A5002057785- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- MicroRNA in disease regulation
- Graph Theory and Algorithms
- Data Management and Algorithms
- Cancer-related molecular mechanisms research
- Microbial Metabolic Engineering and Bioproduction
- Advanced Graph Neural Networks
- RNA modifications and cancer
- Gene Regulatory Network Analysis
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Advanced Database Systems and Queries
- Extracellular vesicles in disease
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Data Mining Algorithms and Applications
- Algorithms and Data Compression
- CRISPR and Genetic Engineering
- Complex Network Analysis Techniques
- RNA regulation and disease
- Advanced Proteomics Techniques and Applications
- Genomics and Chromatin Dynamics
University of Verona
2016-2025
University of Palermo
2023-2025
University of Catania
2008-2018
Courant Institute of Mathematical Sciences
2007-2012
New York University
2007-2009
University of Toronto
2007
Modern search engines answer keyword-based queries extremely efficiently. The impressive speed is due to clever inverted index structures, caching, a domain-independent knowledge of strings, and thousands machines. Several research efforts have attempted generalize keyword keytree keygraph searching, because trees graphs many applications in next-generation database systems. This paper surveys both algorithms applications, giving some emphasis our own work.
<h3>Background</h3> Pancreatic ductal adenocarcinoma (PDAC) is a highly devastating disease with an overall 5-year survival rate of less than 8%. New evidence indicates that PDAC cells release pro-inflammatory metabolites induce marked alteration normal hematopoiesis, favoring the expansion and accumulation myeloid-derived suppressor (MDSCs). We report here patients show increased levels both circulating tumor-infiltrating MDSC-like cells. <h3>Methods</h3> The frequency MDSC subsets in...
Here we elucidate the effect of Alzheimer disease (AD)-predisposing genetic backgrounds, APOE4, PSEN1ΔE9, and APPswe, on functionality human microglia-like cells (iMGLs). We present a physiologically relevant high-yield protocol for producing iMGLs from induced pluripotent stem cells. Differentiation is directed with small molecules through primitive erythromyeloid progenitors to re-create microglial ontogeny yolk sac. The express signature genes respond ADP intracellular Ca2+ release...
The current COVID-19 pandemic presents unprecedent new challenges to public health and medical care delivery. To control viral transmission, social distancing measures have been implemented all over the world, interrupting access routine for many individuals with neurological diseases. Cognitive disorders are common in conditions, e.g., stroke, traumatic brain injury, Alzheimer's disease other types of dementia, Parkinson's parkinsonian syndromes, multiple sclerosis, should be addressed by...
Microglia are the endogenous immune cells of brain and act as sensors pathology to maintain homeostasis eliminate potential threats. In Alzheimer's disease (AD), toxic amyloid beta (Aβ) accumulates in forms stiff plaques. late-onset AD accounting for 95% all cases, this is thought be due reduced clearance Aβ. Human genome-wide association studies animal models suggest that results from aberrant function microglia. While impact neurochemical pathways on microglia had been broadly studied,...
GraphGrep is an application-independent method for querying graphs, finding all the occurrences of a subgraph in database graphs. The interface to regular expression graph query language Glide that combines features from Xpath and Smart. incorporates both single node variable-length wildcards. Our algorithm uses hash-based fingerprinting represent graphs abstract form filter database. has been tested on databases size up 16,000 molecules performs well this entire range.
Graphs can represent biological networks at the molecular, protein, or species level. An important query is to find all matches of a pattern graph target graph. Accomplishing this inherently difficult (NP-complete) and efficiency heuristic algorithms for problem may depend upon input graphs. The common aim existing eliminate unsuccessful mappings as early inexpensively possible.We propose new subgraph isomorphism algorithm which applies search strategy significantly reduce space without...
Abstract Motivation: The identification of drug–target interaction (DTI) represents a costly and time-consuming step in drug discovery design. Computational methods capable predicting reliable DTI play an important role the field. Recently, recommendation relying on network-based inference (NBI) have been proposed. However, such approaches implement naive topology-based do not take into account features within domain. Results: In this article, we present new NBI method, called domain...
MicroRNAs are small noncoding RNAs that play an important role in the regulation of various biological processes through their interaction with cellular messenger RNAs. They frequently dysregulated cancer and have shown great potential as tissue-based markers for classification prognostication. microRNAs also present extracellular human body fluids such serum, plasma, saliva, urine. Most circulating plasma serum cofractionate Argonaute2 (Ago2) protein. However, been found membrane-bound...
