OP
Octávio S. Paulo
Genetic VariationPhylogenyBiological EvolutioncoffeeSelection, GeneticTranscriptomefunctional analysisQuercusCoffeaGene Expression Regulation, Plant
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
76 papers in the corpus · 1994–2026Conservation profile of the largest Palearctic silverfish and Europe's largest cave-adapted terrestrial insect: Squamatinia algharbica (Zygentoma, Nicoletiidae).41835978 · Reboleira, Ana Sofia P S, Galhofa, Davide, Viegas, Mariana et al.2026 · 0 citationsBiodiversity data journal. 2026;14:e171822
Natural selection preserves trans-specific chloroplast diversity in a Mediterranean evergreen oak.41092295 · de Sousa, Filipe, Bilro, João, Viegas, Mariana Bray et al.2026 · 0 citationsJournal of evolutionary biology. 2026;39(1):122-136
Identification of tuna species used by the Portuguese canning industry through a DNA-based approach.41290749 · Silva, Maria Inês, Viegas, Mariana Bray, Sousa, Filipe et al.2025 · 0 citationsScientific reports. 2025;15(1):41802
Mito-nuclear discordance reveals introgressive hybridization following vicariance and secondary contact in Iberian scorpions (Buthidae: Buthus).41126048 · Blasco-Aróstegui, Javier, Simone, Yuri, Paulo, Octávio S et al.2025 · 4 citationsBMC ecology and evolution. 2025;25(1):112
Prediction of Antibiotic Resistance Genes in Cyanobacterial Strains by Whole Genome Sequencing.40572139 · Balata, Duarte, Rosado, Tânia, Pina-Martins, Francisco et al.2025 · 1 citationMicroorganisms. 2025;13(6)
Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection.39730618 · Vieira, Ana Rita, de Sousa, Filipe, Bilro, João et al.2024 · 5 citationsScientific reports. 2024;14(1):30977
Building a Portuguese coalition for biodiversity genomics.39289491 · Marques, João P, Alves, Paulo C, Amorim, Isabel R et al.2024 · 5 citationsnpj biodiversity. 2024;3(1):27
Transcriptomic Analyses Reveal That Coffea arabica and Coffea canephora Have More Complex Responses under Combined Heat and Drought than under Individual Stressors.39063237 · Marques, Isabel, Fernandes, Isabel, Paulo, Octávio S et al.2024 · 14 citationsInternational journal of molecular sciences. 2024;25(14)
Ovule Transcriptome Analysis Discloses Deregulation of Genes and Pathways in Sexual and Apomictic Limonium Species (Plumbaginaceae).37107659 · Caperta, Ana D, Fernandes, Isabel, Conceição, Sofia I R et al.2023 · 5 citationsGenes. 2023;14(4)
Overexpression of Water-Responsive Genes Promoted by Elevated CO2 Reduces ROS and Enhances Drought Tolerance in Coffea Species.36834624 · Marques, Isabel, Fernandes, Isabel, Paulo, Octávio S et al.2023 · 15 citationsInternational journal of molecular sciences. 2023;24(4)
Correction: A first look at sea-lavenders genomics - can genome wide SNP information tip the scales of controversy in the Limonium vulgare species complex?36737677 · Pina-Martins, Francisco, Caperta, Ana D, Conceicao, Sofia I R et al.2023 · 1 citationBMC plant biology. 2023;23(1):76
A first look at sea-lavenders genomics - can genome wide SNP information tip the scales of controversy in the Limonium vulgare species complex?36642719 · Pina-Martins, Francisco, Caperta, Ana D, Conceição, Sofia I R et al.2023 · 7 citationsBMC plant biology. 2023;23(1):34
Integrative analysis reveals the divergence and speciation between sister Sooty Copper butterflies Lycaena bleusei and L. tityrus.36621583 · Marabuto, Eduardo, Nunes, Miguel S, Martins, Renata et al.2023 · 4 citationsMolecular phylogenetics and evolution. 2023;180:107699
Testing drivers of acoustic divergence in cicadas (Cicadidae: Tettigettalna).36514855 · Mendes, Raquel, Nunes, Vera L, Marabuto, Eduardo et al.2023 · 4 citationsJournal of evolutionary biology. 2023;36(2):461-479
Salt Stress Tolerance in Casuarina glauca: Insights from the Branchlets Transcriptome.36365395 · Fernandes, Isabel, Paulo, Octávio S, Marques, Isabel et al.2022 · 10 citationsPlants (Basel, Switzerland). 2022;11(21)
Worldwide Population Structure of the Coffee Rust Fungus Hemileia vastatrix Is Strongly Shaped by Local Adaptation and Breeding History.35322716 · Rodrigues, Ana Sofia B, Silva, Diogo Nuno, Várzea, Vitor et al.2022 · 19 citationsPhytopathology. 2022;112(9):1998-2011
