Raquel Silva

Investigador/Outro

I was awarded the PhD in Biology with the study of the molecular mechanisms involved in the evolution of a genetic code alteration (Silva et al., 2007) and, as a post-doctoral fellow, I have studied the role of mRNA mistranslation on cell physiology, degeneration and aging (Silva et al., 2009). As a Research Associate in the Population Genetics group at IPATIMUP, I became interested in the evolution of proteins and metabolic pathways, in particular, the dynamics of the NAD metabolic network and its roles in health and disease. These enzymes have been implicated in aging, infection and disease, and are the targets of a novel class of antitumor drugs (Duarte-Pereira et al., 2016). I am also involved in the development of bioinformatics tools to detect genome rearrangements and pathogen signatures, with implications for diagnosis and therapeutics (Silva et al., 2015). Additional lines of investigation are maintained in collaboration, to address the mechanisms of anti-fungal resistance in clinical isolates (Branco et al., 2017), and to predict the impact of human mutations (Azevedo et al., 2017). I have integrated the multidisciplinary project "New Strategies Applied to Neuropathological Disorders" (2013-2015), a collaboration between the bioinformatics group, the Chemistry Department and Health School from the University of Aveiro, and researchers from German Universities. I currently participate as a team member in the projects "NETDIAMOND:NEw Targets in DIAstolic heart failure: from coMOrbidities to persoNalizeD medicine" (2016-2019) and "pAGE:Life-long protein aggregation" (2017-2020).

Paper

A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans

Silva, R. , Gomes, A.C.. (2007). A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans. Genome Biology
Paper

A transcriptomics approach to unveiling the mechanisms of in vitro evolution towards fluconazole resistance of a Candida glabrata Clinical Isolate

Silva, R. , Cavalheiro, M.. (2019). A transcriptomics approach to unveiling the mechanisms of in vitro evolution towards fluconazole resistance of a Candida glabrata Clinical Isolate. Antimicrobial Agents and Chemotherapy
Paper

An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

Silva, R. , Pratas, D.. (2015). An alignment-free method to find and visualise rearrangements between pairs of DNA sequences. Scientific Reports
Other

Assisted Mining and Curation of Genomic Variants using Egas

Silva, R. (2015). Assisted Mining and Curation of Genomic Variants using Egas.
Paper

Codon-triplet context unveils unique features of the Candida albicans protein coding genome

Silva, R. , Moura, G.R.. (2007). Codon-triplet context unveils unique features of the Candida albicans protein coding genome. BMC Genomics
Paper

Comparative context analysis of codon pairs on an ORFeome scale.

Silva, R. , Moura, G.. (2005). Comparative context analysis of codon pairs on an ORFeome scale.. Genome biology
Paper

Critical roles for a genetic code alteration in the evolution of the genus Candida

Silva, R. , Silva, R.M.. (2007). Critical roles for a genetic code alteration in the evolution of the genus Candida. EMBO Journal
Book

Dissimilar symmetric word pairs in the human genome

Silva, R. , Tavares, A.H.. (2017). Dissimilar symmetric word pairs in the human genome. Advances in Intelligent Systems and Computing
Paper

DNA word analysis based on the distribution of the distances between symmetric words

Silva, R. , Tavares, A.H.M.P.. (2017). DNA word analysis based on the distribution of the distances between symmetric words. Scientific Reports
Paper

Environmental azole fungicide, prochloraz, can induce cross-resistance to medical triazoles in Candida glabrata

Silva, R. , Faria-Ramos, I.. (2014). Environmental azole fungicide, prochloraz, can induce cross-resistance to medical triazoles in Candida glabrata. FEMS Yeast Research
Paper

Epidemiology and susceptibility profile to classic antifungals and over-the-counter products of Malassezia clinical isolates from a Portuguese University Hospital: a prospective study

Silva, R. , Pedrosa, A.F.. (2019). Epidemiology and susceptibility profile to classic antifungals and over-the-counter products of Malassezia clinical isolates from a Portuguese University Hospital: a prospective study. Journal of medical microbiology
Paper

Evolution of the genetic code in yeasts

Silva, R. , Miranda, I.. (2006). Evolution of the genetic code in yeasts. Yeast
Paper

Evolution of the NET (NocA, Nlz, Elbow, TLP-1) protein family in metazoans: Insights from expression data and phylogenetic analysis

Silva, R. , Pereira, F.. (2016). Evolution of the NET (NocA, Nlz, Elbow, TLP-1) protein family in metazoans: Insights from expression data and phylogenetic analysis. Scientific Reports
Paper

Exceptional Symmetry by Genomic Word: A Statistical Analysis

Silva, R. , Afreixo, V.. (2017). Exceptional Symmetry by Genomic Word: A Statistical Analysis. Interdisciplinary Sciences: Computational Life Sciences
Book

Exceptional symmetry profile: A genomic word analysis

Silva, R. , Afreixo, V.. (2016). Exceptional symmetry profile: A genomic word analysis. Advances in Intelligent Systems and Computing
Paper

Extensive regulation of nicotinate phosphoribosyltransferase (NAPRT) expression in human tissues and tumors

Silva, R. , Duarte-Pereira, S.. (2016). Extensive regulation of nicotinate phosphoribosyltransferase (NAPRT) expression in human tissues and tumors. Oncotarget
Other

FALCON-meta: a method to infer metagenomic composition of ancient DNA

Silva, R. , Diogo Pratas. (2018). FALCON-meta: a method to infer metagenomic composition of ancient DNA.
Paper

