2024

• Lopes, L. E.; Batista, M. N. M. ; Reis, J. N. ; Fernandes, A. M. ; Heming, N. M. ; Magnago, G. ; Nacif, J. A. ; Nogueira, W. ; Rodrigues, M. ; Vasconcelos, M. F. (2024) Two centuries of ornithological exploration of the Rio Doce Basin, southeastern Brazil. Part II?A catalogue of its birds and a gazetteer. Zootaxa, 5532, 1–558.
• Fernandes, Alexandre M. ; Cohn-Haft, Mario ; Silveira, Luís Fábio ; Aleixo, Alexandre ; Nascimento, Nathália ; Urban Olsson (2024) Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon. Molecular Phylogenetics and Evolution, 198, 108–117.

2022

• Fernandes, Alexandre M. ; de Melo, Alyson Vieira ; da Silva, Andreza Maria (2022) CIGANAS, as origens enigmáticas da ave com ‘cabelos’ para trás. Ciência Hoje. 393, 1–10.
• Ferreira, Maria Eduarda Alves ; Marques, Rodrigo Ferraz Jardim ; Leite, Hélio Francisco (2022) New record of the bat falcon (Falco rufigularis) in northeastern Brazil: Implications for its future distribution under climate change. Biologia. 77, 2619–2624.
• Veras, Aurea Palloma Bezerra Barbosa ; de Almeida, Cauê Guion ; de Moraes, Lorena Lima ; Fernandes, Alexandre M. (2022) Ethnoornithology and bird conservation in afro-descendant communities in the brazilian Caatinga. Ethnobiology Letters. 13, 1–15.

2020

• Gomes, Regina Carolina Ferreira De Souza ; Teixeira, Bárbara Luiza Barbosa ; Gusmão, Cássia Lima Silva ; Fernandes, Alexandre M. (2020) Humidity effects on avian blood parasites in the Caatinga of Brazil. Ornithology Research. doi:10.1007/s43388-020-00009-y.
• Moura, Carina C. M.; Fernandes, Alexandre M.; Aleixo, Alexandre; De Araujo, Helder F. P.; De Freitas Mariano, Erich; Wink, Michael (2020) Evolutionary history of the Pectoral Sparrow Arremon taciturnus: evidence for diversification during the Late Pleistocene. IBIS. doi.org/10.1111/ibi.12813

2019

• Silva, Sofia Marques; Peterson, A. Townsend; Carneiro, Lincoln; Burlamaqui,Tibério César Tortola; Ribas, Camila C.; Sousa-Neves, Tiago; Miranda, Leonardo S.; Fernandes, Alexandre M.; D'horta, Fernando M.; Araújo-Silva, Lucas Eduardo; Batista, Romina; Bandeira, Cinthia H. M. M.; Dantas, Sidnei M.; Ferreira, Mateus; Martins, Denise M.; Oliveira, Joiciane; Rocha, Tainá C.; Sardelli, Carla H.; Thom, Gregory; Rêgo, Péricles Sena; Santos, Marcos Pérsio; Sequeira, Fernando; Vallinoto, Marcelo; Aleixo, Alexandre A (2019) Dynamic continental moisture gradient drove Amazonian bird diversification. Science Advances. doi:10.1126/sciadv.aat5752.
• Da Silva, Erasmo Andrade; De Araujo, Helder Farias Pereira; Aleixo, Alexandre; Antonelli, Alexandre; Fernandes, Alexandre M. (2019) The effects of climate change on the distribution of South American antbirds (Thamnophilus punctatus complex) as affected by niche divergences and contact zone interactions between species. Journal of Ornithology. 161, 229–241.

