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André M. Machado has completed his Master in Biotechnology in 2016 (University of Lisbon - Instituto Superior Técnico) and Bachelor in Biology in 2013 (University of Lisbon - Faculty of Science). Recently in 2020 he has started his PhD in Biology in the Faculty of Science - University of Porto.  Overall, since 2016, he has worked as Bioinformatician in the Interdisciplinary Centre of Marine and Environmental Research (University do Porto) where he has published 52 articles in a broad range of international journals. Additionally, in the last five years, he has participated in eight projects, four as Researcher Fellow and four as a team member, and he started his Phd in 2020. Working in a large spectrum of areas such as Evolution, Omics, Biotechnology, Water Resources, and Bioinformatics, he had the opportunity to collaborate with more than 200 different co-authors in scientific papers. Furthermore, he regularly attends scientific meetings and workshops where he presented several posters and oral presentations. Regarding the communication of science, André M. Machado has done a specific effort in advertising his work, by attending several tv/radio shows and giving or participating in interviews on the media.
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Identification

Personal identification

Full name
André Miguel Moreira Machado

Citation names

  • Machado, André
  • Andre M. Machado

Author identifiers

Ciência ID
721C-EFE7-B597
ORCID iD
0000-0002-6857-7581
Google Scholar ID
DfmwjpsAAAAJ&hl
Researcher Id
AAG-2386-2020
Scopus Author Id
57198516098

Email addresses

  • andre.machado@ciimar.up.pt (Professional)

Telephones

Telephone
  • (+351) 223401831 Ext.: 431 (Professional)

Addresses

  • CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental . Novo Edifí­cio do Terminal de Cruzeiros do Porto de Leixões , Avenida General Norton de Matos, S/N , 4450-208 , Matosinhos, Matosinhos, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Evolutionary Biology
  • Natural sciences - Biological Sciences - Biology
  • Natural sciences - Earth and Environmental Sciences - Water Resources
  • Engineering and Technology - Environmental Biotechnology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Elementary (A2) Elementary (A2) Elementary (A2) Elementary (A2)
Portuguese (Mother tongue)
Education
Degree Classification
2020/09/01 - 2024/08/31
Ongoing
 Biologia (Doutoramento)
Universidade do Porto Faculdade de Ciências, Portugal
2022/11/15 - 2022/11/17
Concluded
 “Ready for BioData Management?” – Data Stewards For Life Sciences Consolidation Course (Diploma de especialização)
BioData.pt, Portugal

Instituto Gulbenkian de Ciência, Portugal
2022/02/20 - 2022/10/01
Concluded
 Data Stewardship Program for the Life Sciences (Curso de Especialização Tecnológica)
BioData.pt, Portugal
2016
Concluded
 Master in Biotechnology (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Evolution and Bioinformatics Analysis of the Drug:H+ Antiporter Family 1 (DHA1) in the hemiascomycetes yeasts." (THESIS/DISSERTATION)
 15
2013/02 - 2013/05
Attended
 English course (Outros)
Major in Level B2
Universidade de Lisboa Faculdade de Letras, Portugal
 16
2012/12 - 2013/02
Attended
 English course (Outros)
Major in Level B1
Universidade de Lisboa Faculdade de Letras, Portugal
 15
2013
Concluded
 Bachelor's degree in Biology (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
"N/A" (THESIS/DISSERTATION)
 13
Affiliation

Science

Category
Host institution 		Employer
2019/05/01 - 2020/07/30 Researcher (Research) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2018/09/01 - 2019/03/29 Researcher (Research) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2016/09/01 - 2018/08/31 Researcher (Research) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2015/02/01 - 2016/06/01 Research Trainee (Research) Universidade de Lisboa Instituto Superior Técnico, Portugal
2013/07/01 - 2013/09/01 Research Trainee (Research) Universidade de Lisboa Faculdade de Ciências, Portugal
2013/04/01 - 2013/07/01 Researcher (Research) Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2013/02/01 - 2013/03/29 Research Trainee (Research) Universidade de Lisboa Faculdade de Ciências, Portugal
Projects

Grant

Designation Funders
2020/09/01 - 2024/08/31 MetaDef - The Evolution of the Chemical DEFensome in METAzoa
DFA/BD/8069/2020
PhD Student Fellow
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Associação para a Inovação e Desenvolvimento da FCT
Ongoing

