • Aires T, Moalic Y, Serrao EA, Arnaud-Haond S. Hologenome theory supported by cooccurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa). FEMS Microbiol Ecol. 2015;91(7):fiv067. doi:10.1093/femsec/fiv067.
  • Baptista P, Reis F, Pereira E, et al. Soil DNA pyrosequencing and fruitbody surveys reveal contrasting diversity for various fungal ecological guilds in chestnut orchards. Environ Microbiol Rep. 2015. doi:10.1111/1758-2229.12336.
  • Barros I, Divya B, Martins I, Vandeperre F, Santos RS, Bettencourt R. Post-capture immune gene expression studies in the deep-sea hydrothermal vent mussel Bathymodiolus azoricus acclimatized to atmospheric pressure. Fish Shellfish Immunol. 2015;42(1):159-70. doi:10.1016/j.fsi.2014.10.018.
  • Buscardo E, Rodríguez-Echeverría S, Freitas H, De Angelis P, Pereira JS, Muller LAH. Contrasting soil fungal communities in Mediterranean pine forests subjected to different wildfire frequencies. Fungal Divers. 2014;70(1):85-99. doi:10.1007/s13225-014-0294-5.
  • Cardoso JMS, Fonseca L, Gomes P, Egas C, Abrantes I. Molecular characterization and functional analysis of a calponin gene from the pinewood nematode. Smith JA, ed. For Pathol. 2015;45(6):467-473. doi:10.1111/efp.12196.
  • Cerqueira T, Pinho D, Egas C, et al. Microbial diversity in deep-sea sediments from the Menez Gwen hydrothermal vent system of the Mid-Atlantic Ridge. Mar Genomics. 2015;24 Pt 3:343-55. doi:10.1016/j.margen.2015.09.001.
  • Cleary DFR, Becking LE, Polónia ARM, Freitas RM, Gomes NCM. Composition and predicted functional ecology of mussel-associated bacteria in Indonesian marine lakes. Antonie Van Leeuwenhoek. 2015;107(3):821-34. doi:10.1007/s10482-014-0375-1.
  • Cleary DFR, de Voogd NJ, Polónia ARM, Freitas R, Gomes NCM. Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia. Microb Ecol. 2015;70(4):889-903. doi:10.1007/s00248-015-0632-5.
  • Coelho FJRC, Cleary DFR, Rocha RJM, et al. Unraveling the interactive effects of climate change and oil contamination on laboratory-simulated estuarine benthic communities. Glob Chang Biol. 2015;21(5):1871-86. doi:10.1111/gcb.12801.
  • Cruz A, Rodrigues R, Pinheiro M, Mendo S. Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin (TBT): Unravelling the effects from the molecular level to the organism. Mar Environ Res. 2015;109:132-9. doi:10.1016/j.marenvres.2015.06.017.
  • de Voogd NJ, Cleary DFR, Polónia ARM, Gomes NCM. Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia. FEMS Microbiol Ecol. 2015;91(4):fiv019. doi:10.1093/femsec/fiv019.
  • DUARTE A, MALEITA C, ABRANTES I, CURTIS R. Tomato root exudates induce transcriptional changes of  Meloidogyne hispanica  genes. Phytopathol Mediterr. 2015;54(1):104-108. doi:10.14601/Phytopathol_Mediterr-14595.
  • Duarte S, Bärlocher F, Trabulo J, Cássio F, Pascoal C. Stream-dwelling fungal decomposer communities along a gradient of eutrophication unraveled by 454 pyrosequencing. Fungal Divers. 2014;70(1):127-148. doi:10.1007/s13225-014-0300-y.
  • Fernandes I, Pereira A, Trabulo J, Pascoal C, Cássio F, Duarte S. Microscopy- or DNA-based analyses: Which methodology gives a truer picture of stream-dwelling decomposer fungal diversity? Fungal Ecol. 2015;18:130-134. doi:10.1016/j.funeco.2015.08.005.
