Alfonso Urso

Alfonso Urso
Italian National Research Council | CNR · Institute for High Performance Computing and Networking ICAR

About

101
Publications
48,216
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910
Citations
Citations since 2017
31 Research Items
638 Citations
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2017201820192020202120222023020406080100120140
2017201820192020202120222023020406080100120140
2017201820192020202120222023020406080100120140
Additional affiliations
February 1994 - November 2000
Università degli Studi di Palermo
Position
  • Research Associate

Publications

Publications (101)
Article
Full-text available
2,2’4,4’-tetrabromodiphenyl ether (PBDE-47) is one of the most widespread environmental brominated flame-retardant congeners which has also been detected in animal and human tissues. Several studies have reported the effects of PBDEs on different health issues, including neurobehavioral and developmental disorders, reproductive health, and alterati...
Article
Full-text available
Many biological systems are characterised by biological entities, as well as their relationships. These interaction networks can be modelled as graphs, with nodes representing bio-entities, such as molecules, and edges representing relations among them, such as interactions. Due to the current availability of a huge amount of biological data, it is...
Chapter
Recent advances in single-cell RNA-sequencing in order to study cells in biology, and the increasing amount of data available, led to the development of algorithms for analyzing single cells from gene expression data. In this work, we propose an artificial intelligence architecture that classifies cell types of human tissue. This architecture combi...
Article
Full-text available
In consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing (direct RNA seq.) experiment using critical oropharyngeal swab samples collected from Italian patients infected with SARS-CoV-2 from the Palermo region in Sicily. Here...
Article
Full-text available
Cytochromes P450 (CYP) are enzymes responsible for the biotransformation of most endogenous and exogenous agents. The expression of each CYP is influenced by a unique combination of mechanisms and factors including genetic polymorphisms, induction by xenobiotics, and regulation by cytokines and hormones. In recent years, Ciona robusta, one of the c...
Article
Full-text available
Tumors undergo dynamic immunoediting as part of a process that balances immunological sensing of emerging neoantigens and evasion from immune responses. Tumor-infiltrating lymphocytes (TILs) comprise heterogeneous subsets of peripheral T cells characterized by diverse functional differentiation states and dependence on TCR specificity gained throug...
Article
Full-text available
The 2,2’4,4’-tetrabromodiphenyl ether (PBDE-47) is one of the most prominent PBDE congeners detected in the environment and in animal and human tissues. Animal model experiments suggested the occurrence of PBDE-induced immunotoxicity leading to different outcomes and recently we demonstrated that this substance can impair macrophage and basophil ac...
Article
Full-text available
The transforming growth factor-β (TGF-β) family of cytokines performs a multifunctional signaling, which is integrated and coordinated in a signaling network that involves other pathways, such as Wintless, Forkhead box-O (FOXO) and Hedgehog and regulates pivotal functions related to cell fate in all tissues. In the hematopoietic system, TGF-β signa...
Chapter
DNA sequences are the basic data type that is processed to perform a generic study of biological data analysis. One key component of the biological analysis is represented by sequence classification, a methodology that is widely used to analyze sequential data of different nature. However, its application to DNA sequences requires a proper represen...
Preprint
Full-text available
Background In consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing experiment using critical oropharyngeal swab samples collected from Italian patients infected with SARS-CoV-2 from the Palermo region in Sicily. Methods He...
Article
Full-text available
Background: Non-coding RNAs include different classes of molecules with regulatory functions. The most studied are microRNAs (miRNAs) that act directly inhibiting mRNA expression or protein translation through the interaction with a miRNAs-response element. Other RNA molecules participate in the complex network of gene regulation. They behave as c...
Article
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The 16th Annual Meeting of the Bioinformatics Italian Society was held in Palermo, Italy, on June 26-28, 2019. More than 80 scientific contributions were presented, including 4 keynote lectures, 31 oral communications and 49 posters. Also, three workshops were organised before and during the meeting. Full papers from some of the works presented in...
Article
Full-text available
The close phylogenetic relationship between Ciona robusta and vertebrates makes it a powerful model for studying innate immunity and the evolution of immune genes. To elucidate the nature and dynamics of the immune response, the molecular mechanisms by which bacterial infection is detected and translated into inflammation and how potential pattern...
