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List of works by Agostinho Antunes

A comprehensive compilation of Iberian Medusozoan data: Diversity, ecology, and omics insights

scientific article published in 2024

A proteomics and transcriptomics investigation of the venom from the barychelid spider Trittame loki (brush-foot trapdoor)

scientific article (publication date: 13 December 2013)

ASSESSING THE TAXONOMIC STATUS OF THE PALAWAN PANGOLIN MANIS CULIONENSIS (PHOLIDOTA) USING DISCRETE MORPHOLOGICAL CHARACTERS

scientific article published in 2005

Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions

scientific article published on 18 August 2015

Adaptive evolution of the Retinoid X receptor in vertebrates

scientific article published on 14 December 2011

Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals ⬇️

scientific article published on November 21, 2011

Adaptive functional divergence of the warm temperature acclimation-related protein (WAP65) in fishes and the ortholog hemopexin (HPX) in mammals

scientific article published on 16 December 2013

Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments

scientific article published on 5 February 2018

Adaptive patterns of mitogenome evolution are associated with the loss of shell scutes in turtles.

scientific article published on 06 June 2017

Advancing Genomics through the Global Invertebrate Genomics Alliance (GIGA)

scientific article

African Origin and Europe-Mediated Global Dispersal of The Cyanobacterium Microcystis aeruginosa

Alignment-Free Methods for the Detection and Specificity Prediction of Adenylation Domains

scientific article published in January 2016

Alignment-free prediction of polygalacturonases with pseudofolding topological indices: experimental isolation from Coffea arabica and prediction of a new sequence.

scientific article

An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species

scientific article

An alignment-free approach for eukaryotic ITS2 annotation and phylogenetic inference

scientific article

Analysis of Pelagia noctiluca proteome Reveals a Red Fluorescent Protein, a Zinc Metalloproteinase and a Peroxiredoxin

scientific article published on 3 March 2017

Annotated features of domestic cat - Felis catus genome

scientific article

Application of real-time PCR in the assessment of the toxic cyanobacterium Cylindrospermopsis raciborskii abundance and toxicological potential.

scientific article

Atractaspis aterrima toxins: the first insight into the molecular evolution of venom in side-stabbers

scientific article

Avian Binocularity and Adaptation to Nocturnal Environments: Genomic Insights from a Highly Derived Visual Phenotype

scientific article published on 01 August 2019

Beyond the beaten path: improving natural products bioprospecting using an eco-evolutionary framework - the case of the octocorals

scientific article

Biological toxins and medicinal chemistry: research and therapeutic tools

scientific article published on 01 January 2015

Bone-associated gene evolution and the origin of flight in birds

scientific article

Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat

scientific article published on 23 October 2014

Characterization of the First Conotoxin from Conus ateralbus, a Vermivorous Cone Snail from the Cabo Verde Archipelago

scientific article published on 24 July 2019

Combining genetic and demographic data for the conservation of a Mediterranean marine habitat-forming species

scientific article (publication date: 2015)

Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses

scientific article published on 30 November 2019

Comparative evolutionary genomics of the HADH2 gene encoding Abeta-binding alcohol dehydrogenase/17beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)

scientific article

Comparative genomics reveals insights into avian genome evolution and adaptation

scientific article

Comparative study of topological indices of macro/supramolecular RNA complex networks.

scientific article

Complexity of avian evolution revealed by family-level genomes

scientific article published in April 2024

Computational optimization of AG18051 inhibitor for amyloid-β binding alcohol dehydrogenase enzyme

Computational study of the covalent bonding of microcystins to cysteine residues – a reaction involved in the inhibition of the PPP family of protein phosphatases ⬇️

scientific article published on January 9, 2012

Conopeptides from Cape Verde Conus crotchii

scientific article

Contribution of DNA-typing to bushmeat surveys: assessment of a roadside market in south-western Nigeria

article

Correction: Morphological and Genetic Evidence for Multiple Evolutionary Distinct Lineages in the Endangered and Commercially Exploited Red Lined Torpedo Barbs Endemic to the Western Ghats of India

scientific article published in PLoS ONE

Corrigendum to: Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA)

scholarly article published in Invertebrate Systematics

Cylindrospermopsin: occurrence, methods of detection and toxicology.