FKS2 mutations associated with decreased echinocandin susceptibility of Candida glabrata following anidulafungin therapy

Silva, R. , Costa-de-Oliveira, S.. (2011). FKS2 mutations associated with decreased echinocandin susceptibility of Candida glabrata following anidulafungin therapy. Antimicrobial Agents and Chemotherapy
Paper

Fluconazole and voriconazole resistance in Candida parapsilosis is conferred by gain-of-function mutations in MRR1 transcription factor gene

Silva, R. , Branco, J.. (2015). Fluconazole and voriconazole resistance in Candida parapsilosis is conferred by gain-of-function mutations in MRR1 transcription factor gene. Antimicrobial Agents and Chemotherapy
Paper

Gains, losses and changes of function after gene duplication: Study of the metallothionein family

Silva, R. , Moleirinho, A.. (2011). Gains, losses and changes of function after gene duplication: Study of the metallothionein family. PLoS ONE
Book

Identification of DNA CpG islands using inter-dinucleotide distances

Silva, R. , Afreixo, V.. (2015). Identification of DNA CpG islands using inter-dinucleotide distances. Communications in Computer and Information Science
Paper

Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance

Silva, R. , Branco, J.. (2017). Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance. Clinical Microbiology and Infection
Paper

Improving the in silico assessment of pathogenicity for compensated variants

Silva, R. , Azevedo, L.. (2016). Improving the in silico assessment of pathogenicity for compensated variants. European Journal of Human Genetics
Paper

In vivo and in vitro acquisition of resistance to voriconazole by Candida krusei

Silva, R. , Ricardo, E.. (2014). In vivo and in vitro acquisition of resistance to voriconazole by Candida krusei. Antimicrobial Agents and Chemotherapy
Paper

Malassezia species retrieved from skin with pityriasis versicolor, seborrhoeic dermatitis and skin free of lesions: a comparison of two sampling methods

Silva, R. , Pedrosa, A.F.. (2018). Malassezia species retrieved from skin with pityriasis versicolor, seborrhoeic dermatitis and skin free of lesions: a comparison of two sampling methods. British Journal of Dermatology
Paper

Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard

Silva, R. , D. Pratas. (2018). Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard. Genes
Other

Microevolution in a Natural Population of Daphnia longispina

Silva, R. (2010). Microevolution in a Natural Population of Daphnia longispina. Interdisciplinary Studies on Environmental Chemistry - Biological Responses to Contaminants
Paper

Mining clinical attributes of genomic variants through assisted literature curation in Egas

Silva, R. , Matos, S.. (2016). Mining clinical attributes of genomic variants through assisted literature curation in Egas. Database
Book

Mutation analysis in PARK2 gene uncovers patterns of associated genetic variants

Silva, R. , Castro, L.. (2014). Mutation analysis in PARK2 gene uncovers patterns of associated genetic variants. Advances in Intelligent Systems and Computing
Paper

Nampt and Naprt1: Novel polymorphisms and distribution of variants between normal tissues and tumor samples

Silva, R. , Duarte-Pereira, S.. (2014). Nampt and Naprt1: Novel polymorphisms and distribution of variants between normal tissues and tumor samples. Scientific Reports
Paper

Overview of the interactive task in BioCreative V

Silva, R. , Wang, Q.. (2016). Overview of the interactive task in BioCreative V. Database
Paper

The Evolutionary Portrait of Metazoan NAD Salvage

Silva, R. , Carneiro, J.. (2013). The Evolutionary Portrait of Metazoan NAD Salvage. PLoS ONE
Paper

The exceptional genomic word symmetry along DNA sequences

Silva, R. , Afreixo, V.. (2016). The exceptional genomic word symmetry along DNA sequences. BMC Bioinformatics
Paper

The mitochondrial genome of the pinewood nematode (Bursaphelenchus xylophilus) lineage introduced in Europe

Silva, R. , Moreira, C.. (2014). The mitochondrial genome of the pinewood nematode (Bursaphelenchus xylophilus) lineage introduced in Europe. Mitochondrial DNA
Paper

The Role of Recombination in the Origin and Evolution of Alu Subfamilies

Silva, R. , Teixeira-Silva, A.. (2013). The Role of Recombination in the Origin and Evolution of Alu Subfamilies. PLoS ONE
Paper

The yeast PNC1 longevity gene is up-regulated by mRNA mistranslation

Silva, R. , Silva, R.M.. (2009). The yeast PNC1 longevity gene is up-regulated by mRNA mistranslation. PLoS ONE
Paper

Three minimal sequences found in Ebola virus genomes and absent from human DNA

Silva, R. , Silva, R.M.. (2015). Three minimal sequences found in Ebola virus genomes and absent from human DNA. Bioinformatics
Paper

Transcriptional profiling of azole-resistant Candida parapsilosis strains

Silva, R. , Silva, A.P.. (2011). Transcriptional profiling of azole-resistant Candida parapsilosis strains. Antimicrobial Agents and Chemotherapy
Book

Visualization of distinct DNA regions of the modern human relatively to a neanderthal genome

Silva, R. , Pratas, D.. (2017). Visualization of distinct DNA regions of the modern human relatively to a neanderthal genome. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Paper

Yeast as a model organism for studying the evolution of non-standard genetic codes.

Silva, R. , Silva, R.M.. (2004). Yeast as a model organism for studying the evolution of non-standard genetic codes.. Briefings in functional genomics & proteomics
Paper

Yeast proteome map (update 2006)

Silva, R. , Perrot, M.. (2007). Yeast proteome map (update 2006). Proteomics