Chapter
In this paper, we explore the interaction between miRNA and deregulated proteins in some pathologies. Assuming that miRNA can influence mRNA and consequently the proteins regulation, we explore this connection by using an interaction matrix derived from miRNA-target data and PPI network interactions. From this interaction matrix and the set of dere...
Article
Full-text available
Background: In silico experiments, with the aid of computer simulation, speed up the process of in vitro or in vivo experiments. Cancer therapy design is often based on signalling pathway. MicroRNAs (miRNA) are small non-coding RNA molecules. In several kinds of diseases, including cancer, hepatitis and cardiovascular diseases, they are often dere...
Article
Full-text available
Abstract The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was “Methods, tools and platforms for Personalised Medicine in the Big Data Era”, but the traditional topics of the meeting series were also included in the event. About 40 scientific contributions were presented, in...
Article
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Background microRNAs act as regulators of gene expression interacting with their gene targets. Current bioinformatics services, such as databases of validated miRNA-target interactions and prediction tools, usually provide interactions without any information about what tissue that interaction is more likely to appear nor information about the type...
Article
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Background: Several online databases provide a large amount of biomedical data of different biological entities. These resources are typically stored in systems implementing their own data model, user interface and query language. On the other hand, in many bioinformatics scenarios there is often the need to use more than one resource. The availab...
Chapter
Several recent works have shown that K-mer sequence representation of a DNA sequence can be used for classification or identification of nucleosome positioning related sequences. This representation can be computationally expensive when k grows, making the complexity in spaces of exponential dimension. This issue affects significantly the classific...
Article
Full-text available
Background: An open challenge in translational bioinformatics is the analysis of sequenced metagenomes from various environmental samples. Of course, several studies demonstrated the 16S ribosomal RNA could be considered as a barcode for bacteria classification at the genus level, but till now it is hard to identify the correct composition of meta...
Conference Paper
The development of high throughput technology in biological and medical domains has seen a growing intervention of informatics support. Indeed, the big amount of data produced is difficult to analyse and interpret in terms of time consuming and number of different resources used. In this context, the challenge would be to have an integrated and mul...
Preprint
Full-text available
Nowadays, a huge amount of biomedical data of different biological entities is provided by many online databases and services, each with its own data model, user interface and query language. However, typical bioinformatics scenarios require the use of more than one resource. Therefore, the availability of a single bioinformatics platform that inte...
Preprint
Full-text available
Nowadays, a huge amount of biomedical data of different biological entities is provided by many online databases and services, each with its own data model, user interface and query language. However, typical bioinformatics scenarios require the use of more than one resource. Therefore, the availability of a single bioinformatics platform that inte...
Article
Full-text available
MotivationNon-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically relevant roles has opened the way to develop methods able to discriminate between the different ncRNA classes. Moreover, the lack...
Conference Paper
Full-text available
The proliferation of biological research data generated and shared openly online is of huge benefit to the scientific community, but there are often significant challenges to overcome before it can be integrated from different sources and re-used to gain new knowledge. This paper introduces BioGrakn, which is a graph-based deductive database, combi...
Conference Paper
In the last decade, biological tasks became much more complex and often their solution requires the simultaneous use of several different resources. Examples of typical bioinformatics scenarios are given by the gene functional studies, the study of microRNA Single Nucleotide Polymorphisms in cancer disease, or the study of protein motifs linked to...
Article
Full-text available
Background MicroRNAs (miRNAs) are small non-coding RNA sequences with regulatory functions to post-transcriptional level for several biological processes, such as cell disease progression and metastasis. MiRNAs interact with target messenger RNA (mRNA) genes by base pairing. Experimental identification of miRNA target is one of the major challenges...
Conference Paper
The era of “big data” arose the need to have computational tools in support of biological tasks. Many types of bioinformatics tools have been developed for different biological tasks as target, pathway and gene set analysis, but integrated resources able to incorporate a unique web interface, and to manage a biological scenario involving many diffe...
Conference Paper
Full-text available
Monolithic applications are the most common development paradigm but they have some drawback related to the maintenance, upgrading and scaling. Microservice architectures were recently proposed in order to solve some of these issues, because they are simpler to scale and more flexible. Both architectures use a database and this component can act as...