scientific article

De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin

scientific article

Differential Evolution and Neofunctionalization of Snake Venom Metalloprotease Domains.

scientific article

Differential evolution and neofunctionalization of snake venom metalloprotease domains

scientific article published on 12 December 2012

Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes

scientific article

Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

scientific article published in 2023

Diversification of a single ancestral gene into a successful toxin superfamily in highly venomous Australian funnel-web spiders

scientific article

Dracula's children: molecular evolution of vampire bat venom.

scientific article published on 5 June 2013

EASER: Ensembl Easy Sequence Retriever

scientific article

Emerging viruses in the Felidae: shifting paradigms

scientific article

Engineering protein fragments via evolutionary and protein-protein interaction algorithms: De novo design of peptide inhibitors for FO F1 -ATP synthase

scientific article published on 05 November 2020

Evidence of unique and generalist microbes in distantly related sympatric intertidal marine sponges (Porifera: Demospongiae)

scientific article (publication date: 2013)

Evolution of CRISPs Associated with Toxicoferan-Reptilian Venom and Mammalian Reproduction ⬇️

scientific article published on 01 February 2012

Evolution of separate predation- and defence-evoked venoms in carnivorous cone snails

scientific article

Evolution stings: the origin and diversification of scorpion toxin peptide scaffolds ⬇️

scientific article published on 13 December 2013

Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species

scientific article (publication date: February 2006)

Evolutionary genomics and adaptive evolution of the Hedgehog gene family (Shh, Ihh and Dhh) in vertebrates

scientific article

Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone.

scientific article

Exploring the adenylation domain repertoire of nonribosomal peptide synthetases using an ensemble of sequence-search methods

scientific article

FIV cross-species transmission: an evolutionary prospective

scientific article

First occurrence of cylindrospermopsin in Portugal: a contribution to its continuous global dispersal

scientific article

First report on the occurrence of microcystins in planktonic cyanobacteria from Central Mexico

scientific article

Fish lateral line innovation: insights into the evolutionary genomic dynamics of a unique mechanosensory organ

scientific article

Gathering computational genomics and proteomics to unravel adaptive evolution

scientific article

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds

scientific article

Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (Isurus oxyrinchus)

scientific article published in 2022

Genetic Evidence for Contrasting Wetland and Savannah Habitat Specializations in Different Populations of Lions (Panthera leo).

scientific article published on 22 December 2015

Genetic characterization of Microcystis aeruginosa isolates from Portuguese freshwater systems

scientific article published on 4 June 2016

Genetic diversity and structure of the invasive toxic cyanobacterium Cylindrospermopsis raciborskii.

scientific article published on 25 February 2011

Genetic variability of the invasive cyanobacteria Cylindrospermopsis raciborskii from Bir M'cherga reservoir (Tunisia).

scientific article

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

scientific article

Genomic Signatures of Divergent Ecological Strategies in a Recent Radiation of Neotropical Wild Cats

publication published on 01 June 2022

Genomic legacy of the African cheetah, Acinonyx jubatus

scientific article

Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts.

scientific article

Graph Theory-Based Sequence Descriptors as Remote Homology Predictors

scientific article published on 23 December 2019

How the Protein Architecture of RNases III Influences their Substrate Specificity?

scientific article

IMPACT: Integrated Multiprogram Platform for Analyses in ConTest ⬇️

scientific article published on March 16, 2011

IMPACT_S: integrated multiprogram platform to analyze and combine tests of selection

scientific article

Initial sequence and comparative analysis of the cat genome

scientific article

Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola.

scientific article published in June 2018

Insights into the toxicological properties of a low molecular weight fraction from Zoanthus sociatus (Cnidaria).

scientific article published on 13 August 2013

Intraspecific venom variation in the medically significant Southern Pacific Rattlesnake (Crotalus oreganus helleri): biodiscovery, clinical and evolutionary implications

scientific article published on 24 January 2014

Isolation and characterization of microsatellite markers in pangolins (Mammalia, Pholidota,Manisspp.)

scientific article published in 2006

Jellyfish Bioactive Compounds: Methods for Wet-Lab Work

scientific article

LMAP: Lightweight Multigene Analyses in PAML.