Contract

Designation Funders
2018/10/15 - 2021/10/14 E-IMUNO: Applying elasmobranch immunogenetics to fisheries management and the study of vertebrate adaptive immunity
PTDC/ASP-PES/28053/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2018/07/02 - 2021/07/01 EvoDis-The Metazoan Endocrine System in the Anthropocene Epoch: from EVOlution to DISruption.
PTDC/CTA-AMB/31342/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2019/05/01 - 2020/07/30 The Sea and the Shore, Architecture and Marine Biology: The Impact of Sea Life on the Built Environment
PTDC/ART-DAQ/29537/2017
A&B/BM/2019-006
Research Fellow
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/09/01 - 2019/03/29 CORAL - Sustainable Ocean Exploitation: Tools and Sensors
NORTE-01-0145-FEDER-000036
CORAL_BI-MSc_2018-037
Research Fellow
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluded
2018/09 - 2019/03 CORAL - Sustainable Ocean Exploitation: Tools and Sensors
CORAL_BI-MSc_2018-037
NORTE-01-0145-FEDER-000036
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
2016/09/01 - 2018/08/29 Marinfo - Integrated Platform for Marine Data Acquisition and Analysis
NORTE-01-0145-FEDER-000031
MARINFO/BI/2016-037
Research Fellow
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2013/04/01 - 2013/07/01 Role of a patatin-like lipid acyl hydrolase in membrane degradation under water deficit: Integrating molecular and physiological approaches in Arabidopsis.
PTDC/AGR-AAM/103721/2008
Research Fellow
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Conference poster
  1. Castro, L.F.C.; Lopes-Marques, M.; Fonseca, M.; Alves, L.Q.; Andre M. Machado; Ruivo, R.. "Mammalian habitat transitions and the power of the “LossOme”.". Paper presented in Annual meeting of The Society for Molecular Biology & Evolution (SMBE 2019), 2019.
  2. Andre M. Machado; Silva, F.C.; Ferraz, R.; Ruivo, R.; Fonseca, E.; Santos, M.; Páscoa, I.; et al. "PPAR gamma evolution in teleosts: gene duplication, retention, and loss.". Paper presented in XII Congress of Asociación Ibérica de Endocrinologia Comparada (AIEC 2019), 2019.
  3. Ferraz, R.; Andre M. Machado; Ozório, R.; Oliveira, R.; Castro, L.F.C.. "From the Amazon: A comprehensive liver transcriptome of the teleost tambaqui, Colossoma Macropomum.". Paper presented in 5th Genomics in Aquaculture symposium (GIA2018), 2018.
  4. Castro, L.F.C.; Fonseca, E.; Andre M. Machado; Ruivo, R.; Lopes-Marques, M.; Fonseca, M.; Santos, M.. "The "Neglected": the "insightful" repertoire of nuclear receptors in Protostomes.". Paper presented in 7th meeting of the European Society for Evolutionary Developmental Biology (EED), 2018.
  5. Andre M. Machado; Serrapoulou, E.; Castro, L.F.C.; Vasconcelos, V.; Cunha, I.. "De novo assembly of the cement gland transcriptome of two stalked cirripede barnacles.". Paper presented in 31st CONGRESS of the European Society of Comparative Physiology and Biochemistry (ESCPB), 2018.
  6. Fonseca, E.; Andre M. Machado; Ruivo, R.; Corado, F.S.; Santos, M.; Castro, L.F.C.. "Preservation and loss of the Pregnane X Receptor in chondrichthyans shed light into the early evolution of detoxification mechanisms in gnathostomes.". Paper presented in 31st CONGRESS of the European Society of Comparative Physiology and Biochemistry (ESCPB), 2018.
  7. Castro, L.F.C.; Andre M. Machado; Lopes-Marques, M.; Fonseca, M.; Barbosa, S.; Ruivo, R.. "When less is more: the role of gene loss in phenotypic diversification.". Paper presented in Genome 10K and Genome Science Conference, 2017.
  8. Dias, P.J.; Andre M. Machado; Zhang, K.; Blake, T.; Monteiro, P.T.; Sá-Correia, I.. "Yeast Drug:H+ antiporters: comparative genomic and phylogenetic analyses and design and implementation of a dedicated database.". Paper presented in Microbiotec’15, 2015.
