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A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida).
Gomes-Dos-Santos A, Froufe E, Pfeiffer JM, Johnson NA, Smith CH, Machado AM, C Castro LF, Do VT, Hattori A, Garrison N, Whelan NV, Bolotov IN, Vikhrev IV, Kondakov AV, Ghamizi M, Prié V, Bogan AE, Lopes Lima M. Gomes-Dos-Santos A, et al. Among authors: machado am. Mol Ecol Resour. 2023 Aug;23(6):1403-1422. doi: 10.1111/1755-0998.13802. Epub 2023 Apr 24. Mol Ecol Resour. 2023. PMID: 37092367
"Out of the Can": A Draft Genome Assembly, Liver Transcriptome, and Nutrigenomics of the European Sardine, Sardina pilchardus.
Machado AM, Tørresen OK, Kabeya N, Couto A, Petersen B, Felício M, Campos PF, Fonseca E, Bandarra N, Lopes-Marques M, Ferraz R, Ruivo R, Fonseca MM, Jentoft S, Monroig Ó, da Fonseca RR, C Castro LF. Machado AM, et al. Genes (Basel). 2018 Oct 9;9(10):485. doi: 10.3390/genes9100485. Genes (Basel). 2018. PMID: 30304855 Free PMC article.
Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes.
Fonseca E, Machado AM, Vilas-Arrondo N, Gomes-Dos-Santos A, Veríssimo A, Esteves P, Almeida T, Themudo G, Ruivo R, Pérez M, da Fonseca R, Santos MM, Froufe E, Román-Marcote E, Venkatesh B, Castro LFC. Fonseca E, et al. Among authors: machado am. Gen Comp Endocrinol. 2020 Sep 1;295:113527. doi: 10.1016/j.ygcen.2020.113527. Epub 2020 Jun 8. Gen Comp Endocrinol. 2020. PMID: 32526329
Shedding light on the Chimaeridae taxonomy: the complete mitochondrial genome of the cartilaginous fish Hydrolagus mirabilis (Collett, 1904) (Holocephali: Chimaeridae).
Gomes-Dos-Santos A, Vilas-Arrondo N, Machado AM, Veríssimo A, Pérez M, Baldó F, Castro LFC, Froufe E. Gomes-Dos-Santos A, et al. Among authors: machado am. Mitochondrial DNA B Resour. 2021 Feb 9;6(2):420-422. doi: 10.1080/23802359.2020.1870887. Mitochondrial DNA B Resour. 2021. PMID: 33659699 Free PMC article.
The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758).
Gomes-Dos-Santos A, Lopes-Lima M, Machado AM, Marcos Ramos A, Usié A, Bolotov IN, Vikhrev IV, Breton S, Castro LFC, da Fonseca RR, Geist J, Österling ME, Prié V, Teixeira A, Gan HM, Simakov O, Froufe E. Gomes-Dos-Santos A, et al. Among authors: machado am. DNA Res. 2021 May 2;28(2):dsab002. doi: 10.1093/dnares/dsab002. DNA Res. 2021. PMID: 33755103 Free PMC article.
A mitochondrial genome assembly of the opal chimaera, Chimaera opalescens Luchetti, Iglésias et Sellos 2011, using PacBio HiFi long reads.
Vilas-Arrondo N, Gomes-Dos-Santos A, Pérez M, Baldó F, Veríssimo A, Catarino D, Machado AM, Román-Marcote E, Bañón R, Froufe E, Castro LFC. Vilas-Arrondo N, et al. Among authors: machado am. Mitochondrial DNA B Resour. 2022 Mar 2;7(3):434-437. doi: 10.1080/23802359.2022.2044403. eCollection 2022. Mitochondrial DNA B Resour. 2022. PMID: 35274036 Free PMC article.
The gill transcriptome of threatened European freshwater mussels.
Gomes-Dos-Santos A, Machado AM, Castro LFC, Prié V, Teixeira A, Lopes-Lima M, Froufe E. Gomes-Dos-Santos A, et al. Among authors: machado am. Sci Data. 2022 Aug 13;9(1):494. doi: 10.1038/s41597-022-01613-x. Sci Data. 2022. PMID: 35963883 Free PMC article.
177 results