Filipe Pereira

Filipe Pereira
IDENTIFICA | University of Coimbra | University of Porto

PhD
Researcher | PhD in Genetics

About

271
Publications
59,473
Reads
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2,259
Citations
Introduction
My main research interest is the study of the DNA molecule using computational and biochemical methods. My research activity goes from the computational prediction of alternative DNA structures to the history of animal populations. I also develop molecular diagnostic systems and databases for biological identifications at different levels. More details at: http://fpereira.portugene.com/
Additional affiliations
January 2020 - present
University of Coimbra
Position
  • Researcher
July 2013 - July 2018
University of Porto
Position
  • Researcher
January 2009 - June 2013
University of Porto
Position
  • PostDoc Position
Education
September 2004 - September 2009
Faculty of Sciences, University of Porto; IPATIMUP and Smurfit Institute, Trinity College, Dublin, Ireland
Field of study
  • Genetics

Publications

Publications (271)
Article
Full-text available
The domestication of livestock represented a crucial step in human history. By using endogenous retroviruses as genetic markers, we found that sheep differentiated on the basis of their “retrotype” and morphological traits dispersed across Eurasia and Africa via separate migratory episodes. Relicts of the first migrations include the Mouflon, as we...
Article
Full-text available
The quest for a universal and efficient method of identifying species has been a longstanding challenge in biology. Here, we show that accurate identification of species in all domains of life can be accomplished by multiplex analysis of variable-length sequences containing multiple insertion/deletion variants. The new method, called SPInDel, is ab...
Article
Full-text available
Mitochondrial DNA (mtDNA) deletions are a primary cause of mitochondrial disease and are believed to contribute to the aging process and to various neurodegenerative diseases. Despite strong observational and experimental evidence, the molecular basis of the deletion process remains obscure. In this study, we test the hypothesis that the primary ca...
Article
Full-text available
Mitochondrial DNA (mtDNA) rearrangements cause a wide variety of highly debilitating and often fatal disorders and have been implicated in aging and age-associated disease. Here we present a meta-analytical study of mtDNA deletions (n = 730) and partial duplications (n = 37) using information from more than 300 studies published over the last 30 ye...
Article
Full-text available
The new SARS-CoV-2 poses a significant threat to human health but many aspects of its basic biology remain unknown. Its genome encodes accessory genes that differ significantly within coronaviruses and contribute to the virus pathogenicity. Among accessory genes, open reading frame 8 (ORF8) stands out by being highly variable and showing structural...
Article
Full-text available
SARS-CoV-2 has affected people worldwide as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV-1 responsible for the 2002–2003 SARS outbreak in Asia. Research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Like other beta coronaviruses, RNA-RNA interactions occur b...
Article
Full-text available
By their paternal transmission, Y‐chromosomal haplotypes are sensitive markers of population history and male‐mediated introgression. Previous studies identified biallelic single‐nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y‐chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic par...
Article
SARS-CoV-2 non-structural protein 1 (Nsp1) is a virulence factor that inhibits the translation of host mRNAs and interacts with viral RNA. To date, hundreds of mutations (base substitutions, deletions, and insertions) have been reported in SARS-CoV-2 Nsp1. Despite the relevance of Nsp1, a few studies have been conducted to understand the effect of...
Article
Full-text available
TOPIIA topoisomerases are required for the regulation of DNA topology by DNA cleavage and re-ligation and are important targets of antibiotic and anticancer agents. Humans possess two TOPIIA paralogue genes (TOP2A and TOP2B) with high sequence and structural similarity but distinct cellular functions. Despite their functional and clinical relevance...
Preprint
Full-text available
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic par...
Article
Full-text available
Domestic sheep were introduced in Mexico by the Spanish settlers in the 16 th century. Nowadays, Mexico hosts several sheep breeds, adapting and evolving in both farming and traditional livestock production systems and different climate conditions. Research on the diversity of ovine genetic resources is urgently needed to prevent and reverse geneti...
Preprint
Full-text available
SARS-CoV-2 has affected people all over the world as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV responsible for the 2002-2003 SARS outbreak in Asia. Intense research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Similar to other betacoronaviruses, long-ran...
Preprint
Full-text available
SARS-CoV-2 non-structural protein 1 (Nsp1) is a virulence factor that inhibits the translation of host mRNAs and interact with viral RNA. Despite the relevance of Nsp1, few studies have been conducted to understand the effect of mutations on Nsp1 structure and function. Here, we provide a molecular dynamics simulation of SARS-CoV-2 Nsp1, wild type...
Article