Population structure in Quercus suber L. revealed by nuclear microsatellite markers.35729909 · Sousa, Filipe, Costa, Joana, Ribeiro, Carla et al.2023 · 16 citationsPeerJ. 2022;10:e13565
Global urban environmental change drives adaptation in white clover.35298255 · Santangelo, James S, Ness, Rob W, Cohan, Beata et al.2022 · 193 citationsScience (New York, N.Y.). 2022;375(6586):1275-1281
Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data.34131518 · Seabra, Sofia G, Rodrigues, Ana S B, Silva, Sara E et al.2024 · 11 citationsPeerJ. 2021;9:e11425
A Transcriptomic Approach to Understanding the Combined Impacts of Supra-Optimal Temperatures and CO2 Revealed Different Responses in the Polyploid Coffea arabica and Its Diploid Progenitor C. canephora.33803866 · Marques, Isabel, Fernandes, Isabel, Paulo, Octávio S et al.2021 · 26 citationsInternational journal of molecular sciences. 2021;22(6)
Using gradient Forest to predict climate response and adaptation in Cork oak.33484040 · Vanhove, Mathieu, Pina-Martins, Francisco, Coelho, Ana Cristina et al.2021 · 56 citationsJournal of evolutionary biology. 2021;34(6):910-923
Transcriptomic Leaf Profiling Reveals Differential Responses of the Two Most Traded Coffee Species to Elevated [CO2].33287164 · Marques, Isabel, Fernandes, Isabel, David, Pedro H C et al.2021 · 17 citationsInternational journal of molecular sciences. 2020;21(23)
Corrigendum to "Molecular phylogeny and DNA barcoding in the meadow-spittlebug Philaenus spumarius (Hemiptera, Cercopidae) and its related species" [Mol. Phylogenet. Evol. 56 (2010) 462-467].32781419 · Seabra, S G, Pina-Martins, F, Marabuto, E et al.2020 · 2 citationsMolecular phylogenetics and evolution. 2020;152:106888
Correction to: Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources.32209049 · Rodrigues, Ana S B, Silva, Sara E, Pina-Martins, Francisco et al.2020 · 0 citationsBMC genetics. 2020;21(1):36
Highly regional population structure of Spondyliosoma cantharus depicted by nuclear and mitochondrial DNA data.32132605 · Neves, Ana, Vieira, Ana Rita, Sequeira, Vera et al.2020 · 8 citationsScientific reports. 2020;10(1):4063
Standardised inventories of spiders (Arachnida, Araneae) of Macaronesia II: The native forests and dry habitats of Madeira archipelago (Madeira and Porto Santo islands).31992947 · Malumbres-Olarte, Jagoba, Boieiro, Mário, Cardoso, Pedro et al.2022 · 15 citationsBiodiversity data journal. 2020;8:e47502
Genome-Wide Signatures of Selection in Colletotrichum kahawae Reveal Candidate Genes Potentially Involved in Pathogenicity and Aggressiveness.31275287 · Vieira, Ana, Silva, Diogo Nuno, Várzea, Vitor et al.2024 · 19 citationsFrontiers in microbiology. 2019;10:1374
Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity.31174340 · Romeiras, Maria M, Pena, Ana Rita, Menezes, Tiago et al.2019 · 16 citationsInternational journal of molecular sciences. 2019;20(11)
Genomic signatures of introgression between commercial and native bumblebees, Bombus terrestris, in western Iberian Peninsula-Implications for conservation and trade regulation.30976302 · Seabra, Sofia G, Silva, Sara E, Nunes, Vera L et al.2023 · 36 citationsEvolutionary applications. 2019;12(4):679-691
New insights into adaptation and population structure of cork oak using genotyping by sequencing.30358018 · Pina-Martins, Francisco, Baptista, João, Pappas, Georgios et al.2019 · 95 citationsGlobal change biology. 2019;25(1):337-350
Novel insights on colonization routes and evolutionary potential of Colletotrichum kahawae, a severe pathogen of Coffea arabica.30073748 · Vieira, Ana, Silva, Diogo Nuno, Várzea, Victor et al.2019 · 19 citationsMolecular plant pathology. 2018;19(11):2488-2501
Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust.29328532 · Silva, Diogo Nuno, Várzea, Vítor, Paulo, Octávio Salgueiro et al.2019 · 47 citationsMolecular plant pathology. 2018;19(7):1742-1753