  • Landi M, Araújo A, Lobo J, et al. Ancient DNA in Archaeological Garum Remains from the South of Portugal. In: Oliveira C, Morais R, Cerdán ÁM, eds. Chromatography and DNA analysis in archaeology. Esposende: Municipio de Esposende; 2015.
  • Martins MJF, Lago-Leston A, Anjos A, et al. A transcriptome resource for Antarctic krill (Euphausia superba Dana) exposed to short-term stress. Mar Genomics. 2015;23:45-7. doi:10.1016/j.margen.2015.04.008.
  • Martins P, Navarro RVV, Coelho FJRC, Gomes NCM. Development of a molecular methodology for fast detection of Photobacterium damselae subspecies in water samples. Aquaculture. 2015;435:137-142. doi:10.1016/j.aquaculture.2014.09.028.
  • Miguel A, de Vega-Bartol J, Marum L, et al. Characterization of the cork oak transcriptome dynamics during acorn development. BMC Plant Biol. 2015;15(1):158. doi:10.1186/s12870-015-0534-1.
  • Oliveira J, Negrão L, Fineza I, et al. New splicing mutation in the choline kinase beta (CHKB) gene causing a muscular dystrophy detected by whole-exome sequencing. J Hum Genet. 2015;60(6):305-12. doi:10.1038/jhg.2015.20.
  • Pearson GA, Lago-Leston A, Cánovas F, et al. Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula. ISME J. 2015;9(10):2275-89. doi:10.1038/ismej.2015.40.
  • Pegoraro N, Calado R, Duarte LN, et al. Molecular analysis of skin bacterial assemblages from codfish and pollock after dry-salted fish production. J Food Prot. 2015;78(5):983-9. doi:10.4315/0362-028X.JFP-14-390.
  • Pereira R, Oliveira J, Ferraz L, Barros A, Santos R, Sousa M. Mutation analysis in patients with total sperm immotility. J Assist Reprod Genet. 2015;32(6):893-902. doi:10.1007/s10815-015-0474-6.
  • Pinto C, Pinho D, Cardoso R, et al. Wine fermentation microbiome: a landscape from different Portuguese wine appellations. Front Microbiol. 2015;6:905. doi:10.3389/fmicb.2015.00905.
  • Polónia ARM, Cleary DFR, Freitas R, de Voogd NJ, Gomes NCM. The putative functional ecology and distribution of archaeal communities in sponges, sediment and seawater in a coral reef environment. Mol Ecol. 2015;24(2):409-23. doi:10.1111/mec.13024.
  • Ramos AA, Weydmann A, Cox CJ, Canário AVM, Serrão EA, Pearson GA. A transcriptome resource for the copepod Calanus glacialis across a range of culture temperatures. Mar Genomics. 2015;23:27-9. doi:10.1016/j.margen.2015.03.014.
  • Riquelme C, Câmara S, Dapkevicius M de LNE, et al. Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food). Int J Food Microbiol. 2015;192:86-94. doi:10.1016/j.ijfoodmicro.2014.09.031.
  • Rosado T, Mirão J, Candeias A, Caldeira AT. Characterizing microbial diversity and damage in mural paintings. Microsc Microanal. 2015;21(1):78-83. doi:10.1017/S1431927614013439.
  • Serrazina S, Santos C, Machado H, et al. Castanea root transcriptome in response to Phytophthora cinnamomi challenge. Tree Genet Genomes. 2015;11(1):6. doi:10.1007/s11295-014-0829-7.
  • Vaz-Moreira I, Varela AR, Pereira T V., Fochat RC, Manaia CM. Multidrug Resistance in Quinolone-Resistant Gram-Negative Bacteria Isolated from Hospital Effluent and the Municipal Wastewater Treatment Plant. Microb Drug Resist. 2015:mdr.2015.0118. doi:10.1089/mdr.2015.0118.
  • Yim B, Winkelmann T, Ding G-C, Smalla K. Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis - contribution to improved aboveground apple plant growth? Front Microbiol. 2015;6:1224. doi:10.3389/fmicb.2015.01224.