scientific article

LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation

scientific article published on 30 December 2019

Life on the edge: the long-term persistence and contrasting spatial genetic structure of distinct brown trout life histories at their ecological limits

scientific article published on 17 February 2006

Low Genetic Diversity and High Invasion Success of Corbicula fluminea (Bivalvia, Corbiculidae) (Müller, 1774) in Portugal. ⬇️

scientific article

MDPI Oceans: A New Publication Channel for Open Access Science Focused on the Ocean

scientific article published on 12 August 2019

Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments

scientific article

Measuring phylogenetic signal between categorical traits and phylogenies

scholarly article by Rui Borges et al published 25 October 2018 in Computer applications in the biosciences : CABIOS

Microcystin-LR Detected in a Low Molecular Weight  Fraction from a Crude Extract of Zoanthus sociatus

scientific article

Mitochondrial haplotype diversity among Portuguese brown trout Salmo trutta L. populations: relevance to the post-pleistocene recolonization of northern Europe

scientific article published in June 2000

Mitochondrial introgressions into the nuclear genome of the domestic cat.

scientific article published on 28 July 2007

Molecular Forensics into the Sea: How Molecular Markers Can Help to Struggle Against Poaching and Illegal Trade in Precious Corals?

Molecular and phylogenetic characterization of potentially toxic cyanobacteria in Tunisian freshwaters.

scientific article

Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases

scientific article

Molecular evolution of vertebrate neurotrophins: co-option of the highly conserved nerve growth factor gene into the advanced snake venom arsenalf

scientific article (publication date: 2013)

Molecular phylogeny and evolution of the proteins encoded by coleoid (cuttlefish, octopus, and squid) posterior venom glands

scientific article

Morphological and genetic evidence for multiple evolutionary distinct lineages in the endangered and commercially exploited red lined torpedo barbs endemic to the Western Ghats of India

scientific article (publication date: 2013)

Morphological, toxicological and molecular characterization of a benthic Nodularia isolated from Atlantic estuarine environments

scientific article

Non-linear models based on simple topological indices to identify RNase III protein members

scientific article published on 28 December 2010

Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida

scientific article published on 28 July 2015

Pangolin genomes and the evolution of mammalian scales and immunity

scientific article published on 10 August 2016

Parabolic variation in sexual selection intensity across the range of a cold-water pipefish: implications for susceptibility to climate change.

scientific article

Phylogenetic, chemical and morphological diversity of cyanobacteria from Portuguese temperate estuaries

scientific article

Phylogeny and biogeography of cyanobacteria and their produced toxins.

scientific article

Phylogeny and biogeography of the invasive cyanobacterium Cylindrospermopsis raciborskii

scientific article

Phylogeny of microcystins: evidence of a biogeographical trend?

scientific article published on 9 November 2012

Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification.

scientific article

Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns.

scientific article published on 09 September 2016

Postglacial range expansion shaped the spatial genetic structure in a marine habitat-forming species: Implications for conservation plans in the Eastern Adriatic Sea

Proteogenomic Characterization of the Cement and Adhesive Gland of the Pelagic Gooseneck Barnacle Lepas anatifera

scientific article published in 2021

Proteomic Analyses of the Unexplored Sea Anemone Bunodactis verrucosa.

scientific article

Putative Antimicrobial Peptides of the Posterior Salivary Glands from the Cephalopod Octopus vulgaris Revealed by Exploring a Composite Protein Database

scientific article published on 30 October 2020

Pyrosequencing characterization of the microbiota from Atlantic intertidal marine sponges reveals high microbial diversity and the lack of co-occurrence patterns

scientific article published on 20 May 2015

Response to Comment by Faurby, Werdelin and Svenning

scientific article

Risk assessment of cyanobacteria toxic metabolites on freshwater ecosystems applying molecular methods

scientific article published in 2022

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

scholarly article

Sea anemone (Cnidaria, Anthozoa, Actiniaria) toxins: an overview

scientific article

Seasonal dynamics of Microcystis spp. and their toxigenicity as assessed by qPCR in a temperate reservoir

scientific article published on 29 September 2011

ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes

scientific article published on 07 July 2020

Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host-Microbe Interactions by Revealing Diverse Antimicrobial Peptides

scientific article published on 13 July 2020

Small Molecules in the Cone Snail Arsenal

scientific article published on 30 September 2015

Squeezers and leaf-cutters: differential diversification and degeneration of the venom system in toxicoferan reptiles.