  9. Andre M. Machado; Silvestre, S.; Arrabaça, J.D.; Matos, A.R.. "Changes is soybean leaf lipid composition in response to drought and identification of candidate drought-induced phospholipase A genes.". Paper presented in 21 st International Symposium on Plant Lipids 2014, 2014.
  10. Machado, A.M.; Arrabaça, J.D.; Matos, A.R.. "Phospholipases A in soybean: gene identification and expression in response to drought.". Paper presented in XIII Congresso Luso - Espanhol de Fisiologia Vegetal, 2013.
  11. Andre M. Machado; Silvestre, S.; Da Silva, I.V.; Da Silva, A.B.; Da Silva, J.M.; Arrabaça, J.D.; Matos, A.R.. "Study of the contribution of the patatin-like pPLAIIa to drought tolerance using genetically modified Arabidopsis plants.". Paper presented in XIII Congresso Luso-Espanhol de Fisiologia Vegetal, 2013.
  12. Andre M. Machado; Arrabaça, J.D.; Matos, A.R.. "Searching for drought-induced phospholipase A genes: a comparative analysis between Soybean and Arabidopsis.". Paper presented in Plant Symposium "Oxidative stress and cell death in plants: mechanisms and implications", 2013.
Journal article
  1. Sergio Fernández-Boo; André Machado; L. Filipe C. Castro; Rita Azeredo; Benjamin Costas. "Unravelling the main immune repertoire of Paracentrotus lividus following Vibrio anguillarum bath challenge". Fish & Shellfish Immunology (2024): https://doi.org/10.1016/j.fsi.2024.109431.
    10.1016/j.fsi.2024.109431
  2. André M. Machado; Rodrigo Samico; Marcos Domingues; Andreas Hagemann; Luísa M.P. Valente; Arne M. Malzahn; André Gomes-dos-Santos; et al. "A whole-body transcriptome assembly of the annelid worm Hediste diversicolor". Marine Genomics (2024): http://dx.doi.org/10.1016/j.margen.2024.101084.
    10.1016/j.margen.2024.101084
  3. Rute da Fonseca; Paula F. Campos; Alba Rey-Iglesia; Gustavo V. Barroso; Lucie A. Bergeron; Manuel Nande; Tuya, F; et al. "Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia". Genes (2024): https://www.mdpi.com/2073-4425/15/2/170.
    10.3390/genes15020170
  4. André Gomes-dos-Santos; Nair Vilas-Arrondo; André M. Machado; Esther Román-Marcote; Jose Luís Del Río Iglesias; Francisco Baldó; Montse Pérez; et al. "Mitochondrial replication's role in vertebrate mtDNA strand asymmetry". Open Biology (2023): https://doi.org/10.1098/rsob.230181.
    10.1098/rsob.230181
  5. Bernardo Pinto; André M. Machado; J. Miguel Cordeiro; Salman Malakpour Kolbadinezhad; Elza Fonseca; José Pedro Andrade; Jorge Palma; et al. "Extensive gene loss parallels kidney aglomerulism in Syngnathidae". Current Biology (2023): http://dx.doi.org/10.1016/j.cub.2023.08.045.
    10.1016/j.cub.2023.08.045
  6. André Gomes-dos-Santos; Elsa Froufe; John M. Pfeiffer; Nathan Johnson; Chase Smith; André M. Machado; Luis Filipe Castro; et al. "A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)". Molecular Ecology Resources (2023): http://dx.doi.org/10.1111/1755-0998.13802.
    10.1111/1755-0998.13802
  7. André Gomes-dos-Santos; Elsa Froufe; André M Machado; Jasna Lajtner; Ján Cernecký; L Filipe C. Castro; Manuel Lopes Lima. "A PacBio Hi-Fi Genome Assembly of the Painter’s Mussel, Unio pictorum (Linnaeus, 1758)". Genome Biology and Evolution (2023): http://dx.doi.org/10.1093/gbe/evad116.
    10.1093/gbe/evad116
  8. André Gomes-dos-Santos; Manuel Lopes-Lima; M. André Machado; Amílcar Teixeira; L. Filipe C. Castro; Elsa Froufe. "PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793". Scientific Data (2023): https://doi.org/10.1038/s41597-023-02251-7.
    10.1038/s41597-023-02251-7
  9. André Gomes-dos-Santos; Manuel Lopes-Lima; André M. Machado; Thomas Forest; Guillaume Achaz; Amílcar Teixeira; Vincent Prié; L. Filipe C. Castro; Elsa Froufe. "The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)". Gigabyte (2023): https://doi.org/10.46471/gigabyte.81.
    10.46471/gigabyte.81