2014 

  • M. Adam, A. Westphal, J. Hallmann, and H. Heuer. (2014) Specific Microbial Attachment to Root Knot Nematodes in Suppressive Soil. Appl. Environ. Microbiol. 80:2679-2686. doi:10.1128/AEM.03905-13.
  • A. C. Alves, A. Etxebarria, A. K. Soutar, C. Martin, and M. Bourbon. (2014) Novel functional APOB mutations outside LDL-binding region causing familial hypercholesterolaemia. Hum. Mol. Genet. 23 (7): 1817-1828. DOI:10.1093/hmg/ddt573. 
  • S. Arnaud-Haond, R. Candeias, E. A. Serrão, S. J. L. Teixeira. (2014) Microsatellite markers developed through pyrosequencing allow clonal discrimination in the invasive alga Caulerpa taxifolia. Conservation Genetics Resources 5:667-669. doi:10.1007/s12686-013-9878-8.
  • Bettencourt, R., Rodrigues, M., Barros, I., Cerqueira, T., Freitas, C., Costa, V., Pinheiro, M., Egas, C., Santos, R. S. (2014) Site-related differences in gene expression and bacterial densities in the mussel Bathymodiolus azoricus from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites. Fish & Shellfish Immunology. 39:343-353. doi:10.1016/j.fsi.2014.05.024.
  • N. C. Coelho, E. A. Serrão, F. Alberto. (2014) Characterization of fifteen microsatellite markers for the kelp Laminaria ochroleuca and cross species amplification within the genus. Conservation Genet Resour. 6:949-950. doi:10.1007/s12686-014-0249-x.
  • Ding G-C, Radl V, Schloter-Hai B, Jechalke S, Heuer H, Smalla K, Schloter M (2014) Dynamics of Soil Bacterial Communities in Response to Repeated Application of Manure Containing Sulfadiazine. PLoS ONE 9(3): e92958. doi: 10.1371/journal.pone.0092958.
  • Egas, C., Barroso, C., Froufe, H., Pacheco, J., Albuquerque, L., da Costa, M. (2014) Complete genome sequence of the radiation-resistant bacterium Rubrobacter radiotolerans RSPS-4. Standards in Genomic Sciences. 9(3). doi:10.4056/sigs.5661021.
  • Newton C.M. Gomes, Daniel F.R. Cleary, Ana C.C. Pires, Adelaide Almeida, Angela Cunha, Leda C.S. Mendonça-Hagler, Kornelia Smalla. (2014) Assessing variation in bacterial composition between the rhizospheres of two mangrove tree species. Estuarine, Coastal and Shelf Science.139:40-45. doi.org/10.1016/j.ecss.2013.12.022.
  • Pinto C, Pinho D, Sousa S, Pinheiro M, Egas C, et al. (2014) Unravelling the Diversity of Grapevine Microbiome. PLoS ONE 9(1): e85622. doi:10.1371/journal.pone.0085622.
  • Hardoim C, Cúcio ACB, Esteves AIS, Berg G, Xavier JR, Cox CJ and Costa R. Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges Front Microbiol. 2014; 5:611. doi: 10.3389/fmicb.2014.00611.
  • Hardoim, C. C. P. and Costa, R. (2014), Temporal dynamics of prokaryotic communities in the marine sponge Sarcotragus spinosulus. Molecular Ecology, 23: 3097–3112. doi: 10.1111/mec.12789.
  • Lopes, A. R., Manaia, C. M. and Nunes, O. C. (2014) Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing. FEMS Microbiology Ecology, 87: 650–663. doi: 10.1111/1574-6941.12253.
  • J. M. Marques, T. F. da Silva, R. E. Vollu, A. F. Blank, G. Ding, L. Seldin, and K. Smalla. (2014) Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants. FEMS Microbiology Ecology. 2014. 88:424–435. doi: 10.1111/1574-6941.12313.
  • F. O. Morais-Silva, A. M. Rezende, C. Pimentel, C. I. Santos, C. Clemente, A. Varela–Raposo, D. M. Resende, S. M. da Silva, L. M. de Oliveira, M. Matos, D. A. Costa, O. Flores, J. C. Ruiz and C. Rodrigues-Pousada. (2014) Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus. MicrobiologyOpen 2014; 3(4): 513–530 doi:10.1002/mbo3.184.