2018

• Moura, Carina C. M.; De Araujo, Helder F. P.; Aleixo, Alexandre; Wink, Michael; Fernandes, Alexandre M. (2018) The role of landscape change and paleoclimatic events in shaping the evolutionary history of the Polioptila Gnatcatchers (Passeriformes, Polioptilidae) with emphasis on species associated with open habitats. Journal of Avian Biology. doi.org/10.1111/jav.01692.
• Andermann, Tobias; Fernandes, Alexandre M.; Olsson, Urban; Töpel, Mats; Pfeil, Bernard; Oxelman, Bengt; Aleixo, Alexandre; Faircloth, Brant C; Antonelli, Alexandre (2018) Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements. Systematic Biology, doi: 10.1093/sysbio/syy039.
• Ferreira, Mateus; Fernandes, Alexandre M.; Aleixo, Alexandre; Antonelli, Alexandre; Olsson, Urban; Bates, John M.; Cracraft, Joel; Ribas, Camila (2018). Evidence for mtDNA capture in the jacamar Galbula leucogastra / chalcothorax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin. Molecular Phylogenetics and Evolution.

2016

• Lopes, Leonardo E.; Fernandes, Alexandre M.; Medeiros, Matthew C. I.; Marini, Miguel Ângelo (2016) A classification scheme for avian diet types. Journal of Field Ornithology, 87, 309–322.

2015

• Fernandes, A. M.; Conh-Haft, M.; Hrbek, T.; Farias, I. P. (2015) Rivers acting as barriers for bird dispersal in the Amazon. Revista Brasileira de Ornitologia, 22, 361–371.

2014

• Fernandes, A. M.; Wink, M.; Sardelli, C.; Aleixo, A. (2014) Multiple speciation across the Andes and throughout Amazonia: the case of the spot-backed antbird species complex. Journal of Biogeography, 41, 1094–1104.
• Fernandes, A. M. (2014) Phylogeographie und Artbildung von ausgewählten Singvogelarten im Amazonas-Gebiet Implikationen für die historische Biogeographie und den Artenschutz. Vogelwarte, 52, 49 –50.
• Aleixo, A.; Peterson, A. T.; Araujo-Silva, L. E.; Bandeira, C. H. M. M.; Batista, R. S. S.; Burlamaqui, T.; Dantas, S.; Fernandes, A. M.; Ferreira, M.; Martins, D. M.; Rego, P. S.; Ribas, C. C.; Rocha, T. C.; Santos, M. P. D.; Sardelli, Carla H.; Sequeira, F. G.; Soares, L. M. S.; Souza, B. R. S.; Costa, S. A.; Souza-Neves, T.; Thom, G.; Vallinoto, M. (2014) In: Instabilidade climática e diversificação de espécies na Amazônia. Cenários para a Amazônia: Clima, Biodiversidade e Uso da Terra. (ed. T. Emilio, F. Luizão). 43–53. 1ed. Manaus: INPA.

2013

• Cohn-Haft, M.; Junior, M.A.S.; Fernandes, A.M.; Ribas, C (2013) A new species of Cyanocorax jay from savannas of the central Amazon. In: Handbook of the birds of the world, Special Volume: New Species and Global Index. (ed. J. del Hoyo, A. Elliott, J. Sargatal, D. A. Christie), 48–53. Lynx Edicions, USA. ISBN-13: 978-84-96553-88-0.
• Fernandes, A.M. (2013) Fine-scale endemism of Amazonian birds in a threatened landscape. Biodiversity and Conservation, 22, 2683–2694.
• Fernandes, A.M.; Gonzalez, J.; Wink, M.; Aleixo, A. (2013) Multilocus phylogeography of the Wedge-billed Woodcreeper Glyphorynchus spirurus (Aves, Furnariidae) in lowland Amazonia: Widespread cryptic diversity and paraphyly reveal a complex diversification pattern. Molecular Phylogenetics and Evolution, 66, 270–282.

2012

• Fernandes, A.M.; Wink, M.; Aleixo, A. (2012) Phylogeography of the Chestnut-tailed Antbird (Myrmeciza hemimelaena) clarifies the role of rivers in Amazonian biogeography. Journal of Biogeography, 39, 1524–1535.