Conference Paper
Full-text available
Deep learning neural networks are capable to extract significant features from raw data, and to use these features for classification tasks. In this work we present a deep learning neural network for DNA sequence classification based on spectral sequence representation. The framework is tested on a dataset of 16S genes and its performances, in term...
Conference Paper
Full-text available
Microservice architectures are used as alternative to monolithic applications because they are simpler to scale and more flexible. Microservices require a careful design because each service component should be simple and easy to develop. In this paper, a new microservice pattern is proposed: a database that can be considered a microservice by itse...
Conference Paper
Full-text available
Current bioinformatics databases provide huge amounts of different biological entities such as genes, proteins, diseases, microRNA, annotations, literature references. In many case studies, a bioinformatician often needs more than one type of resource in order to fully analyse his data. In this paper, we introduce BioGraphDB, a bioinformatics datab...
Conference Paper
Full-text available
Analysis and classification of sequences is one of the key research areas in bioinformatics. The basic tool for sequence analysis is alignment, but there are also other techniques that can be used. Frequency Chaos Game Representation is a technique that builds an image characteristic of the sequence The paper describes the first experiment in the u...
Conference Paper
Full-text available
In this paper, an extension of a MultiModel NoSQL database is proposed in order to transform it on an ebXML registry, a complete system for Business-to-Business (B2B) information exchange. It can be used as key component of the interoperability infrastructure developed within the OpenInFSE project. OrientDB has been chosen as MultiModel NoSQL datab...
Conference Paper
Full-text available
IT complexity in enterprise today continues to grow at a dizzying rate. Technology innovation, vendor heterogeneity, and business demands are major reasons why organizations are exposed to new risks, based on the gaps opened between the options and features of each IT element and product, and how they are implemented to support a well-defined polic...
Poster
Full-text available
RNA sequencing (RNA-seq) is a New Generation Sequencing (NGS) method used for the analysis of transcripts and differential gene expression profiles. MicroRNA (miRNAs, 22--25 nt long) are, among small non coding RNAs (sncRNA) obtained through RNA-seq, key regulators in multiple cellular functions, as they play a crucial role in different physiologic...
Poster
Full-text available
MicroRNAs (miRNAs) are small non coding RNAs with regulatory functions to post-transcriptional level. They play an important role in molecular and cellular mechanisms, thanks to their ability to bind and interact with many RNA messengers (mRNAs) of coding product involved in a wide range of biological pathways, cellular status, and conditions. We p...
Chapter
The “cythosome c oxidase subunits 1” (COI) gene is used for identification of species, and it is one of the so-called DNA barcode genes. Identification of species, even using DNA barcoding can be difficult if the biological examples are degraded. Spectral representation of sequences and the General Regression Neural Network (GRNN) can give some int...
Conference Paper
In the identification of living species through the analysis of their DNA sequences, the mitochondrial “cytochrome c oxidase subunit 1” (COI) gene has proved to be a good DNA barcode. Nevertheless, the quality of the full length barcode sequences often can not be guaranteed because of the DNA degradation in biological samples, so that only short se...
Article
In this paper, an alignment-free method for DNA barcode classification that is based on both a spectral representation and a neural gas network for unsupervised clustering is proposed. In the proposed methodology, distinctive words are identified from a spectral representation of DNA sequences. A taxonomic classification of the DNA sequence is then...
Conference Paper
Full-text available
The traditional Java API for Registries (JAXR) provides a useful way for Java developers to use a single simple abstraction API to access a variety of registries. The unified JAXR information model (Infomodel), which describes content and metadata within registries, provides a simple way to access registries information. However, when a JAXR regist...
Article
Full-text available
Studies on genomic sequences for classification and taxonomic identification have a leading role in the biomedical field and in the analysis of biodiversity. These studies are focusing on the so-called barcode genes, representing a well defined region of the whole genome. Recently, alignment-free techniques are gaining more importance because they...
Article
Full-text available
MicroRNAs (miRNAs) are important key regulators in multiple cellular functions, due to their a crucial role in different physiological processes. MiRNAs are differentially expressed in specific tissues, during specific cell status, or in different diseases as tumours. RNA sequencing (RNA-seq) is a Next Generation Sequencing (NGS) method for the ana...