  • V. Oliveira, Newton C.M. Gomes, Daniel F.R. Cleary, A. Almeida, Artur M.S. Silva, Mário M.Q. Simões, H. Silva, A. Cunha. Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons. FEMS Microbiology Ecology. 2014, 90 (3) 647-662; DOI:10.1111/1574-6941.12425.
  • J. B. Pereira-Leal, I. A. Abreu, C. S. Alabaça, M. H. Almeida, P. Almeida, T. Almeida, M. I. Amorim, S. Araújo, H. Azevedo, A. Badia, D. Batista, A. Bohn, T. Capote, I. Carrasquinho, I. Chaves, A. C. Coelho, M. M. R. Costa, R. Costa, A. Cravador, C. Egas, C. Faro, A. M. Fortes, A. S. Fortunato, M. J. Gaspar, S. Gonçalves, J. Graça, M. Horta, V. Inácio, J. M. Leitão, T. Lino-Neto, L. Marum, J. Matos, D. Mendonça, A. Miguel, C. M. Miguel, L. Morais-Cecílio, I. Neves, F. Nóbrega, M. M. Oliveira, R. Oliveira, M. S. Pais, J. A. Paiva, O. S. Paulo, M. Pinheiro, J. A. P. Raimundo, J. C. Ramalho, A. I. Ribeiro, T. Ribeiro, M. Rocheta, A. I. Rodrigues, J. C. Rodrigues, N. J. M. Saibo, T. E. Santo, A. M. Santos, P. Sá-Pereira, M. Sebastiana, F. Simões, R. S. Sobral, R. Tavares, R. Teixeira, C. Varela, M. M. Veloso and C. P. P. Ricardo. (2014) A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. BMC Genomics, 15:371. doi:10.1186/1471-2164-15-371.
  • Rocheta M, Sobral R, Magalhães J, Amorim MI, Ribeiro T, Pinheiro M, Egas C, Morais-Cecílio L, Costa MMR. 2014. Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber. Frontiers in Plant Science. 5. Doi:10.3389/fpls.2014.00599.      
  • S. Schreiter, G-C. Ding, R. Grosch, S. Kropf, K. Antweiler, K. Smalla. Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce. FEMS Microbiology Ecology. 2014, 90 (3) 718-730; DOI:10.1111/1574-6941.12430.
  • S. Schreiter, G. Ding, H. Heuer, G. Neumann, M. Sandmann, R. Grosch, S. Kropf and K. Smalla. (2014) Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce. Front Microbiol. 2014; 5:144. doi:10.3389/fmicb.2014.00144.
  • Sebastiana M, Vieira B, Lino-Neto T, Monteiro F, Figueiredo A, et al. (2014) Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling. PLoS ONE 9(5): e98376. doi: 10.1371/journal.pone.0098376.
  • Simoes MJ, Lobo C., Egas C, Nunes S, Carmona S, Costa MA, Duarte T, Ribeiro L, Faro C, Cunha-Vaz J. Genetic variants in ICAM1, PPARGC1A and MTHFR are potentially associated with different phenotypes of diabetic retinopathy. Ophthalmologica 2014. 232(3):156-62. doi: 10.1159/000365229.
  • Sergio Stefanni, Raul Bettencourt, Miguel Pinheiro, Gianluca De Moro, Lucia Bongiorni, and Alberto Pallavicini. 2014. Transcriptome of the Deep-Sea Black Scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation. International Journal of Genomics 2014, Article ID 267482, 21 pages. doi:10.1155/2014/267482.
  • Teixeira, R. T., Fortes, A. M., Pinheiro, C., and Pereira, H. (2014) Comparison of good- and bad-quality cork: application of high-throughput sequencing of phellogenic tissue. J Exp Bot. 2014 Sep;65(17):4887-905. doi: 10.1093/jxb/eru252.
  • A. Weydmann, N. C. Coelho, A. A. Ramos, E. A. Serrão, G. A. Pearson. (2014) Microsatellite markers for the Arctic copepod Calanus glacialis and cross-amplification with C. finmarchicus. Conservation Genet Resour. 6:1003-1005.