  10. Fabiana Neves; Antonio Muñoz-Mérida; André M. Machado; Tereza Almeida; Arnaud Gaigher; Pedro J. Esteves; L. Filipe C. Castro; Ana Veríssimo. "Corrigendum: Uncovering a 500 million year old history and evidence of pseudogenization for TLR15". Frontiers in Immunology (2023): http://dx.doi.org/10.3389/fimmu.2023.1216338.
    10.3389/fimmu.2023.1216338
  11. Fabiana Neves; Antonio Muñoz-Mérida; André M. Machado; Tereza Almeida; Arnaud Gaigher; Pedro J. Esteves; L. Filipe C. Castro; Ana Veríssimo. "Uncovering a 500 million year old history and evidence of pseudogenization for TLR15". Frontiers in Immunology (2022): http://dx.doi.org/10.3389/fimmu.2022.1020601.
    10.3389/fimmu.2022.1020601
  12. Osamu Nishimura; John Rozewicki; Kazuaki Yamaguchi; Kaori Tatsumi; Yuta Ohishi; Tazro Ohta; Masaru Yagura; et al. "Squalomix: shark and ray genome analysis consortium and its data sharing platform". F1000Research (2022): http://dx.doi.org/10.12688/f1000research.123591.1.
    10.12688/f1000research.123591.1
  13. André Gomes-dos-Santos; André M. Machado; L. Filipe C. Castro; Vincent Prié; Amílcar Teixeira; Manuel Lopes-Lima; Elsa Froufe. "The gill transcriptome of threatened European freshwater mussels". Scientific Data (2022): https://doi.org/10.1038/s41597-022-01613-x.
    10.1038/s41597-022-01613-x
  14. Renato B. Ferraz; Rômulo V. Paixão; Mónica Lopes-Marques; André M. Machado; Ana L. Salaro; L. Filipe C. Castro; Óscar Monroig; Fernanda L.A. O'Sullivan. "The repertoire of the elongation of very long-chain fatty acids (Elovl) protein family is conserved in tambaqui (Colossoma macropomum): Gene expression profiles offer insights into the sexual differentiation process". Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology (2022): http://dx.doi.org/10.1016/j.cbpb.2022.110749.
    10.1016/j.cbpb.2022.110749
  15. Nande, M.; Monroig, Ó.; Andre M. Machado; Castro, L.F.C.; Lopes-Marques, M.; Capitão, A.; Navarro, J.C.. "Dietary lipids as modulators of fatty acid profile and gene expression patterns on body compartments of Octopus vulgaris paralarvae". Aquaculture 556 (2022): 738293. http://dx.doi.org/10.1016/j.aquaculture.2022.738293.
    10.1016/j.aquaculture.2022.738293
  16. Vilas-Arrondo, Nair; Gomes-dos-Santos, André; Pérez, Montse; Baldó, Francisco; Veríssimo, Ana; Catarino, Diana; Andre M. Machado; et al. "A mitochondrial genome assembly of the opal chimaera, Chimaera opalescens Luchetti, Iglésias et Sellos 2011, using PacBio HiFi long reads". Mitochondrial DNA Part B 7 3 (2022): 434-437. http://dx.doi.org/10.1080/23802359.2022.2044403.
    10.1080/23802359.2022.2044403
  17. Neuparth, T.; Alves, N.; Machado, A.M.; Pinheiro, M.; Montes, R.; Rodil, R.; Barros, S.; et al. "Neuroendocrine pathways at risk? Simvastatin induces inter and transgenerational disruption in the keystone amphipod Gammarus locusta". Aquatic Toxicology 244 (2022): 106095. http://dx.doi.org/10.1016/j.aquatox.2022.106095.
    10.1016/j.aquatox.2022.106095
  18. Machado, André M.; Gomes-dos-Santos, André; Fonseca, Miguel M.; da Fonseca, Rute R.; Veríssimo, Ana; Felício, Mónica; Capela, Ricardo; et al. "A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource". Gigabyte 2022 (2022): 1-21. http://dx.doi.org/10.46471/gigabyte.40.
    10.46471/gigabyte.40
  19. Machado, André M.; Fernández-Boo, Sergio; Nande, Manuel; Pinto, Rui; Costas, Benjamin; Castro, L. Filipe C.. "The male and female gonad transcriptome of the edible sea urchin, Paracentrotus lividus: Identification of sex-related and lipid biosynthesis genes". Aquaculture Reports 22 (2022): 100936. http://dx.doi.org/10.1016/j.aqrep.2021.100936.
    10.1016/j.aqrep.2021.100936
  20. Páscoa, Inês; Fonseca, Elza; Ferraz, Renato; Machado, André M.; Conrado, Francisca; Ruivo, Raquel; Cunha, Isabel; Castro, Luís Filipe C.. "The Preservation of PPAR¿ Genome Duplicates in Some Teleost Lineages: Insights into Lipid Metabolism and Xenobiotic Exploitation". Genes 13 1 (2022): 107. http://dx.doi.org/10.3390/genes13010107.
