Rocha, J., Crespí, A.L., García-Barruso, M., Kozlowski, G., Almeida, R., Honrado, J., Talavera, S. and Amich, F. 2011. Morpho-environmental characterization of the genus Baldellia Parl. (Alismataceae) in the iberian Peninsula, Balearic Islands and North Morocco. Plant viosystems - An International Journal Dealing with all Aspects of Plant Biology. First published on: 01 June 2011 (iFirst). DOI: 10.1080/11263504.2011.557096

Alonso, J.M., Honrado, J. P. & Silva, R.A. 2011. Biodiversidade, Recursos Naturais e Biotecnologia In Ferraz, A.I. & Rodrigues, A.C. (Eds.). Biotecnologia, Ambiente e Desenvolvimento Sustentável. Publindústria, Edições Técnicas. Porto. ISBN: 978-972-8953-81-2

Vicente, J., Randin, C.F., Gonçalves, J., Metzger, M., Lomba, A., Honrado, J. and Guisan, A. (2011) Where will conflicts between alien and rare species occur after climate and land-use change? A test with a novel combined modeling approach. Biological Invasions. 13:1209–1227

Cerqueira Y,  Araújo C, Vicente J, Pereira HM & Honrado J (2010) "Ecological and Cultural Consequences of Agricultural Abandonment in the Peneda-Gerês National Park (Portugal)" Chapter 2 in: Evelpidou N, Figueiredo T, Mauro F, Tecim V & Vassilopoulos A (Eds.) "Natural Heritage from East to West". 1st Edition., 2010, XIII, 363 p., Hardcover. ISBN: 978-3-642-01576-2. Springer 

Honrado, J., J. Vicente, A. Lomba, P. Alves, J. A. Macedo, R. Henriques, H. Granja & F. B. Caldas (2010). Fine-scale patterns of vegetation assembly in the monitoring of changes in coastal sand-dune landscapes. Web Ecology, 9: 82–95.

Macedo, J. A., P. Alves, A. Lomba, J. Vicente, H. Hespanhol, R. Henriques, H. Granja & J. Honrado (2010). On the interest of plant functional classifications to study community-level effects of increased disturbance on coastal dune vegetation. Acta Botanica Gallica. 157(2): 305-315

Torres J., J.C. Brito, M.J. Vasconcelos, L. Catarino, J. Gonçalves & J. Honrado (2010). Ensemble models of habitat suitability relate chimpanzee (Pan troglodytes) conservation to forest and landscape dynamics in Western Africa. Biological Conservation 143: 416-425.

Lomba, A., Pellissier, L., Randin, C., Vicente, J., Moreira, F., Honrado, J., Guisan, A. (2010) Overcoming the rare species modelling paradox: A novel hierarchical framework applied to an Iberian endemic plant. Biological Conservation 143, 2647-2657.

Vicente J, Alves P, Randin C, Guisan A and Honrado J (2010) What drives invasibility? A multi-model inference test and spatial modelling of alien plant species richness patterns in Northern Portugal. Ecography  33(6):1081-1092

Neto C, Costa JC, Honrado J and Capelo J (2008). Phytosociologic associations and Natura 2000 habitats of Portuguese coastal sand dunes. Fitosociologia, 44: 29-36

Lomba A, Alves P and Honrado J (2008). Endemic sand-dune vegetation from Northwest Iberian Peninsula: Diversity, dynamics and significance for bioindication and monitoring of coastal landscapes. Journal of Coastal Research, 24(2b):113-121 .

Honrado J, F.B. Caldas, P. Alves, J. Vicente (2008). "Biodiversidade e Recursos Biológicos: Vegetação e flora vascular". In: J.M. Alonso (coord.) "As condições naturais do território de Ponte de Lima". Município de Ponte de Lima.

Alves P, Lomba A, Ortiz S, Caldas FB and Honrado J (2007) Two new endemic megaforb (Galio-Urticetea) vegetation types from North-western Portugal. Silva Lusitana, 14: 275-279.

Honrado J, Alves P, Lomba A, Vicente J, Silva G, Nepomuceno H and Caldas FB (2007). Perennial vegetation of coastal sand dunes in northern Portugal. Silva Lusitana, 14: 269-275.

Capelo J, Mesquita S, Costa JC, Ribeiro S, Arsénio P, Neto C, Monteiro T, Aguiar C, Honrado J, Espírito-Santo D and Lousã M (2007). A methodological approach to potential vegetation modeling using GIS techniques and phytosociological expert-knowledge: application to mainland Portugal. Phytocoenologia, 37:399-415.