Full-text available
DNA topoisomerase III beta (TOP3B) is unique by operating on both DNA and RNA substrates to regulate gene expression and genomic stability. Mutations in human TOP3B are linked to neurodevelopmental and cognitive disorders, highlighting its relevance for human health. Despite the emerging importance of TOP3B, its precise cellular functions and evolu...
Article
Full-text available
The mitochondrial genome of Neurospora crassa has been less studied than its nuclear counterpart, yet it holds great potential for understanding the diversity and evolution of this important fungus. Here we describe a new mitochondrial DNA (mtDNA) complete sequence of a N. crassa wild type strain. The genome with 64,839 bp revealed 21 protein codin...
Preprint
Full-text available
SARS-CoV-2 non-structural protein 1 (Nsp1) is a virulence factor that inhibits the innate immune response and translation of host mRNAs. Despite the relevance of Nsp1, few studies have been conducted to understand the effect of mutations on Nsp1 structure and function. Here, we provide a molecular dynamics simulation of SARS-CoV-2 and SARS-CoV-1 Ns...
Article
Full-text available
The SARS-CoV-2 Variant of Concern 202012/01 (VOC) is rapidly spreading worldwide owing to its substantial transmission advantage. The variant has changes in critical sites of the spike protein with potential biological significance. Moreover, VOC-202012/01 has a mutation that inactivates the ORF8 protein, whose absence can change the clinical featu...
Article
Full-text available
The SARS-CoV-2 Variant of Concern 202012/01 (VOC-202012/01) emerged in southeast England and rapidly spread worldwide. This variant is believed to be more transmissible, with all attention being given to its spike mutations. However, VOC-202012/01 has also a mutation (Q27stop) that truncates the ORF8, a likely immune evasion protein. Removal of ORF...
Article
Full-text available
Natural compounds have had increasing applications in the biotechnological sector, with a large fraction of these substances being channeled to the pharmaceutical industry due to their important pharmacological properties. The discovery of new bioactive molecules with novel mechanisms of action constitutes a promising solution for the design of alt...
Article
Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications’ field, the major current difficulties result from the lack of standards and genetic databases as well as...
Preprint
Full-text available
The ability to detect the SARS-CoV-2 in a widespread epidemic is crucial for screening of carriers and for the success of quarantine efforts. Methods based on real-time reverse transcription polymerase chain reaction (RT-qPCR) and sequencing are being used for virus detection and characterization. However, RNA viruses are known for their high genet...
Data
The CoV2ID evaluates molecular methods for detection of SARS-CoV-2 and treatment of COVID-19. The database evaluates available oligonucleotide sequences (PCR primers, RT-qPCR probes, etc.) considering the genetic diversity of the virus. Updated sequences alignments are used to constantly verify the theoretical efficiency of available testing method...
Article
Full-text available
The filamentous fungus Neurospora crassa is a popular model organism used in a wide range of biochemical and genetic studies and vastly used in mitochondrial research. Despite the relevance of mitochondria in N. crassa biology, no method for quantification of mitochondrial DNA (mtDNA) is currently available. Quantitative real‐time PCR (qPCR) is a p...
Article
Domestic sheep were introduced in Mexico by the Spanish settlers in the 16th century. Nowadays, Mexico hosts several sheep breeds, adapting and evolving in both farming and traditional livestock production systems and different climate conditions. Research on the diversity of ovine genetic resources is urgently needed to prevent and reverse genetic...
Preprint
Full-text available
The male-specific part of the Y-chromosome is in mammalian and many other species the longest haplotype that is inherited without recombination. By its paternal transmission it has a small effective population size in species with dominant males. In several species, Y-chromosomal haplotypes are sensitive markers of population history and introgress...
Poster
Full-text available
Genome rearrangements have an important role in evolution and are key events in the development of many diseases. Mitochondrial DNA (MtDNA) is associated to a series of rearrangement events, such as deletions, insertions, transpositions, inversions, duplications, and tandem duplication random loss (TDRL). We already detected the cruciform and hairp...
Article
Full-text available
Amphibians are the focus of a recent debate and public attention owing to the global decline in their populations worldwide. Amphibians are one of the most threatened and poorly known groups of vertebrates in several geographic areas, even though they play a central role in their own ecosystems. At different levels, amphibians make their contributi...
Article
Full-text available
The identification of species in casework samples is of fundamental importance for forensic investigations. Laboratories are increasingly compelled to provide accurate and fast identifications in trace materials left on crime scenes, wildlife poaching, illegal trade of protected species, fraudulent food products cases, etc. However, the field of no...
Preprint
Full-text available