    10.3390/genes13010107
  21. Ferreira, Daniela; Figueiredo, Joana; Laureano, Gonçalo; Machado, André; Arrabaça, João Daniel; Duarte, Bernardo; Figueiredo, Andreia; Matos, Ana Rita. "Membrane remodelling and triacylglycerol accumulation in drought stress resistance: The case study of soybean phospholipases A". Plant Physiology and Biochemistry 169 (2021): 9-21. http://dx.doi.org/10.1016/j.plaphy.2021.10.033.
    10.1016/j.plaphy.2021.10.033
  22. Alves, Luís Q.; Ruivo, Raquel; Valente, Raul; Fonseca, Miguel M.; Machado, André M.; Plön, Stephanie; Monteiro, Nuno; et al. "A drastic shift in the energetic landscape of toothed whale sperm cells". Current Biology 31 16 (2021): 3648-3655.e9. http://dx.doi.org/10.1016/j.cub.2021.05.062.
    10.1016/j.cub.2021.05.062
  23. Almeida, Tereza; Ohta, Yuko; Gaigher, Arnaud; Muñoz-Mérida, Antonio; Neves, Fabiana; Castro, L. Filipe C.; Machado, André M.; et al. "A Highly Complex, MHC-Linked, 350 Million-Year-Old Shark Nonclassical Class I Lineage". The Journal of Immunology 207 3 (2021): 824-836. http://dx.doi.org/10.4049/jimmunol.2000851.
    10.4049/jimmunol.2000851
  24. Barros-García, David; Gomes-dos-Santos, André; Machado, André M.; Castro, L. Filipe C.; de Carlos, Alejandro; Bañón, Rafael; Bruno, Isabel; Arronte, Juan C.; Froufe, Elsa. "Complete mitogenome of the Oven's halosaur, Halosaurus ovenii (Elopomorpha; Notacanthiformes)". Mitochondrial DNA Part B 6 4 (2021): 1571-1572. http://dx.doi.org/10.1080/23802359.2021.1914518.
    10.1080/23802359.2021.1914518
  25. Domínguez-Pérez, Dany; Almeida, Daniela; Wissing, Josef; Machado, André M.; Jänsch, Lothar; Antunes, Agostinho; Castro, Luís Filipe; et al. "Proteogenomic Characterization of the Cement and Adhesive Gland of the Pelagic Gooseneck Barnacle Lepas anatifera". International Journal of Molecular Sciences 22 7 (2021): 3370. http://dx.doi.org/10.3390/ijms22073370.
    10.3390/ijms22073370
  26. Gomes-dos-Santos, André; Lopes-Lima, Manuel; Machado, André M; Marcos Ramos, António; Usié, Ana; Bolotov, Ivan N; Vikhrev, Ilya V; et al. "The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)". DNA Research 28 2 (2021): http://dx.doi.org/10.1093/dnares/dsab002.
    10.1093/dnares/dsab002
  27. Gomes-dos-Santos, André; Machado, André M.; Aranha, Sofia Graça; Dias, Ester; Veríssimo, Ana; Castro, L. Filipe C.; Froufe, Elsa. "The complete mitochondrial genome of the endemic Iberian pygmy skate Neoraja iberica Stehmann, Séret, Costa, & Baro 2008 (Elasmobranchii, Rajidae)". Mitochondrial DNA Part B 6 3 (2021): 848-850. http://dx.doi.org/10.1080/23802359.2021.1884030.
    10.1080/23802359.2021.1884030
  28. Gomes-dos-Santos, André; Vilas-Arrondo, Nair; Machado, André M.; Veríssimo, Ana; Pérez, Montse; Baldó, Francisco; Castro, L. Filipe C.; Froufe, Elsa. "Shedding light on the Chimaeridae taxonomy: the complete mitochondrial genome of the cartilaginous fish Hydrolagus mirabilis (Collett, 1904) (Holocephali: Chimaeridae)". Mitochondrial DNA Part B 6 2 (2021): 420-422. http://dx.doi.org/10.1080/23802359.2020.1870887.
    10.1080/23802359.2020.1870887
  29. Neuparth, T.; Machado, A.M.; Montes, R.; Rodil, R.; Barros, S.; Alves, N.; Ruivo, R.; et al. "Transgenerational inheritance of chemical-induced signature: A case study with simvastatin". Environment International 144 (2020): 106020. http://dx.doi.org/10.1016/j.envint.2020.106020.
    10.1016/j.envint.2020.106020
  30. Espregueira Themudo, Gonçalo; Alves, Luís Q.; Machado, André M.; Lopes-Marques, Mónica; da Fonseca, Rute R.; Fonseca, Miguel; Ruivo, Raquel; Castro, L. Filipe C.. "Losing Genes: The Evolutionary Remodeling of Cetacea Skin". Frontiers in Marine Science 7 (2020): http://dx.doi.org/10.3389/fmars.2020.592375.
    10.3389/fmars.2020.592375