Honrado J, Alves P, Lomba A, Torres J and Caldas FB (2007). Ecology, Diversity and Conservation of Relict Laurel-Leaved Mesophytic Scrublands in Mainland Portugal. Acta Botanica Gallica, 154:63-77.

Honrado J (2005). Carici piluliferae-Genistetum triacanthi, a new heath association from Northwestern Portugal. Silva Lusitana, 13: 127-131.

Lomba A, Honrado J, Granja H, Favennec J and Vidal-Romaní J (2005). Geomorphology and Vegetation: A Contribution for a Synthesis on Erosion vs. Stability Bioindicators of the Coastal Zone. Proceedings Book of ICCCM’05 International Conference on Coastal Conservation and Management in the Atlantic and Mediterranean, pp.495-501

Alves H, Honrado J, Alves P, Vieira C and Séneca A (2004) - A Flora e a Vegetação da Serra da Aboboreira. In: M. Nunes (coord.) - Serra da Aboboreira - a Terra, o Homem e os Lobos. Câmara Municipal de Amarante, Amarante. pp. 71-79.

Honrado J (2004). Syntaxonomy of riparian woodlands in North-Western Portugal (Galician-Portuguese and Juresian sectors).Silva Lusitana, 12: 255-256.

Honrado J, Alves P, Alves HN and Caldas FB (2004) - A vegetação do Alto Minho: Esboço fitossociológico da vegetação natural do extremo noroeste de Portugal (sectores Galaico-Português e Geresiano). Quercetea 5: 3-102.

Lomba A, Torres J, Alves H and Honrado J (2004). GIS applied to landscape valuation and management in coastal areas. Proceedings of the 7th International Symposium Littoral 2004, 770-771.

Honrado J, Alves P, Lomba A, Rocha I, Torres J, Ortíz S and Caldas FB (2004). A new association of perennial nitrophilous vegetation from North-western Iberian Peninsula. Acta Botanica Gallica, 151: 393-399.

Vieira C, Honrado JJ, Séneca A and Caldas FB (2003). Comunidades Higrófilas Herbáceas (Classes Isoeto-Littorelletea, Montio-Cardaminetea, Phragmito-Magnocaricetea e Potametea) no Parque Nacional da Peneda-Gerês (Noroeste de Portugal Continental). Quercetea 4: 93-112

Alves P, Honrado J and Caldas FB (2003). Perennial shade tolerant nitrophilous vegetation (class Galio-Urticetea) of Northwestern Portugal: Allio triquetri-Urticetum membranaceae ass. nova. Stvdia Botanica, 22: 17-26.

Alves P, Honrado J and Caldas FB (2003). Sagino procumbentis-Sibthorpietum europaeae, a new association within class Montio fontanae-Cardaminetea amarae from Northwestern Portugal. Lazaroa, 24: 33-36.

Honrado J, Alves P, Aguiar C, Ortiz S and Caldas FB (2003) - Juresian riparian birch woodlands: Carici reuterianae-Betuletum celtibericae as. Nova. Silva Lusitana 11(2), 237-241.

Honrado J (2003). A Vegetação Natural de Portugal Continental. In: Maravalhas E (Ed.). As Borboletas de Portugal. Vento Norte. pp. 143-166.

Honrado J, Alves P, Alves HN and Caldas FB (2003) – Ten new syntaxa from the miniense biogeographic subsector (Northwest Portugal). Silva lusitana 10 (2): 247-259

Honrado J, Alves P, Alves HN & Caldas FB (2002) - Natural and Semi-natural Vegetation of the “Alto Minho”. In: J. Honrado, H.N. Alves & F.B. Caldas (eds.) - Flora and Vegetation of the “Alto Minho”. Excursion Guide of the “IV ALFA Meeting”. Associação Lusitana de Fitossociologia, Porto. pp. 18-57.

Honrado J, Alves P, Alves HN and Caldas FB (2002) - Vascular Flora of the “Alto Minho”. In: J. Honrado, H.N. Alves & F.B. Caldas (eds.) - Flora and Vegetation of the “Alto Minho”. Excursion Guide of the “IV ALFA Meeting”. Associação Lusitana de Fitossociologia, Porto. pp. 58-80.

Honrado J, Pereira R, Araújo R, Alves P, Santos G, Matos J, Alves HN, Sousa-Pinto I and Caldas FB (2002) - Classification and mapping of terrestrial and inter-tidal vegetation in the Atlantic Coast of Northern Portugal. Actas do Congresso “Littoral 2002”: 211-215.