Conference Paper
Today Workflow Management Systems (WFMS), like Taverna and Kepler, have a very important place in the everyday work of the scientist. These tools support the access to computational resources and act as interface for building complex data processing chains. The next step is to support decisions of the researcher on autonomously developing workflow...
Technical Report
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Secondo quanto definito dalle linee guida nazionali del Ministero della Salute, il Fascicolo Sanitario Elettronico è composto dall'insieme di dati e documenti digitali di tipo sanitario e socio-sanitario generati da eventi clinici presenti e trascorsi, riguardanti l'assistito. La gestione di queste informazioni sul territorio nazionale ha richiesto...
Conference Paper
Taxonomic classification of genomic sequences is usually based on evolutionary distance obtained by alignment. In this work we introduce a novel alignment-free classification approach based on probabilistic topic modeling. Using a k-mer (small fragments of length k) decomposition of DNA sequences and the Latent Dirichlet Allocation algorithm, we bu...
Article
Full-text available
Background In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to design and execute scientific workflows and aid in silico experimentation. The availability of fast unsupervised methods for clust...
Conference Paper
In this paper we present an application of the neural gas network to the classification of the DNA barcode sequences. The proposed method is based on the identification of distinctive words, extracted from the spectral representation of DNA sequences. In particular we calculated the "signatures" that are a characteristic of the DNA sequence at diff...
Article
Specific expert systems are used for supporting, speeding-up and adding precision to in silico experimentation in many domains. In particular, many experimentalists exhibit a growing interest in workflow management systems for making a pipeline of experiments. Unfortunately, these types of systems do not integrate a systematic approach or a support...
Article
Full-text available
Background The key idea of DNA barcode initiative is to identify, for each group of species belonging to different kingdoms of life, a short DNA sequence that can act as a true taxon barcode. DNA barcode represents a valuable type of information that can be integrated with ecological, genetic, and morphological data in order to obtain a more consis...
Article
Full-text available
Background We introduce a Knowledge-based Decision Support System (KDSS) in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed scenario, our KDSS is able to suggest both strategies and tools, according to the features of input dataset. Our system provides a navigable workflow for...
Chapter
Full-text available
In this paper it is introduced a new methodology for the analysis of barcode sequences. Barcode DNA is a very short nucleotide se-quence, corresponding for the animal kingdom to the mitochondrial gene cytochrome c oxidase subunit 1, that acts as a unique element for identi-fication and taxonomic purposes. Traditional barcode analysis uses well cons...
Conference Paper
Background / Purpose: Ontologies represent formal structures to define and organize knowledge of a specific application domain. Our purpose is to provide an ontological structure in order to add the functionalities and capability of a DSS to the more recent workflow management systems. We called our ontological approach Data Problem Solver Workfl...
Conference Paper
In this paper a new intelligent system designed to support the researcher in the development of a workflow for bioinformatics experiments is presented. The proposed system is capable to suggest one or more strategies in order to resolve the selected problem and to support the user in the assembly of a workflow for complex experiments, using a a Kno...
Conference Paper
Ontologies are formal knowledge representation models. Knowledge organization is a fundamental requirement in order to develop Knowledge-Based systems. In this paper we present Data-Problem-Solver (DPS) approach, a new ontological paradigm that allows the knowledge designer to model and represent a Knowledge Base (KB) for expert systems. Our approa...
Article
The Self-Organizing Map (SOM) is a popular unsupervised neural network able to provide effective clustering and data visualization for multidimensional input datasets. In this paper, we present an application of the simulated annealing procedure to the SOM learning algorithm with the aim to obtain a fast learning and better performances in terms of...
Article
Full-text available
The Self-Organizing Map (SOM) algorithm is widely used for building topographic maps of data represented in a vectorial space, but it does not operate with dissimilarity data. Soft Topographic Map (STM) algorithm is an extension of SOM to arbitrary distance measures, and it creates a map using a set of units, organized in a rectangular lattice, def...
Article
Full-text available
In this work a method for building maps represent-ing topographic visualization of bacteria taxonomy is presented. The method uses ba