  31. Neuparth, Teresa; Machado, André M.; Montes, Rosa; Rodil, Rosario; Barros, Susana; Alves, Nélson; Ruivo, Raquel; et al. "Transcriptomic data on the transgenerational exposure of the keystone amphipod Gammarus locusta to simvastatin". Data in Brief 32 (2020): 106248. http://dx.doi.org/10.1016/j.dib.2020.106248.
    10.1016/j.dib.2020.106248
  32. Fonseca, Elza; Machado, André M.; Vilas-Arrondo, Nair; Gomes-dos-Santos, André; Veríssimo, Ana; Esteves, Pedro; Almeida, Tereza; et al. "Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes". General and Comparative Endocrinology 295 (2020): 113527. http://dx.doi.org/10.1016/j.ygcen.2020.113527.
    10.1016/j.ygcen.2020.113527
  33. Azevedo, Joana; Antunes, Jorge T.; Machado, André M.; Vasconcelos, Vitor; Leão, Pedro N.; Froufe, Elsa. "Monitoring of biofouling communities in a Portuguese port using a combined morphological and metabarcoding approach". Scientific Reports 10 1 (2020): http://dx.doi.org/10.1038/s41598-020-70307-4.
    10.1038/s41598-020-70307-4
  34. Ferraz, Renato B.; Machado, André M.; Navarro, Juan C.; Cunha, Isabel; Ozório, Rodrigo; Salaro, Ana L.; Castro, L. Filipe C.; Monroig, Óscar. "The fatty acid elongation genes elovl4a and elovl4b are present and functional in the genome of tambaqui (Colossoma macropomum)". Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 245 (2020): 110447. http://dx.doi.org/10.1016/j.cbpb.2020.110447.
    10.1016/j.cbpb.2020.110447
  35. Andre M. Machado; Antonio Muñoz-Merida; Elza Fonseca; Ana Verissimo; Rui Pinto; Mónica Felício; Rute R. da Fonseca; Elsa Froufe; L. Filipe C.Castro. "Liver transcriptome resources of four commercially exploited teleost species". Scientific Data (2020): http://dx.doi.org/10.1038/s41597-020-0565-9.
    10.1038/s41597-020-0565-9
  36. Domínguez-Pérez, Dany; Almeida, Daniela; Wissing, Josef; Machado, André M.; Jänsch, Lothar; Castro, Luís Filipe; Antunes, Agostinho; et al. "The Quantitative Proteome of the Cement and Adhesive Gland of the Pedunculate Barnacle, Pollicipes pollicipes". International Journal of Molecular Sciences 21 7 (2020): 2524. http://dx.doi.org/10.3390/ijms21072524.
    10.3390/ijms21072524
  37. Gomes-dos-Santos, André; Arrondo, Nair Vilas; Machado, André M.; Veríssimo, Ana; Pérez, Montse; Román, Esther; Castro, L. Filipe C.; Froufe, Elsa. "The complete mitochondrial genome of the deep-water cartilaginous fish Hydrolagus affinis (de Brito Capello, 1868) (Holocephali: Chimaeridae)". Mitochondrial DNA Part B 5 2 (2020): 1810-1812. http://dx.doi.org/10.1080/23802359.2020.1749154.
    10.1080/23802359.2020.1749154
  38. Barros-García, David; Gomes-dos-Santos, André; Machado, André M.; Castro, L. Filipe C.; de Carlos, Alejandro; Bañón, Rafael; Bruno, Isabel; Arronte, Juan C.; Froufe, Elsa. "Complete mitogenome of the shortfin spiny eel, Notacanthus bonaparte (Elopomorpha; Notacanthiformes)". Mitochondrial DNA Part B 5 2 (2020): 1421-1422. http://dx.doi.org/10.1080/23802359.2020.1736672.
    10.1080/23802359.2020.1736672
  39. da Fonseca, Rute R; Couto, Alvarina; Machado, Andre M; Brejova, Brona; Albertin, Carolin B; Silva, Filipe; Gardner, Paul; et al. "A draft genome sequence of the elusive giant squid, Architeuthis dux". GigaScience 9 1 (2020): http://dx.doi.org/10.1093/gigascience/giz152.
    10.1093/gigascience/giz152
  40. Machado, André M.; Sarropoulou, Elena; Castro, L. Filipe C.; Vasconcelos, Vitor; Cunha, Isabel. "An important resource for understanding bio-adhesion mechanisms: Cement gland transcriptomes of two goose barnacles, Pollicipes pollicipes and Lepas anatifera (Cirripedia, Thoracica)". Marine Genomics 45 (2019): 16-20. http://dx.doi.org/10.1016/j.margen.2018.11.001.
    10.1016/j.margen.2018.11.001
  41. Fonseca, Elza S. S.; Ruivo, Raquel; Machado, André M.; Conrado, Francisca; Tay, Boon-Hui; Venkatesh, Byrappa; Santos, Miguel M.; Castro, L. Filipe C.. "Evolutionary Plasticity in Detoxification Gene Modules: The Preservation and Loss of the Pregnane X Receptor in Chondrichthyes Lineages". International Journal of Molecular Sciences 20 9 (2019): 2331. http://dx.doi.org/10.3390/ijms20092331.