scientific article

Statistical Inferences Applying Non-Parametric Data on Cyanobacterial Investigations: Contributions to Water Quality and New Trends under Global Changes on Portuguese Freshwater Ecosystems

scientific article published in 2022

Structural and functional implications of positive selection at the primate angiogenin gene

scientific article

Structural and molecular diversification of the Anguimorpha lizard mandibular venom gland system in the arboreal species Abronia graminea

scientific article published on 17 November 2012

Structural divergence and adaptive evolution in mammalian cytochromes P450 2C

article

Subspecies genetic assignments of worldwide captive tigers increase conservation value of captive populations

scientific article

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

scientific article published on 3 May 2018

Sympatric Asian felid phylogeography reveals a major Indochinese-Sundaic divergence

scientific article

TI2BioP: Topological Indices to BioPolymers. Its practical use to unravel cryptic bacteriocin-like domains.

scientific article published on 19 June 2010

The Harderian gland transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, three colubroid snakes from Cuba

scientific article published on 01 December 2018

The Quantitative Proteome of the Cement and Adhesive Gland of the Pedunculate Barnacle, Pollicipes pollicipes

scientific article published on 05 April 2020

The adaptive evolution of the mammalian mitochondrial genome

scientific article (publication date: 4 March 2008)

The chemical ecology of cyanobacteria ⬇️

scientific article

The complete phylogeny of pangolins: scaling up resources for the molecular tracing of the most trafficked mammals on Earth.

scientific article

The era of reference genomes in conservation genomics

scientific article published in March 2022

The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics

scientific article

The evolutionary history of extinct and living lions

scientific article published on 04 May 2020

The genetic diversity of two invasive sympatric bivalves (Corbicula fluminea and Dreissena polymorpha) from Lakes Garda and Maggiore, Northern Italy

scientific article published on 26 December 2019

The late Miocene radiation of modern Felidae: a genetic assessment

scientific article

The lek mating system of the worm pipefish (Nerophis lumbriciformis): a molecular maternity analysis and test of the phenotype-linked fertility hypothesis

scientific article

The phosphoprotein phosphatase family of Ser/Thr phosphatases as principal targets of naturally occurring toxins ⬇️

scientific article published on February 1, 2011

The role of gene duplication and unconstrained selective pressures in the melanopsin gene family evolution and vertebrate circadian rhythm regulation

scientific article (publication date: 2012)

The role of nuclear genes in intraspecific evolutionary inference: genealogy of the transferrin gene in the brown trout

scientific article published in August 2002

The swinholide biosynthetic gene cluster from a terrestrial cyanobacterium Nostoc sp. UHCC 0450. ⬇️

scientific article published on 17 November 2017

Three-fingered RAVERs: Rapid Accumulation of Variations in Exposed Residues of snake venom toxins

scientific article

Transcriptomic Characterization of the South American Freshwater Stingray Potamotrygon motoro Venom Apparatus.

scientific article published on 18 December 2018

Unraveling a 146 years old taxonomic puzzle: validation of Malabar snakehead, species-status and its relevance for channid systematics and evolution

scientific article published in 2011

Unusual symbiotic cyanobacteria association in the genetically diverse intertidal marine sponge Hymeniacidon perlevis (Demospongiae, Halichondrida)

scientific article

Validating the use of colouration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers

scientific article published on 6 August 2013

Vomeronasal Receptors in Vertebrates and the Evolution of Pheromone Detection.

scientific article published on 28 November 2016

What's behind these scales? Comments to "The complete mitochondrial genome of Temminck's ground pangolin (Smutsia temminckii; Smuts, 1832) and phylogenetic position of the Pholidota (Weber, 1904)".

scientific article published on 19 March 2015

White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability

scientific article published on 19 February 2019

Whole Genome Sequencing of the Symbiont Pseudovibrio sp. from the Intertidal Marine Sponge Polymastia penicillus Revealed a Gene Repertoire for Host-Switching Permissive Lifestyle.

scientific article published on 31 October 2015

Whole-Genome Comparisons Among the Genus Shewanella Reveal the Enrichment of Genes Encoding Ankyrin-Repeats Containing Proteins in Sponge-Associated Bacteria

article

Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds

scientific article

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