2013

  • Abbasi, M., Paquete, L., Liefooghe, A., Pinheiro, M. and Matias P. (2013) Improvements on bicriteria pairwise sequence alignment: algorithms and applications. Bioinformatics 29(8):996-1003 doi:10.1093/bioinformatics/btt098. 
  • Aires, T., Serrão, E. A., Kendrick, G., Duarte, C. M. and Arnaud-Haond, S. (2013). Invasion is a community affair: Clandestine followers in the bacterial community associated to green algae, Caulerpa racemosa, track the invasion source. PloS One, 8(7):e68429. doi:10.1371/journal.pone.0068429.
  • Arnaud-Haond, S., Candeias, R., Serrão, E. A. and Teixeira, S. J. (2013). Microsatellite markers developed through pyrosequencing allow clonal discrimination in the invasive alga Caulerpa taxifoliaConservation Genetics Resources, 5(3):667–669. doi:10.1007/s12686-013-9878-8.
  • Bettencourt, R., Rodrigues, M. I., Barros, I., Cerqueira, T., Freitas, C., Costa, V., Pinheiro, M., Egas, C. and Santos, R. S. (2013). Differential gene expression in the mussel Bathymodiolus azoricus from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites. Biogeosciences Discussions, 10(2):2013–2038. doi:10.5194/bgd-10-2013-2013.
  • Carneiro, A. R., Jucá Ramos, R. T., Baraúna, R. A., de Sá, P. H., Marinho Almeida, D., Barbosa, S., Pereira A, Alves, A., Egas, C., Correia, A., Henriques, I. and Silva, A. (2013). Draft Genome Sequence of Serratia fonticola LMG 7882T Isolated from Freshwater. Genome Announcements, 1(6). doi:10.1128/genomeA.00971-13.
  • Cleary, D. F. R., Becking, L. E., de Voogd, N. J., Pires, A. C. C., Polónia, A. R. M., Egas, C. and Gomes, N. C. M. (2013). Habitat- and host-related variation in sponge bacterial symbiont communities in Indonesian waters. FEMS Microbiology Ecology, 85(3):465–82. doi:10.1111/1574-6941.12135.
  • Coelho, F.J., Rocha, R.J., Pires, A.C., Ladeiro, B., Castanheira, J.M., Costa, R., Almeida, A., Cunha, A., Lillebø, A.I., Ribeiro, R., Pereir,a R., Lopes, I., Marques, C., Moreira-Santos, M., Calado, R., Cleary, D.F. and Gomes, N.C. (2013). Development and validation of an experimental life support system for assessing the effects of global climate change and environmental contamination on estuarine and coastal marine benthic communities. Global Change Biology, 19(8): 2584–95. doi:10.1111/gcb.12227.
  • Ding, G.-C., Pronk, G. J., Babin, D., Heuer, H., Heister, K., Kögel-Knabner, I. and Smalla, K. (2013). Mineral composition and charcoal determine the bacterial community structure in artificial soils. FEMS Microbiology Ecology, 86(1):15–25. doi:10.1111/1574-6941.12070.
  • Figueiredo, J., Simões, M. J., Gomes, P., Barroso, C., Pinho, D., Conceição, L., Fonseca, L., Abrantes, I., Pinheiro, M. and Egas, C. (2013). Assessment of the Geographic Origins of Pinewood Nematode Isolates via Single Nucleotide Polymorphism in Effector Genes. PloS One, 8(12):e83542. doi:10.1371/journal.pone.0083542.
  • Gomes, N. C. M., Manco, S. C., Pires, A. C. C., Gonçalves, S. F., Calado, R., Cleary, D. F. R. and Loureiro, S. (2013). Richness and composition of sediment bacterial assemblages in an Atlantic port environment. The Science of the Total Environment, 452-453:172–80. doi:10.1016/j.scitotenv.2013.02.017.
  • Henriques, I., Jucá Ramos, R. T., Baraúna, R. A., de Sá, P. H., Marinho Almeida, D., Carneiro, A. R., Barbosa, S., Pereira, A., Alves, A., Saavedra, M.J., Egas, C., Silva, A. and Correia, A. (2013). Draft Genome Sequence of Serratia fonticola UTAD54, a Carbapenem-Resistant Strain Isolated from Drinking Water. Genome Announcements, 1(6). doi:10.1128/genomeA.00970-13.
  • Lopes, A. R., Manaia, C. M. and Nunes, O. C. (2013). Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing. FEMS Microbiology Ecology. doi:10.1111/1574-6941.12253.
  • Martins, P., Cleary, D. F. R., Pires, A. C. C., Rodrigues, A. M., Quintino, V., Calado, R. and Gomes, N. C. M. (2013). Molecular Analysis of Bacterial Communities and Detection of Potential Pathogens in a Recirculating Aquaculture System for Scophthalmus maximus and Solea senegalensis. PloS One, 8(11):e80847. doi:10.1371/journal.pone.0080847.
  • Vaz-Moreira, I., Egas, C., Nunes, O. C. and Manaia, C. M. (2013). Bacterial diversity from the source to the tap: a comparative study based on 16S rRNA gene-DGGE and culture-dependent methods. FEMS Microbiology Ecology, 83(2):361–74. doi:10.1111/1574-6941.12002.
  • Vieira, R., Simões, M. J., Carmona, S., Egas, C., Faro, C. and Figueiredo, A. (2013). Identification of DLEC1 D215N Somatic Mutation in Formalin Fixed Paraffin Embedded Melanoma and Melanocytic Nevi Specimens. Journal of Skin Cancer, ID 469671. doi:10.1155/2013/469671.

