A5009037969- Mitochondrial Function and Pathology
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Metabolism and Genetic Disorders
- Gene expression and cancer classification
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- Bacteriophages and microbial interactions
- Explainable Artificial Intelligence (XAI)
- Hippo pathway signaling and YAP/TAZ
- DNA Repair Mechanisms
- Microtubule and mitosis dynamics
- Genomics and Chromatin Dynamics
- Telomeres, Telomerase, and Senescence
- Genomic variations and chromosomal abnormalities
- Signaling Pathways in Disease
- ATP Synthase and ATPases Research
- RNA modifications and cancer
- Genomics and Rare Diseases
- Cancer Cells and Metastasis
- Nuclear Structure and Function
- Cancer Genomics and Diagnostics
- Microbial Community Ecology and Physiology
University of Pavia
2022-2024
University of Trieste
2020-2022
University of Bologna
2014-2022
University of Pisa
2022
AREA Science Park
2020-2021
University of Bari Aldo Moro
2014-2016
University of Sannio
2014-2015
National Research Council
2014
Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies
2014
University of Milan
2014
Abstract Motivation: The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome whole-genome studies (WXS WGS) has risen the demand effective pipelines to accurately measure heteroplasmy easily recognize most functionally important mitochondrial variants among a huge number candidates. To this purpose, we developed MToolBox, highly automated pipeline reconstruct analyze human DNA from high-throughput data. Results: MToolBox implements an computational...
Whole Exome Sequencing (WES) is one of the most used and cost-effective next generation technologies that allows sequencing all nuclear exons. Off-target regions may be captured if they present high sequence similarity with baits. Bioinformatics tools have been optimized to retrieve a large amount WES off-target mitochondrial DNA (mtDNA), by exploiting aspecificity probes, partially overlapping Nuclear Sequences (NumtS). The 1000 Genomes project represents widest resources extract mtDNA...
Tumor organoids are tridimensional cell culture systems that generated in vitro from surgically resected patients’ tumors. They can be propagated maintaining several features of the tumor origin, including cellular and genetic heterogeneity, thus representing a promising tool for precision cancer medicine. Here, we established patient-derived (PDOs) different breast subtypes (luminal A, luminal B, human epidermal growth factor receptor 2 (HER2)-enriched, triple negative). The model showed...
The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. is intended to support both population geneticists as well clinicians undertaking the task assess pathogenicity specific mtDNA mutations. wide application next-generation sequencing (NGS) has provided an enormous volume high-resolution data at low price, increasing availability data, which called for cogent significant expansion content that more than tripled in...
Assigning a pathogenic role to mitochondrial DNA (mtDNA) variants and unveiling the potential involvement of genome in diseases are challenging tasks human medicine. Assuming that rare more likely be damaging, we designed phylogeny-based prioritization workflow obtain reliable pool candidate for further investigations. The relies on an exhaustive functional annotation through mtDNA extraction pipeline MToolBox includes Macro Haplogroup Consensus Sequences filter out fixed evolutionary report...
Abstract Pathways that direct the selection of telomerase-dependent or recombination-based, alternative lengthening telomere (ALT) maintenance pathway in cancer cells are poorly understood. Using human lung and tumor organoids we show formation 2,2,7-trimethylguanosine (TMG) cap structure at telomerase RNA 5′ end by Trimethylguanosine Synthase 1 (TGS1) is central for recruiting to telomeres engaging Cajal bodies maintenance. TGS1 depletion inhibition natural nucleoside sinefungin impairs...
The Metabolome and Transcriptome are mutually communicating within cancer cells, this interplay is translated into the existence of quantifiable correlation structures between gene expression metabolite abundance levels. Studying these correlations could provide a novel venue understanding discovery biomarkers pharmacological strategies, as well laying foundation for prediction quantities by leveraging information from more widespread transcriptomics data. In current paper, we investigate...
Deep learning has already revolutionised the way we process a wide range of data, in many areas our daily life. The ability to learn abstractions and relationships from heterogeneous provided impressively accurate prediction classification tools handle increasingly big datasets. This significant impact on growing wealth omics datasets, with unprecedented opportunity for better understanding complexity living organisms. While this revolution is transforming analyse these explainable deep...
Abstract Next-Generation Sequencing (NGS) is being increasingly adopted in clinical settings as a tool to increase diagnostic yield genetically determined pathologies. However, for patients critical conditions the time-to-results of data analysis crucial rapid diagnosis and response. Sentieon DNASeq Clara Parabricks Germline are two widely used pipelines ultra-rapid NGS analysis, but their high computational demands often exceed resources available many healthcare facilities. Cloud...
Amplicon sequencing of the nuclear ribosomal 5S RNA gene arrays is highly promising for genotaxonomy, to resolve species' genetic resources and tracing evolution. However, huge amount data retrieved with this approach difficult manage prone redundancy, error, computational difficulties. Reducing per sample without losing conveyed molecular-phylogenetic signal therefore a crucial step downstream analyses. In work, we compared Operational Taxonomic Units (OTUs) Sequence Variants (ASVs) from...
Horizontal gene transfer (HGT) is well described in prokaryotes: it plays a crucial role evolution, and has functional consequences insects plants. However, less known about HGT humans. Studies have reported bacterial integrations cancer patients, microbial sequences been detected data from well-known human sequencing projects. Few of the existing tools for investigating are highly automated. Thanks to adoption Nextflow life sciences workflows, standards best practices curated by communities...
Abstract Horizontal gene transfer (HGT) is well described in prokaryotes, it plays a crucial role evolution, and has functional consequences insects plants: less known about HGT Humans. Studies have reported bacterial integrations cancer patients, microbial sequences been detected data from well-known Human sequencing projects. Few of the existing tools to investigate are highly automated. Thanks adoption Nextflow for life sciences work-flows, standards best practices curated by communities...