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Chapter and Conference Paper
A Gene Ontology-Driven Wide and Deep Learning Architecture for Cell-Type Classification from Single-Cell RNA-seq Data
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 express...
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Chapter
Classification of Sequences with Deep Artificial Neural Networks: Representation and Architectural Issues
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 methodo...
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Article
Open AccessBITS2019: the sixteenth annual meeting of the Italian society of bioinformatics
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 commun...
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Article
Open AccessmiRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions
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 interac...
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Chapter and Conference Paper
Identification of Key miRNAs in Regulation of PPI Networks
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...
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Article
Open AccessMiRNA therapeutics based on logic circuits of biological pathways
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-...
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Article
Open AccessThe 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes
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”, bu...
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Article
Open AccessmiRTissue: a web application for the analysis of miRNA-target interactions in human tissues
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 provi...
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Article
Open AccessBioGraph: a web application and a graph database for querying and analyzing bioinformatics resources
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 ...
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Article
Open AccessDeep learning models for bacteria taxonomic classification of metagenomic data
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 ...
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Chapter and Conference Paper
Variable Ranking Feature Selection for the Identification of Nucleosome Related Sequences
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 com...
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Article
Open AccessnRC: non-coding RNA Classifier based on structural features
Non-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...
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Chapter and Conference Paper
Gremlin Language for Querying the BiographDB Integrated Biological Database
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 th...
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Chapter and Conference Paper
A Problem-Driven Approach for Building a Bioinformatics GraphDB
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 inter...
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Article
Open AccessMiRNATIP: a SOM-based miRNA-target interactions predictor
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 ...
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Chapter and Conference Paper
Integrated DB for Bioinformatics: A Case Study on Analysis of Functional Effect of MiRNA SNPs in Cancer
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 gen...
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Chapter and Conference Paper
A Deep Learning Approach to DNA Sequence Classification
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 seque...
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Article
Open AccessProbabilistic topic modeling for the analysis and classification of genomic sequences
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...
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Article
Open AccessAnalysis of miRNA expression profiles in breast cancer using biclustering
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...
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Chapter
DNA Barcode Classification Using General Regression Neural Network with Different Distance Models
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...
