A5000359857- Circular RNAs in diseases
- RNA modifications and cancer
- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Single-cell and spatial transcriptomics
- Extracellular vesicles in disease
- Cell Image Analysis Techniques
- RNA Research and Splicing
- Reproductive Biology and Fertility
- Graph Theory and Algorithms
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Advanced Graph Neural Networks
- Cancer-related gene regulation
- RNA and protein synthesis mechanisms
- Ovarian function and disorders
- Renal and related cancers
- Cancer Genomics and Diagnostics
- Gene Regulatory Network Analysis
- DNA and Biological Computing
- Cholangiocarcinoma and Gallbladder Cancer Studies
University of Turin
2019-2025
University of Verona
2020
Background & AimsFecal tests currently used for colorectal cancer (CRC) screening show limited accuracy in detecting early tumors or precancerous lesions. In this respect, we comprehensively evaluated stool microRNA (miRNA) profiles as biomarkers noninvasive CRC diagnosis.MethodsA total of 1273 small RNA sequencing experiments were performed multiple biospecimens. a cross-sectional study, miRNA investigated fecal samples from an Italian and Czech cohort (155 CRCs, 87 adenomas, 96 other...
Abstract Background Artificial Intelligence entails the application of computer algorithms to huge and heterogeneous amount morphodynamic data produced by Time-Lapse Technology. In this context, Machine Learning (ML) methods were developed in order assist embryologists with automatized objective predictive models able standardize human embryo assessment. study, we aimed at developing a novel ML-based strategy identify relevant patterns associated prediction blastocyst development stage on...
Early detection of colorectal cancer (CRC) significantly improves its management and patients' survival. Circular RNAs (circRNAs) are peculiar covalently closed transcripts involved in gene expression modulation whose dysregulation has been extensively reported CRC cells. However, little is known about their alterations the early phases carcinogenesis. In this study, we performed an integrative analysis circRNA profiles RNA-sequencing (RNA-Seq) data 96 cancers, 27 adenomas, matched adjacent...
Abstract Single-cell RNA sequencing (scRNAseq) is an essential tool to investigate cellular heterogeneity. Thus, it would be of great interest being able disclose biological information belonging cell subpopulations, which can defined by clustering analysis scRNAseq data. In this manuscript, we report a that developed for the functional mining single clusters based on Sparsely-Connected Autoencoder (SCA). This allows uncovering hidden features associated with We implemented two new metrics,...
Abstract Background Single-cell RNA sequencing is essential for investigating cellular heterogeneity and highlighting cell subpopulation-specific signatures. applications have spread from conventional to epigenomics, e.g., ATAC-seq. Many related algorithms tools been developed, but few computational workflows provide analysis flexibility while also achieving functional (i.e., information about the data used are saved as metadata) reproducibility a real image of environment generate stored)...
Recent improvements in cost-effectiveness of high-throughput technologies has allowed RNA sequencing total transcriptomes suitable for evaluating the expression and regulation circRNAs, a relatively novel class transcript isoforms with suggested roles transcriptional post-transcriptional gene regulation, as well their possible use biomarkers, due to deregulation various human diseases. A limited number integrated workflows exists prediction, characterization, differential analysis none them...
Recently the increased cost-effectiveness of high-throughput technologies has made available a large number RNA sequencing datasets to identify circular RNAs (circRNAs). However, despite many computational tools were developed predict circRNAs, limited workflows exists and characterize circRNAs. Moreover, best our knowledge, these do not ensure reproducibility require advanced bash scripting skills be correctly installed used. To cope with critical aspects we present Docker4Circ, new...
Abstract Single-cell RNA sequencing (scRNAseq) is an essential tool to investigate cellular heterogeneity. Although scRNAseq has some technical challenges, it would be of great interest being able disclose biological information out cell subpopulations, which can defined by cluster analysis data. In this manuscript, we evaluated the efficacy sparsely-connected autoencoder (SCA) as for functional mining single cells clusters. We show that SCA uses uncover hidden features associated Our...
DNA methylation is a modification playing an important role in several diseases, including cancer. The gold-standard technique for measuring Bisulfite Sequencing (BS). treatment with bisulfite alters the sequence of making analysis BS data computationally difficult. There are many tools analysing but choice which to use difficult due extensive biological and technical variability data. Synthetic real datasets can be exploited evaluate tool performance obtain accurate analysis. Today, Sherman...
Despite many computational tools were developed to predict circular RNAs (circRNAs), a limited number of work-flows exists fully analyse circRNA set ensuring the reproducibility whole analysis. For this purpose, we designed Docker4Circ, work-flow for comprehensive circRNAs analysis composed four modules: prediction (module 1), classification and annotation 2), sequence 3), expression 4). To ensure each function Docker4Circ was embeded into docker image following guideline provided by...
Despite many computational tools were developed to predict circular RNAs (circRNAs), a limited number of work-flows exists fully analyse circRNA set ensuring the reproducibility whole analysis. For this purpose, we designed Docker4Circ, work-flow for comprehensive circRNAs analysis composed four modules: prediction (module 1), classification and annotation 2), sequence 3), expression 4). To ensure each function Docker4Circ was embeded into docker image following guideline provided by...
Despite many computational tools were developed to predict circular RNAs (circRNAs), a limited number of work-flows exists fully analyse circRNA set ensuring the reproducibility whole analysis. For this purpose, we designed Docker4Circ, work-flow for comprehensive analysis circRNAs composed four modules: prediction (module 1), classification and annotation 2), sequence 3), expression 4). To ensure each function Docker4Circ was embeded into docker image following guideline provided by...
Despite many computational tools were developed to predict circular RNAs (circRNAs), a limited number of work-flows exists fully analyse circRNA set ensuring the reproducibility whole analysis. For this purpose, we designed Docker4Circ, work-flow for comprehensive circRNAs analysis composed four modules: prediction (module 1), classification and annotation 2), sequence 3), expression 4). To ensure each function Docker4Circ was embeded into docker image following guideline provided by...
Abstract Background: Graphs are mathematical structures widely used for expressing relationships among elements when representing biomedical and biological information. On top of these representations, several analyses conducted. A common task is the search one substructure, called query, within graph, target. The problem referred to as one-to-one subgraph search, it shown be NP-complete. However, heuristics indexing techniques can applied facilitate search. Such also exploited in context...
Abstract Study question Can morphokinetic features included into Machine Learning (ML) algorithms identify cleavage-stage embryos with the best chance to reach expanded blastocyst stage on day 5? Summary answer A ML algorithm based early can cleaving that will 5. What is known already To date, conventional morphology assessment of human has a limited predictive power further embryo developmental potential. The analysis using Time-Lapse systems (TLS) was introduced in order provide new tool...