Nuno A. Fonseca
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View article: Author Correction: Genomic basis for RNA alterations in cancer
Author Correction: Genomic basis for RNA alterations in cancer Open
View article: MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification
MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification Open
The current study presents MIMt, a new 16S rRNA database for archaea and bacteria's identification, encompassing 47 001 sequences, all precisely identified at species level. In addition, a MIMt2.0 version was created with only curated sequ…
View article: Singing for Anxiety: Exploring the Potentials of Singing in Immersive Virtual Reality to Help Children with Social Anxiety
Singing for Anxiety: Exploring the Potentials of Singing in Immersive Virtual Reality to Help Children with Social Anxiety Open
This paper presents an immersive Virtual Reality application designed for exposure therapy on children suffering from social anxiety. Two different interfaces for communication between the therapist and the client are designed and evaluate…
View article: Exploring Immersion and Spatial Audio Perception in Concerts for Hearing-Impaired and Normal Hearing Audiences
Exploring Immersion and Spatial Audio Perception in Concerts for Hearing-Impaired and Normal Hearing Audiences Open
In this paper we present the results of an investigation performed during a concert designed specifically for individuals with a hearing impairment. We remixed a popular song for the Ambisonic concert hall at The Royal Danish Academy of Mu…
View article: MIMt – A curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification
MIMt – A curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification Open
Motivation Accurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the major issues in metagenomics. This is primarily due to the limitations of commonly u…
View article: The leaf idioblastome of the medicinal plant<i>Catharanthus roseus</i>is associated with stress resistance and alkaloid metabolism
The leaf idioblastome of the medicinal plant<i>Catharanthus roseus</i>is associated with stress resistance and alkaloid metabolism Open
Catharanthus roseus leaves produce a range of monoterpenoid indole alkaloids (MIAs) that include low levels of the anticancer drugs vinblastine and vincristine. The MIA pathway displays a complex architecture spanning different subcellular…
View article: Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes
Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes Open
View article: Idioblasts accumulating anticancer alkaloids in<i>Catharanthus roseus</i>leaves are a unique cell type
Idioblasts accumulating anticancer alkaloids in<i>Catharanthus roseus</i>leaves are a unique cell type Open
Catharanthus roseus leaves produce a range of monoterpenoid indole alkaloids (MIAs) that include low levels of the anticancer drugs vinblastine and vincristine. The MIA pathway displays a complex architecture spanning different subcellular…
View article: Author Correction: Genomic basis for RNA alterations in cancer
Author Correction: Genomic basis for RNA alterations in cancer Open
View article: Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Open
View article: The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot
The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot Open
The Trichoptera are an important component of freshwater ecosystems. In the Iberian Peninsula, 380 taxa of caddisflies are known, with nearly 1/3 of the total species being endemic in the region. A reference collection of morphologically id…
View article: Author Correction: Integrative pathway enrichment analysis of multivariate omics data
Author Correction: Integrative pathway enrichment analysis of multivariate omics data Open
View article: Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower
Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower Open
View article: Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis Open
View article: Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations Open
In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortiumwere listed in the Supplementary Information; however, these members shouldhave been included in themainpaper.The originalArt…
View article: Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes
Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes Open
View article: Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes
Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes Open
View article: DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida)
DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida) Open
The orders Neuroptera and Raphidioptera include the species of insects known as lacewings and snakeflies, respectively. In Portugal, these groups account for over 100 species, some of which are very difficult to identify by morphological a…
View article: Comparative Genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree
Comparative Genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree Open
The recent report of distinct Xanthomonas lineages of Xanthomonas arboricola pv. juglandis and Xanthomonas euroxanthea within the same walnut tree revealed that this consortium of walnut-associated Xanthomonas includes both pathogenic and …
View article: Complete Genome Sequence Obtained by Nanopore and Illumina Hybrid Assembly of Xanthomonas arboricola pv. juglandis CPBF 427, Isolated from Buds of a Walnut Tree
Complete Genome Sequence Obtained by Nanopore and Illumina Hybrid Assembly of Xanthomonas arboricola pv. juglandis CPBF 427, Isolated from Buds of a Walnut Tree Open
We report the genome sequence of Xanthomonas arboricola pv. juglandis strain CPBF 427, which was isolated from early-season buds of a diseased walnut tree, suggesting overwinter potential. This study provides a consistent genomic reference…
View article: Metabarcoding with MinION: Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing
Metabarcoding with MinION: Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing Open
Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection ap…
View article: Evaluating the impact of sampling strategies and bioinformatics on ethanol-based DNA metabarcoding
Evaluating the impact of sampling strategies and bioinformatics on ethanol-based DNA metabarcoding Open
Recent developments on ethanol-based DNA (etDNA) metabarcoding have shown that it is possible to extract meaningful information about macroinvertebrate community diversity and composition from the ethanol used to preserve bulk samples. The…
View article: Tumour gene expression signature in primary melanoma predicts long-term outcomes
Tumour gene expression signature in primary melanoma predicts long-term outcomes Open
View article: Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution
Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution Open
The continuous characterization of genome-wide diversity in population and case–cohort samples, allied to the development of new algorithms, are shedding light on host ancestry impact and selection events on various infectious diseases. Es…
View article: Complete Genome Sequences of Walnut-Associated <i>Xanthomonas euroxanthea</i> Strains CPBF 367 and CPBF 426 Obtained by Illumina/Nanopore Hybrid Assembly
Complete Genome Sequences of Walnut-Associated <i>Xanthomonas euroxanthea</i> Strains CPBF 367 and CPBF 426 Obtained by Illumina/Nanopore Hybrid Assembly Open
We present the complete genome sequences of two Xanthomonas euroxanthea strains isolated from buds of a walnut tree. The whole-genome sequences of strains CPBF 367 and CPBF 426 consist of two circular chromosomes of 4,923,218 bp and 4,883,…
View article: Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci
Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci Open
The human gastrointestinal tract harbors approximately 100 trillion microorganisms with different microbial compositions across geographic locations. In this work, we used RNASeq data from stomach samples of non-disease (164 individuals fr…
View article: The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera
The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera Open
The use of DNA barcoding allows unprecedented advances in biodiversity assessments and monitoring schemes of freshwater ecosystems; nevertheless, it requires the construction of comprehensive reference collections of DNA sequences that rep…
View article: Tumors induce de novo steroid biosynthesis in T cells to evade immunity
Tumors induce de novo steroid biosynthesis in T cells to evade immunity Open
Tumors subvert immune cell function to evade immune responses, yet the complex mechanisms driving immune evasion remain poorly understood. Here we show that tumors induce de novo steroidogenesis in T lymphocytes to evade anti-tumor immunit…
View article: An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile
An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile Open
A better understanding of the response against Tuberculosis (TB) infection is required to accurately identify the individuals with an active or a latent TB infection (LTBI) and also those LTBI patients at higher risk of developing active T…
View article: A user guide for the online exploration and visualization of PCAWG data
A user guide for the online exploration and visualization of PCAWG data Open