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Article
Open AccessData-driven recombination detection in viral genomes
Recombination is a key molecular mechanism for the evolution and adaptation of viruses. The first recombinant SARS-CoV-2 genomes were recognized in 2021; as of today, more than ninety SARS-CoV-2 lineages are d...
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Article
Open AccessThe pancancer overexpressed NFYC Antisense 1 controls cell cycle mitotic progression through in cis and in trans modes of action
Antisense RNAs (asRNAs) represent an underappreciated yet crucial layer of gene expression regulation. Generally thought to modulate their sense genes in cis through sequence complementarity or their act of trans...
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Article
Open AccessHaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2
Accurate and timely monitoring of the evolution of SARS-CoV-2 is crucial for identifying and tracking potentially more transmissible/virulent viral variants, and implement mitigation strategies to limit their ...
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Article
Open AccessLaniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of ...
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Article
Open AccessAccurate detection and quantification of SARS-CoV-2 genomic and subgenomic mRNAs by ddPCR and meta-transcriptomics analysis
SARS-CoV-2 replication requires the synthesis of a set of structural proteins expressed through discontinuous transcription of ten subgenomic mRNAs (sgmRNAs). Here, we have fine-tuned droplet digital PCR (ddPC...
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Open AccessComplete vertebrate mitogenomes reveal widespread repeats and gene duplications
Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.
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Open AccessELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Mo...
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Open AccessTwo novel fish paralogs provide insights into the Rid family of imine deaminases active in pre-empting enamine/imine metabolic damage
Reactive Intermediate Deaminase (Rid) protein superfamily includes eight families among which the RidA is conserved in all domains of life. RidA proteins accelerate the deamination of the reactive 2-aminoacryl...
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Open AccessNo metagenomic evidence of tumorigenic viruses in cancers from a selected cohort of immunosuppressed subjects
The possible existence of yet undiscovered human tumorigenic viruses is still under scrutiny. The development of large-scale sequencing technologies, coupled with bioinformatics techniques for the characteriza...
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Open AccessWhole transcriptome profiling of Late-Onset Alzheimer’s Disease patients provides insights into the molecular changes involved in the disease
Alzheimer’s Disease (AD) is the most common cause of dementia affecting the elderly population worldwide. We have performed a comprehensive transcriptome profiling of Late-Onset AD (LOAD) patients using second...
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Open AccessCoVaCS: a consensus variant calling system
The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and prec...
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Article
Open AccessA-GAME: improving the assembly of pooled functional metagenomics sequence data
Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such “func...
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Open AccessMassive transcriptome sequencing of human spinal cord tissues provides new insights into motor neuron degeneration in ALS
ALS is a devastating and debilitating human disease characterized by the progressive death of upper and lower motor neurons. Although much effort has been made to elucidate molecular determinants underlying th...