    10.3390/ijms20092331
  42. Lopes-Marques, Mónica; Alves, Luís Q.; Fonseca, Miguel M.; Secci-Petretto, Giulia; Machado, André M.; Ruivo, Raquel; Castro, L. Filipe C.. "Convergent inactivation of the skin-specific C-C motif chemokine ligand 27 in mammalian evolution". Immunogenetics 71 5-6 (2019): 363-372. http://dx.doi.org/10.1007/s00251-019-01114-z.
    10.1007/s00251-019-01114-z
  43. Machado, André M.; Ferraz, Renato; Ribeiro, Ricardo do Amaral; Ozório, Rodrigo; Castro, L. Filipe C.. "From the Amazon: A comprehensive liver transcriptome dataset of the teleost fish tambaqui, Colossoma macropomum". Data in Brief 23 (2019): 103751. http://dx.doi.org/10.1016/j.dib.2019.103751.
    10.1016/j.dib.2019.103751
  44. Lopes-Marques, Mónica; Machado, André M; Alves, Luís Q; Fonseca, Miguel M; Barbosa, Susana; Sinding, Mikkel-Holger S; Rasmussen, Marianne Helene; et al. "Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea". Molecular Biology and Evolution 36 6 (2019): 1270-1280. http://dx.doi.org/10.1093/molbev/msz068.
    10.1093/molbev/msz068
  45. Lopes-Marques, Mónica; Ruivo, Raquel; Alves, Luís Q.; Sousa, Nelson; Machado, André M.; Castro, L. Filipe C.. "The Singularity of Cetacea Behavior Parallels the Complete Inactivation of Melatonin Gene Modules". Genes 10 2 (2019): 121. http://dx.doi.org/10.3390/genes10020121.
    10.3390/genes10020121
  46. Oliveira, Diogo; M. Machado, André; Cardoso, Tiago; Lopes-Marques, Mónica; C. Castro, L. Filipe; Ruivo, Raquel. "Identification of a Novel Nucleobase-Ascorbate Transporter Family Member in Fish and Amphibians". Fishes 4 1 (2019): 1. http://dx.doi.org/10.3390/fishes4010001.
    10.3390/fishes4010001
  47. Ferraz, Renato B.; Kabeya, Naoki; Lopes-Marques, Mónica; Machado, André M.; Ribeiro, Ricardo A.; Salaro, Ana L.; Ozório, Rodrigo; Castro, L. Filipe C.; Monroig, Óscar. "A complete enzymatic capacity for long-chain polyunsaturated fatty acid biosynthesis is present in the Amazonian teleost tambaqui, Colossoma macropomum". Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 227 (2019): 90-97. http://dx.doi.org/10.1016/j.cbpb.2018.09.003.
    10.1016/j.cbpb.2018.09.003
  48. Andre M. Machado. "Cetacea are natural knockouts for IL20". Immunogenetics (2018): http://dx.doi.org/10.1007/s00251-018-1071-5.
    10.1007/s00251-018-1071-5
  49. Andre M. Machado. "“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus". Genes (2018): http://dx.doi.org/10.3390/genes9100485.
    10.3390/genes9100485
  50. Lopes-Marques, Mónica; Machado, André M.; Ruivo, Raquel; Fonseca, Elza; Carvalho, Estela; Castro, L. Filipe C.. "Expansion, retention and loss in the Acyl-CoA synthetase “ Bubblegum ” ( Acsbg ) gene family in vertebrate history". Gene 664 (2018): 111-118. http://dx.doi.org/10.1016/j.gene.2018.04.058.
    10.1016/j.gene.2018.04.058
  51. Andre M. Machado. "A resource for sustainable management: De novo assembly and annotation of the liver transcriptome of the Atlantic chub mackerel, Scomber colias". Data in Brief (2018): http://dx.doi.org/10.1016/j.dib.2018.03.013.
    10.1016/j.dib.2018.03.013
  52. Machado, André M.; Almeida, Tereza; Mucientes, Gonzalo; Esteves, Pedro J.; Verissimo, Ana; Castro, L. Filipe C.. "De novo assembly of the kidney and spleen transcriptomes of the cosmopolitan blue shark, Prionace glauca". Marine Genomics 37 (2018): 50-53. http://dx.doi.org/10.1016/j.margen.2017.11.009.
    10.1016/j.margen.2017.11.009
Thesis / Dissertation
  1. Andre M. Machado. "Evolution and Bioinformatics Analysis of the Drug: H+ Antiporter Family 1 (DHA1) in the hemiascomycetes yeasts". Master, Universidade de Lisboa Instituto Superior Técnico, 2016. https://fenix.tecnico.ulisboa.pt/cursos/mbiotec/dissertacao/846778572211587.