2011

• Costa, T.V.V.; Andretti, C.B.; Fernandes, A.M.; Vargas, C.F.; Bechtoldt, C.; Deslandes, V.; Cohn-Haft, M. (2011) Estação Ecológica Juami-Japurá. In: Conservação das aves migratórias neárticas no Brasil (ed by Valente, R.M.). 33–36, Conservation International.

2008

• Fernandes, A.M. & Deslandes, V. (2008) First record of the Slate Colored Seadeaters (Sporophila schistacea, Emberezidae) in Amazonas state, Brazil. Revista Brasileira de Ornitologia, 16, 67–70.
• Lopes, L.E., Malacco, G.E., Vasconcelos, M.F., Carvalho, C.E.A., Duca, C., Fernandes, A.M., Neto, S.D., Marini, M.A. (2008) Aves da região de Unaí e Cabeceira Grande, noroeste de Minas Gerais, Brasil. Revista Brasileira de Ornitologia, 16, 24–32.

2007

• Fernandes, A.M. (2007) Southern range extension for the Red-and-black Grosbeak (Periporphyrus erythromelas, Cardinalidae) Amazonia, Brazil. Revista Brasileira de Ornitologia, 15, 468–469.
• Faria, C.M.A.; Rodrigues, M.; Amaral, F.Q.; Módena, É.; Fernandes, A.M. (2007) Aves de um fragmento de Mata Atlântica no alto Rio Doce, Minas Gerais: colonização e extinção. Revista Brasileira de Zoologia, 24, 23–26.
• Cohn-Haft, M., Pacheco, A.M.F., Bechtoldt, C. L.,Torres, M. F.N., Fernandes, A.M., Sardelli, C. H., Macêdo, I. T. (2007) Inventário ornitológico. In: Biodiversidade do médio Madeira: Bases científicas para propostas de conservação (ed. by L.R. Py-Daniel, C.P. Deus, A.L. Henriques, D.M. Pimpão, M.O. Ribeiro), 145–178. INPA, Manaus.
• Cohn-Haft, M., Naka., L.N., Fernandes, A.M. (2007) Padrões de distribuição da avifauna da várzea dos rios Solimões e Amazonas. In: Conservação da várzea: identifcação e caracterização de regiões biogeográfcas (ed. by A.L.K.M. Albernaz), 287–323, Ibama/ProVárzea, Manaus, Brazil.

2006

• Pinho, J.B.; Morais, D.H.; Lopes. L.E.; Fernandes, A.M. (2006) Life history of Mato Grosso Antbird (Cercomacra melanaria) on the Brazilian Pantanal. Ibis, 148, 321–329.

2005

• Lopes, L.E., Fernandes, A.M., Marini, M. A. (2005) Diet of some Atlantic Forest birds. Ararajuba, 13, 95–103.
• Lopes, L.E., Fernandes, A.M., Marini, M.Â. (2005) Predation on vertebrate by Neotropical passerine birds Lundiana, 6, 57–66.
• Pinho, J.B., Lopes L.E., Fernandes, A.M. (2005) Nest of the Spot-backed Antbird (Hylophylax naevia) and of the Purplish Jay (Cyanocorax cyanomelas) from Brazil. Lundiana, 6, 71–73.

2004

• Lopes, L.E., Fernandes, A.M., Marini, M.Â. (2004) Comsumption of vegetable matter by Furnarioidea. Ararajuba, 11, 235–239.

2003

• Marini, M.Â., Durães, R., Lopes, L.E., Fernandes, A.M., Carvalho, C.A. (2003) Rediscovery of the Scalloped-antbird (Myrmeciza ruficauda, Thamnophilidae) at Minas Gerais state, Brazil. Cotinga, 19, 56–59.

2002

• Marini, M.Â., Lopes, L.E., Fernandes, A.M., Sebaio, F. (2002) Descrição de um ninho de Lepidocolaptes fuscus (Dendrocolaptidae) do nordeste de Minas Gerais, com dados sobre sua dieta e pterilose dos ninhegos. Revista Ararajuba, 10, 95–98.