In recent years, a large number of nucleotide sequences have become available for plant species by the advent of massive parallel sequencing. The use of genomic data has been important for agriculture, food science, medicine or ecology. Despite the increasing amount of data, nucleotide sequences are usually available in public databases as isolated...
Article
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Nature is the major reservoir of biologically active molecules. The urgent need of finding novel molecules for pharmaceutical application is prompting the research of underexplored environments, such as marine ecosystems. Here, we investigated cultivable actinobacteria associated with the macroalgae Laminaria ochroleuca and assessed their potential...
Article
Full-text available
Deletions in the 16.6 kb mitochondrial genome have been implicated in numerous disorders that often display muscular and/or neurological symptoms due to the high-energy demands of these tissues. We describe a catalogue of 4489 putative mitochondrial DNA (mtDNA) deletions, including their frequency and relative read rate, using a combinatorial appro...
Article
Full-text available
Adhesion in barnacles is still poorly understood. The cement gland secretes an insoluble multi-protein complex, which adheres very strongly to a variety of substrates in the presence of water. This adhesion mechanism is bioinspiring for the engineering of new adhesive materials, but to replicate this adhesive system, the genes coding for the cement...
Article
Full-text available
The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More impor...
Conference Paper
In Mexico, sheep were introduced by the Spanish colonizers in the sixteenth century, since then our country hosts a high diversity of breeds of these small ruminants. The national herd is composed of "Creole" sheep and foreign breeds, the latter have contributed to increase the gene pool. Faced with the challenges of climate change, research on the...
Presentation
In Mexico, sheep were introduced by the Spanish colonizers in the sixteenth century, since then our country hosts a high diversity of breeds of these small ruminants. The national herd is composed of "Creole" sheep and foreign breeds, the latter have contributed to increase the gene pool. Faced with the challenges of climate change, research on the...
Article
Full-text available
The correct identification of species in the highly divergent group of plants is crucial for several forensic investigations. Previous works had difficulties in the establishment of a rapid and robust method for the identification of plants. For instance, DNA barcoding requires the analysis of two or three different genomic regions to attain reason...
Article
Full-text available
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic...
Data
Illustrative examples of scenarios of nonhuman genetic material (NHGM) for main evidence in litigations not related with human identification. (PDF)
Data
Illustrative examples of scenarios using nonhuman genetic material (NHGM) for auxiliary evidence in litigations related with human identification. (PDF)
Data
Literature cited in the supplementary material. (PDF)
Article
Full-text available
Here we present a mitogenomic perspective on the evolution of sharks and rays, being a first glance on the complete mitochondrial history of such an old and diversified group of vertebrates. The Elasmobranchii is a diverse subclass of Chondrichthyes, or cartilaginous fish, with about 1200 species of ocean- and freshwater-dwelling fishes spread all...
Article
The Elasmobranchii comprises the diverse and important group of sharks and rays. The group includes some of the ocean's largest predatory fishes, suffering unsustainable fishing activities and is commercially overexploited for their meat and fins. Overfishing has resulted in significant population declines and several species are now considered und...
Article
This work focused on the biodegradation of three structurally related fluoroacetates (FAs), mono- (MFA), di- (DFA) and trifluoroacetate (TFA), using as microbial inocula samples collected from a site with a long history of industrial contamination and activated sludge obtained from a municipal wastewater treatment plant. Biodegradation experiments...
Article
Full-text available
The detection of transgenic animals in food and environmental samples will require the development of reliable screening assays. The identification of junction regions between genetic elements is the unequivocal way to prove the presence of transgene constructs. However, a sample from the transgenic organism or genetic construct is not always avail...
Poster
Unravelling the role of non-B DNA conformations in mitochondrial genome rearrangements
Article
Full-text available
There has been little evaluation of anecdotal sightings as a means to confirm new incursions of invasive species. This paper explores the potential for equivocal information communicated by the media to account for patterns of anecdotal reports. In 2001 it was widely reported that red foxes (Vulpes vulpes) had been deliberately released in the isla...
Article
Full-text available
The human immunodeficiency virus (HIV) is associated with one of the most widespread infectious disease, the acquired immunodeficiency syndrome (AIDS). The development of antiretroviral drugs and methods for virus detection requires a comprehensive analysis of the HIV genomic diversity, particularly in the binding sites of oligonucleotides. Here, w...