Genetic and Genomic Tools to Asssist Sugar Beet Improvement: The Value of the Crop Wild Relatives.29467772 · Monteiro, Filipa, Frese, Lothar, Castro, Sílvia et al.2024 · 85 citationsFrontiers in plant science. 2018;9:74
New data on polymorphism of the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) from the island of São Miguel (Azores).29689902 · Borges, Paulo A V, Rodrigues, Ana S B, Silva, Sara E et al.2018 · 10 citationsZootaxa. 2018;4369(1):144-150
Structure_threader: An improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems.28776963 · Pina-Martins, Francisco, Silva, Diogo N, Fino, Joana et al.2018 · 130 citationsMolecular ecology resources. 2017;17(6):e268-e274
Morphology, songs and genetics identify two new cicada species from Morocco: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. & sp. nov. (Hemiptera: Cicadettini).28264279 · Costa, Gonçalo João, Nunes, Vera L, Marabuto, Eduardo et al.2017 · 5 citationsZootaxa. 2017;4237(3):zootaxa.4237.3.4
Genetic and Morphological Variation of the Forkbeard, Phycis phycis (Pisces, Phycidae): Evidence of Panmixia and Recent Population Expansion along Its Distribution Area.27941988 · Vieira, Ana Rita, Rodrigues, Ana Sofia B, Sequeira, Vera et al.2017 · 28 citationsPloS one. 2016;11(12):e0167045
Revisiting Vitis vinifera Subtilase Gene Family: A Possible Role in Grapevine Resistance against Plasmopara viticola.27933087 · Figueiredo, Joana, Costa, Gonçalo J, Maia, Marisa et al.2023 · 39 citationsFrontiers in plant science. 2016;7:1783
Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources.27846816 · Rodrigues, Ana S B, Silva, Sara E, Pina-Martins, Francisco et al.2017 · 21 citationsBMC genetics. 2016;17(1):144
Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification.27778293 · Ramos, Miguel Jesus Nunes, Coito, João Lucas, Fino, Joana et al.2017 · 20 citationsPlant molecular biology. 2017;93(1-2):151-170
Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes.27621130 · Lopes-Lima, Manuel, Froufe, Elsa, Do, Van Tu et al.2017 · 170 citationsMolecular phylogenetics and evolution. 2017;106:174-191
Genetic Diversity and Physiological Performance of Portuguese Wild Beet (Beta vulgaris spp. maritima) from Three Contrasting Habitats.27630646 · Ribeiro, Isa C, Pinheiro, Carla, Ribeiro, Carla M et al.2016 · 58 citationsFrontiers in plant science. 2016;7:1293
Evolutionary and Biogeographic Insights on the Macaronesian Beta-Patellifolia Species (Amaranthaceae) from a Time-Scaled Molecular Phylogeny.27031338 · Romeiras, Maria M, Vieira, Ana, Silva, Diogo N et al.2016 · 57 citationsPloS one. 2016;11(3):e0152456
Comparative Validation of Conventional and RNA-Seq Data-Derived Reference Genes for qPCR Expression Studies of Colletotrichum kahawae.26950697 · Vieira, Ana, Cabral, Ana, Fino, Joana et al.2016 · 15 citationsPloS one. 2016;11(3):e0150651
Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L.26832927 · Domingos, Sara, Fino, Joana, Cardoso, Vânia et al.2016 · 41 citationsBMC plant biology. 2016;16:38
4Pipe4--A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information.26787189 · Pina-Martins, Francisco, Vieira, Bruno M, Seabra, Sofia G et al.2016 · 5 citationsBMC bioinformatics. 2016;17:41
Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles.26810452 · Domingos, Sara, Fino, Joana, Paulo, Octávio S et al.2016 · 23 citationsPlant science : an international journal of experimental plant biology. 2016;244:40-56
Genomic Patterns of Positive Selection at the Origin of Rust Fungi.26632820 · Silva, Diogo N, Duplessis, Sebastien, Talhinhas, Pedro et al.2016 · 16 citationsPloS one. 2015;10(12):e0143959
Phylogeography and modes of reproduction in diploid and tetraploid halophytes of Limonium species (Plumbaginaceae): evidence for a pattern of geographical parthenogenesis.26424783 · Róis, Ana Sofia, Sádio, Flávio, Paulo, Octávio S et al.2016 · 27 citationsAnnals of botany. 2016;117(1):37-50
p53 gene discriminates two ecologically divergent sister species of pine voles.25990877 · Quina, A S, Bastos-Silveira, C, Miñarro, M et al.2016 · 5 citationsHeredity. 2015;115(5):444-51
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