2012

  • Aires, Tânia, Marbà, N., Serrão, E. A., Duarte, C. M. and Arnaud-Haond, S. (2012). Selective elimination of chloroplastidial DNA for metagenomics of bacteria associated with the green alga Caulerpa taxofolia (Bryopsidophyceae). Journal of Phycology, 48(2):483–490. doi:10.1111/j.1529-8817.2012.01124.x.
  • Cleary, D. F. R., Smalla, K., Mendonça-Hagler, L. C. S. and Gomes, N. C. M. (2012). Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing. PloS One7(1):e29380. doi:10.1371/journal.pone.0029380.
  • Conceição, I. L., Tzortzakakis, E. A., Gomes, P., Abrantes, I. and Cunha, M. J. (2012). Detection of the root-knot nematode Meloidogyne ethiopica in Greece. European Journal of Plant Pathology, 134(3):451–457. doi:10.1007/s10658-012-0027-0.
  • Costa-Matos, L., Batista, P., Monteiro, N., Simões, M., Egas, C., Pereira, J., Pinho, H., Santos, N., Ribeiro, J., Cipriano, MA., Henriques, P., Girão, F., Rodrigues, A. and Carvalho, A. (2012). Liver hepcidin mRNA expression is inappropriately low in alcoholic patients compared with healthy controls. European Journal of Gastroenterology and Hepatology, 24(10):1158–65. doi:10.1097/MEG.0b013e328355cfd0.
  • Ding, G.-C., Heuer, H. and Smalla, K. (2012). Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders. Frontiers in Microbiology3:290. doi:10.3389/fmicb.2012.00290.
  • Egas, C., Pinheiro, M., Gomes, P., Barroso, C. and Bettencourt, R. (2012). The transcriptome of Bathymodiolus azoricus gill reveals expression of genes from endosymbionts and free-living deep-sea bacteria. Marine Drugs, 10(8):1765–83. doi:10.3390/md10081765.
  • Maleita, C. M., Simões, M. J., Egas, C., Curtis, R. H. C. and Abrantes, I. M. (2012). Biometrical, Biochemical, and Molecular Diagnosis of Portuguese Meloidogyne hispanica Isolates. Plant Disease, 96(6):865–874. doi:10.1094/PDIS-09-11-0769-RE.
  • Pires, A. C. C., Cleary, D. F. R., Almeida, A., Cunha, A., Dealtry, S., Mendonça-Hagler, L. C. S., Smalla, K. and Gomes, N. C. M. (2012). Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples. Applied and Environmental Microbiology, 78(16):5520–8. doi:10.1128/AEM.00386-12.
  • Santos, C. S., Pinheiro, M., Silva, A. I., Egas, C. and Vasconcelos, M. W. (2012). Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening. BMC Genomics, 13(1):599. doi:10.1186/1471-2164-13-599.

2011

  • Gomes, N. C., Cleary, D. F., Calado, R. and Costa, R. (2011). Mangrove bacterial richness. Communicative and Integrative Biology, 4(4):419–23. doi:10.4161/cib.4.4.15253
  • Vaz-Moreira, I., Egas, C., Nunes, O. C. and Manaia, C. M. (2011). Culture-dependent and culture-independent diversity surveys target different bacteria: a case study in a freshwater sample. Antonie van Leeuwenhoek, 100(2):245–57. doi:10.1007/s10482-011-9583-0
  • Velada, I., Capela-Silva, F., Reis, F., Pires, E., Egas, C., Rodrigues-Santos, P. and Barros, M. T. (2011). Expression of genes encoding extracellular matrix macromolecules and metalloproteinases in avian tibial dyschondroplasia. Journal of comparative Pathology, 145(2-3):174–86. doi:10.1016/j.jcpa.2010.12.008.

2010

  • Bettencourt, Raul, Pinheiro, M., Egas, C., Gomes, P., Afonso, M., Shank, T. and Santos, R. S. (2010). High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricusBMC Genomics, 11:559. doi:10.1186/1471-2164-11-559.
  • Gomes, N, Clearly, D., Pinto, F., Egas, C., Almeida, A., Cunha, A., Mendonça-Hagler, L. and Smalla, K. (2010). Taking root: enduring effect of rhizosphere bacterial colonization in mangroves. PloS One, 5(11): e14065. doi:10.1371/journal.pone.0014065.

2009

  • Soares, A. R., Pereira, P. M., Santos, B., Egas, C., Gomes, A.C., Arrais, J., Moura, G.R. and Santos, M.A.S. 2009. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics 10:195. (BMC Genomics highly accessed paper).

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