When it becomes completely possible for one to computationally forecast the impacts of harmful substances on humans, would be easier attempt addressing shortcomings existing safety testing chemicals. In this paper, we relay outcomes a community-facing DREAM contest prognosticate nature environment-based compounds, considering their likelihood have disadvantageous health-related effects human populace. Our research quantified cytotoxicity levels in 156 compounds across 884 lymphoblastic lines...
Mesenchymal stromal cells (MSCs) are adult, multipotent of mesodermal origin representing the progenitors all tissues. MSCs possess significant and broad immunomodulatory functions affecting both adaptive innate immune responses once primed by inflammatory microenvironment. Recently, role extracellular vesicles (EVs) in mediating therapeutic effects has been recognized. Nevertheless, molecular mechanisms responsible for properties MSC-derived EVs (MSC-EVs) still poorly characterized....
Abstract Hypoxia induces changes in the secretion of extracellular vesicles (EVs) several non‐neuronal cells and pathological conditions. EVs are packed with biomolecules, such as microRNA(miR)‐21‐5p, which respond to hypoxia. However, true EV association miR‐21‐5p, its functional or biomarker relevance, inadequately characterised. Neurons extremely sensitive cells, it is not known whether neuronal miR‐21‐5p altered upon Here, we characterised temporal profile cell viability neurons under...
Tumors weakly infiltrated by T lymphocytes poorly respond to immunotherapy. We aimed unveil malignancy-associated programs regulating cell entrance, arrest, and activation in the tumor environment. Differential expression of adhesion tissue architecture programs, particularly presence membrane tetraspanin claudin (CLDN)18 as a signature gene, demarcated immune-infiltrated from immune-depleted mouse pancreatic tumors. In human ductal adenocarcinoma (PDAC) non-small lung cancer, CLDN18...
More sophisticated representations of compounds attempt to incorporate not only information on the structure and physicochemical properties molecules, but also knowledge about their biological traits, leading so-called bioactivity profile. The bioactive profiling air pollutants is challenging crucial, as activity toxicological effects have been deeply investigated yet, further exploration could shed light impact pollution complex disorders. Therefore, a signature that simultaneously captures...
miRò is a web-based knowledge base that provides users with miRNA–phenotype associations in humans. It integrates data from various online sources, such as databases of miRNAs, ontologies, diseases and targets, into unified database equipped an intuitive flexible query interface mining facilities. The main goal the establishment which allows non-trivial analysis through sophisticated techniques introduction new layer between genes phenotypes inferred based on miRNAs annotations. Furthermore,...
Abstract Glycogen synthase kinase-3 β (GSK-3 ) has emerged as a critical factor in several pathways involved hippocampal neuronal maintenance and function. In Huntington’s disease (HD), there are early deficits both patients transgenic mouse models, which prompted us to investigate whether disease-specific changes GSK-3 expression may underlie these abnormalities. Thirty-three postmortem samples from HD (neuropathological grades 2–4) age- sex-matched normal control cases were analyzed using...
miRandola (http://mirandola.iit.cnr.it/) is a database of extracellular non-coding RNAs (ncRNAs) that was initially published in 2012, foreseeing the relevance ncRNAs as non-invasive biomarkers. An increasing amount experimental evidence shows are frequently dysregulated diseases. Further, have been discovered different forms, such exosomes, which circulate human body fluids. Thus, 2017 an effort to update and collect accumulating information on spread across scientific publications...
Olfaction is orchestrated by olfactory mucosal cells located in the upper nasal cavity. Olfactory dysfunction manifests early several neurodegenerative disorders including Alzheimer’s disease, however, disease-related alterations to remain poorly described. The aim of this study was evaluate mucosa differences between cognitively healthy individuals and disease patients. We report increased amyloid-beta secretion detail cell-type-specific gene expression patterns, unveiling 240...
Background Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest tumors owing to its robust desmoplasia, low immunogenicity, and recruitment cancer-conditioned, immunoregulatory myeloid cells. These features strongly limit success immunotherapy as a single agent, thereby suggesting need for development multitargeted approach. The goal foster T lymphocyte infiltration within tumor landscape neutralize cancer-triggered immune suppression, enhance therapeutic effectiveness...