Other

Dataset
  1. Tereza Almeida; Yuko Ohta; Arnaud Gaigher; Antonio Muñoz-Merida; Fabiana Neves; L. Filipe C. Castro; André M. Machado; et al. A Highly Complex, MHC-Linked, 350 Million-Year-Old Shark Nonclassical Class I Lineage.. 2021.
    10.6084/m9.figshare.14932545
Activities

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2019 - 2019 BioMarine Business Conventions 2019 (2019/11/04 - 2019/11/05)
Conference (Member of the Organising Committee)

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2018/10/02 - 2018/10/04 BioMarine Business Conventions 2018
Conference
 BioMarine Business Conventions 2018
2018/03/13 - 2018/03/16 Course " de novo Assembly 2018 " The course will provide a hands-on introduction to de novo assembly, followed by in-depth analysis of the key stages in the process.
Workshop
 de novo Assembly 2018
Earlham Institute, United Kingdom
2013 - 2013 Course " GC, SPE e EZ:fast Tecnocroma "
Workshop
 Course " GC, SPE e EZ:fast Tecnocroma "
Universidade de Lisboa Faculdade de Ciências, Portugal
2009/02 - 2009/10 A Evolução de Darwin - Addressing several topics directly or indirectly related with the theory of Darwinian evolution.
Conference
 A Evolução de Darwin - Addressing several topics directly or indirectly related with the theory of Darwinian evolution.
Fundação Calouste Gulbenkian, Portugal

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2020/01/16 Genoma da lula-gigante não é assim tão gigante Equipa liderada por uma investigadora portuguesa sequenciou o genoma completo da lula-gigante, revelando um pouco mais sobre este invertebrado que pode atingir 13 metros de comprimento e pesar mais de 900 quilos. Público
2020/01/16 Investigadores do CIIMAR ajudam a desvendar ADN de "monstro" marinho. Equipa de cientistas conseguiu sequenciar pela primeira vez o genoma completo da lula gigante, oferecendo novas luzes sobre a sua vida no mar profundo. Notícias U.Porto - Universidade do Porto
2018/10/20 CIIMAR coordena estudo sobre genoma da sardinha agora divulgado em revista científica. Estudo coordenado pelo CIIMAR e com apoio de investigadores do IPMA fez progressos sobre a dieta da sardinha e por essa via, sobre a sua produção em cativeiro . Jornal de Economia do Mar
2018/10/18 Investigadores do CIIMAR desvendam genoma da Sardinha. Estudo internacional liderado pelo Centro Interdisciplinar de Investigação Marinha e Ambiental elucida ainda sobre a capacidade daquela espécie em biossintetizar os famosos ómega-3. Notícias U.Porto - Universidade do Porto
2018/10/16 CIIMAR coordena estudo sobre genoma da sardinha agora divulgado em revista científica. APP – Associação dos Portos de Portugal – Noticias
2018/10/13 Eis (finalmente) o genoma da sardinha. E em duplicado. Dois trabalhos independentes realizados com investigadores portugueses de diferentes instituições divulgaram esta semana o genoma da sardinha. É o mesmo genoma da mesma espécie com o mesmo objectivo: disponibilizar uma ferramenta para proteger a sardinha. Público

Interview (tv / radio show)

Program Topic
2018/11/03 - 2018/11/03 Mentes que Brilham Será possível criar sardinha em cativeiro?
2018 - 2018 Os Dias do Futuro - Série de programas semanal, na Antena 1, focado nos investigadores, na inovação e nos projetos de desenvolvimento - Inclui o programa - "Ponto de Partida". Ponto de Partida 94 - Rica Sardinha
Distinctions

Other distinction

2018 Competetive selection course - "de novo Assembly 2018", Mar 2018.
Earlham Institute, United Kingdom