From Computational Logic to Computational Biology
Essays Dedicated to Alfredo Ferro to Celebrate His Scientific Career
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Article
Open AccessEfficacy of High-dose Liraglutide 3.0 mg in Patients with Poor Response to Bariatric Surgery: Real-world Experience and Updated Meta-analysis
Poor response to bariatric surgery, characterized by insufficient weight loss (IWL) or weight regain (WR), poses a significant challenge in obesity treatment. This study aims to assess the effectiveness of lir...
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Chapter
Motif Finding Algorithms: A Performance Comparison
Network motifs are subgraphs of a network that occur more frequently than expected, according to some reasonable null model. They represent building blocks of complex systems such as genetic interaction networ...
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Book
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Article
Open AccessXRF analysis searching for fingerprint elemental profile in south-eastern Sicily tomatoes
The implementation of analytical techniques able to certify food quality and origin in a fast and non-destructive way is becoming a widespread need in the agri-food sector. Among the physical non-destructive t...
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Chapter and Conference Paper
COMBO: A Computational Framework to Analyze RNA-seq and Methylation Data Through Heterogeneous Multi-layer Networks
Multi-layer Complex networks are commonly used for modeling and analysing biological entities. This paper presents a new computational framework called COMBO (Combining Multi Bio Omics) for generating and anal...
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Article
Open AccessNetwork analysis of synovial RNA sequencing identifies gene-gene interactions predictive of response in rheumatoid arthritis
To determine whether gene-gene interaction network analysis of RNA sequencing (RNA-Seq) of synovial biopsies in early rheumatoid arthritis (RA) can inform our understanding of RA pathogenesis and yield improve...
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Article
Open AccessDysregulation of microRNAs and tRNA-derived ncRNAs in mesothelial and mesothelioma cell lines after asbestiform fiber exposure
Experimental evidence demonstrated that fluoro-edenite (FE) can develop chronic respiratory diseases and elicit carcinogenic effects. Environmental exposure to FE fibers is correlated with malignant pleural me...
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Article
Open AccessNETME: on-the-fly knowledge network construction from biomedical literature
The rapidly increasing biological literature is a key resource to automatically extract and gain knowledge concerning biological elements and their relations. Knowledge Networks are helpful tools in the contex...
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Chapter
Computational Methods for Drug Repurposing
The wealth of knowledge and multi-omics data available in drug research has allowed the rise of several computational methods in the drug discovery field, resulting in a novel and exciting strategy called drug...
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Chapter
Computational Resources for the Interpretation of Variations in Cancer
A broad ecosystem of resources, databases, and systems to analyze cancer variations is present in the literature. These are a strategic element in the interpretation of NGS experiments. However, the intrinsic ...
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Chapter
Pathway Analysis for Cancer Research and Precision Oncology Applications
With the advent of OMICs technologies, several bioinformatics methods have been developed to infer biological knowledge from such data. Pathway analysis methodologies help integrate multi-OMICs data and find a...
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Article
Open AccessTemporalRI: subgraph isomorphism in temporal networks with multiple contacts
Temporal networks are graphs where each edge is associated with a timestamp denoting when two nodes interact. Temporal Subgraph Isomorphism (TSI) aims at retrieving all the subgraphs of a temporal network (cal...
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Article
Open AccessRNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis
RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requ...
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Chapter and Conference Paper
NETME: On-the-Fly Knowledge Network Construction from Biomedical Literature
The huge amount of biological literature, which daily increases, represents a strategic resource to automatically extract and gain knowledge concerning relations among biological elements. Knowledge Networks a...
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Chapter and Conference Paper
TemporalRI: A Subgraph Isomorphism Algorithm for Temporal Networks
Temporal networks are graphs where each edge is associated with a timestamp or an interval indicating when an interaction between two nodes happens. The Temporal Subgraph Isomorphism (TSI) problem aims at iden...
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Article
Open AccessEstablish the expected number of induced motifs on unlabeled graphs through analytical models
Complex networks are usually characterized by the presence of small and recurrent patterns of interactions between nodes, called network motifs. These small modules can help to elucidate the structure and the ...
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Article
Risk of acute stroke in patients with retinal artery occlusion: a systematic review and meta-analysis
To estimate the incidence of acute cerebral ischaemia detected by magnetic resonance imaging (MRI) in acute central retinal artery occlusion (CRAO), branch retinal artery occlusion (BRAO) and transient monocul...
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Chapter and Conference Paper
Establish the Expected Number of Injective Motifs on Unlabeled Graphs Through Analytical Models
Network motifs have a central role in explaining the functionality of complex systems. Establishing motif significance requires the computation of the expected number of their occurrences according to a random...
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Article
Open AccessTACITuS: transcriptomic data collector, integrator, and selector on big data platform
Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate d...
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Article
Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics
Many scientific applications entail solving the subgraph isomorphism problem, i.e., given an input pattern graph, find all the subgraphs of a (usually much larger) target graph that are structurally equivalent...
