A5063116840- Mitochondrial Function and Pathology
- Genomics and Phylogenetic Studies
- Metabolism and Genetic Disorders
- RNA and protein synthesis mechanisms
- Renal cell carcinoma treatment
- Metabolomics and Mass Spectrometry Studies
- Machine Learning in Bioinformatics
- Forensic and Genetic Research
- Cancer, Hypoxia, and Metabolism
- Glutathione Transferases and Polymorphisms
- Ferroptosis and cancer prognosis
- Genetic diversity and population structure
- Molecular Biology Techniques and Applications
- Genomics and Rare Diseases
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Biomedical Text Mining and Ontologies
- Epigenetics and DNA Methylation
- Genetic and Kidney Cyst Diseases
- Molecular spectroscopy and chirality
- Genetics, Bioinformatics, and Biomedical Research
- Pacific and Southeast Asian Studies
- Gene expression and cancer classification
- ATP Synthase and ATPases Research
- Yersinia bacterium, plague, ectoparasites research
University of Bari Aldo Moro
2012-2023
Washington Center
2018
University of Washington
2018
National Research Council
2014
Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies
2014
University of Milan
2014
University of Bologna
2014
École Pratique des Hautes Études
2013
Deutsche Forschungsgemeinschaft
2013
Biogem
2010
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...
ACNUC is a database structure and retrieval software for use with either the GenBank or EMBL nucleic acid sequence data collections. The nucleotide textual furnished by both collections are each restructured into that allows on multi-criterion basis. main selection criteria are: species (or higher order taxon), keyword, reference, journal, author, organelle; all logical combinations of these can be used. Direct access to regions code specific product (protein, tRNA rRNA) provided. A...
Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, heteroplasmy, threshold effect, absence splicing, and contextual effects haplogroups. Currently, there are insufficient standardized criteria for assessment, which leads to inconsistencies in clinical reporting. An international working group experts was assembled within Disease Sequence Data Resource Consortium obtained Expert...
Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because methods used missed cause in known gene, novel causative gene could not be identified and/or confirmed. To address these challenges, RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates collation, discovery, sharing, and analysis standardized genome-phenome...
We previously showed that disruptive complex I mutations in mitochondrial DNA are the main genetic hallmark of oncocytic tumors thyroid and kidney. here report a high frequency homoplasmic large panel pituitary head-and-neck tumors. The presence such implicates disassembly respiratory vivo which turn contributes to inability stabilize HIF1α display pseudo-hypoxia. By utilizing transmitochondrial cytoplasmic hybrids (cybrids), we induced shift homoplasmy truncating mutation mitochondria-coded...
Abstract DNA barcoding may be particularly important in influencing ecology, economic issues, and the fundamental crisis facing biodiversity as a standardized, species‐level identification tool for taxonomy assessment. Trees play roles conservation of many land ecosystems, wood trade, definition biogeographical processes; nevertheless, peculiar biological, evolutionary taxonomical features will probably constitute an intriguing challenge to barcoders. We examined whether four marker regions...
HmtDB (http://www.hmtdb.uniba.it:8080/hmdb) is a open resource created to support population genetics and mitochondrial disease studies. The database hosts human genome sequences annotated with variability data, the latter being estimated through application of SiteVar software based on site-specific nucleotide amino acid calculations. annotations are manually curated thus adding value quality information provided end-user. Classifier tools implemented in allow prediction haplogroup for any...
Abstract Background Aerobic glycolysis, namely the Warburg effect, is main hallmark of cancer cells. Mitochondrial respiratory dysfunction has been proposed to be one major causes for such glycolytic shift. This hypothesis revisited as tumors appear undergo waves gene regulation during progression, some which rely on functional mitochondria. In this framework, role mitochondrial complex I still debated, in particular with respect effect DNA mutations metabolism. The aim work provide proof...
Abstract Background Eukaryotic nuclear genomes contain fragments of mitochondrial DNA called NumtS (Nuclear Sequences), whose mode and time insertion, as well their functional/structural role within the genome are debated issues. Insertion sites match with chromosomal breaks, revealing that micro-deletions usually occurring at non-homologous end joining loci become reduced in presence NumtS. Some involved recombination events leading to fragment duplication. Moreover, polymorphic, a feature...
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...
Interest in human mitochondrial genetic data is constantly increasing among both clinicians and researchers, due to the involvement of DNA (mtDNA) a number physiological pathological processes. Thanks new sequencing technologies modern databases, large amount information on mtDNA variability may be exploited gain insights into relationship between variants, phenotypes diseases. To facilitate this process, we have developed HmtVar resource, variant-focused database that allows exploration...
Abstract Background NumtS ( N uclear M i T ochondrial S equences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized nuclear genome. Accurate mapping of avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates) and polymorphic, in terms presence/absence content SNPs, may be used as evolutionary markers...
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...
The colonization of the nuclear genome by mitochondrial DNA is an ongoing process in eukaryotes and plays important role genomic variability. Notwithstanding sequence availability about 100 complete eukaryotic genomes, up to now NumtS distribution has been fully reported for a small number sequenced species. With aim clarify time way evolution, we explored 23 species using intra/interspecies silico approach based on cross-species similarity search deeply investigate evolution mammals. intra-...
MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome phenome bioinformatics resource built by mitochondrial disease community to facilitate clinical diagnosis research investigations of individual patient phenotypes, genomes, genes, variants. A central Web portal (https://mseqdr.org) integrates knowledge from expert-curated databases with genomic phenotype data shared clinicians researchers. also functions as application server for Web-based...
Population genetics studies based on the analysis of mtDNA and mitochondrial disease have produced a huge quantity sequence data related information. These are at present worldwide distributed in differently organised databases web sites not well integrated among them. Moreover it is generally possible for user to submit contemporarily analyse its own comparing them with content given database, both population data.HmtDB well-integrated web-based human bioinformatic resource aimed supporting...
Mitochondrial DNA (mtDNA) mutations have been described in almost all types of cancer. However, their exact role and timing occurrence during tumor development progression are still a matter debate. A Vogelstein-like model is well established for endometrial carcinoma (EC), however, mtDNA has scarcely investigated these tumors despite the fact that mitochondrial biogenesis increase shown to be hallmark type I EC. Here, we screened panel 23 EC tissues matched typical hyperplasia four...
Mitochondrial DNA (mtDNA) mutations leading to the disruption of respiratory complex I (CI) have been shown exhibit anti-tumorigenic effects, at variance with those impairing only function but not assembly complex, which appear contribute positively cancer development. Owing challenges in analysis multi-copy mitochondrial genome, it is yet be determined whether tumour-associated mtDNA lesions occur as somatic modifying factors or germ-line predisposing elements. Here we investigated whole...
We present here a fast and sensitive method designed to isolate short nucleotide sequences which have non-random statistical properties may thus be biologically active. It is based on first order Markov analysis allows us detect statistically significant sequence motifs from six ten nucleotides long are significantly shared (or avoided) in the under investigation. This has been tested set of 521 extracted Eukaryotic Promoter Database (2). Our results demonstrate accuracy efficiency that...
Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include inconsistency in mtDNA nomenclatures, existence multiple reference genomes, and a lack population frequency data. Clinicians need simple bioinformatics tool that user-friendly, bioinformaticians powerful informatics resource programmatic usage. Here, we report development functionality MSeqDR Variant Tool set (mvTool),...
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...