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Article
Open AccessData-driven recombination detection in viral genomes
Recombination is a key molecular mechanism for the evolution and adaptation of viruses. The first recombinant SARS-CoV-2 genomes were recognized in 2021; as of today, more than ninety SARS-CoV-2 lineages are d...
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Article
Open AccessPublisher Correction: Social and economic variables explain COVID-19 diffusion in European regions
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Article
Open AccessSocial and economic variables explain COVID-19 diffusion in European regions
At the beginning of 2020, Italy was the country with the highest number of COVID-19 cases, not only in Europe, but also in the rest of the world, and Lombardy was the most heavily hit region of Italy. The obje...
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Chapter and Conference Paper
Towards an Explorable Conceptual Map of Large Language Models
Large Language Models (LLMs) have revolutionized the current landscape of Natural Language Processing, enabling unprecedented advances in text generation, translation, summarization, and more. Currently, limit...
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Chapter and Conference Paper
Fine-Tuning Large Enterprise Language Models via Ontological Reasoning
Large Language Models (LLMs) exploit fine-tuning as a technique to adapt to diverse goals, thanks to task-specific training data. Task specificity should go hand in hand with domain orientation, that is, the s...
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Article
Open AccessCoV2K model, a comprehensive representation of SARS-CoV-2 knowledge and data interplay
Since the outbreak of the COVID-19 pandemic, many research organizations have studied the genome of the SARS-CoV-2 virus; a body of public resources have been published for monitoring its evolution. While we e...
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Chapter and Conference Paper
A Comprehensive Approach for the Conceptual Modeling of Genomic Data
The human genome is traditionally represented as a DNA sequence of three billion base pairs. However, its intricacies are captured by many more complex signals, representing DNA variations, the expression of g...
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Article
Open AccessSocioeconomic differences and persistent segregation of Italian territories during COVID-19 pandemic
Lockdowns implemented to address the COVID-19 pandemic have disrupted human mobility flows around the globe to an unprecedented extent and with economic consequences which are unevenly distributed across terri...
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Article
Open AccessData-driven analysis of amino acid change dynamics timely reveals SARS-CoV-2 variant emergence
Since its emergence in late 2019, the diffusion of SARS-CoV-2 is associated with the evolution of its viral genome. The co-occurrence of specific amino acid changes, collectively named ‘virus variant’, require...
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Article
Open AccessIdentifying collateral and synthetic lethal vulnerabilities within the DNA-damage response
A pair of genes is defined as synthetically lethal if defects on both cause the death of the cell but a defect in only one of the two is compatible with cell viability. Ideally, if A and B are two synthetic le...
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Article
Open AccessSystematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes
Chromatin compartmentalization reflects biological activity. However, inference of chromatin sub-compartments and compartment domains from chromosome conformation capture (Hi-C) experiments is limited by data ...
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Chapter and Conference Paper
CoV2K: A Knowledge Base of SARS-CoV-2 Variant Impacts
In spite of the current relevance of the topic, there is no universally recognized knowledge base about SARS-CoV-2 variants; viral sequences deposited at recognized repositories are still very few, and the pro...
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Chapter and Conference Paper
Show, Don’t Tell. Reflections on the Design of Multi-modal Conversational Interfaces
Conversational Agents are the future of Human-Computer Interaction. Technological advancements in Artificial Intelligence and Natural Language Processing allow the development of Conversational Agents that sup...
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Article
Open AccessA multi-layer approach to disinformation detection in US and Italian news spreading on Twitter
We tackle the problem of classifying news articles pertaining to disinformation vs mainstream news by solely inspecting their diffusion mechanisms on Twitter. This approach is inherently simple compared to existi...
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Article
Open AccessSearch and comparison of (epi)genomic feature patterns in multiple genome browser tracks
Genome browsers are widely used for locating interesting genomic regions, but their interactive use is obviously limited to inspecting short genomic portions. An ideal interaction is to provide patterns of reg...
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Article
Open AccessNAUTICA: classifying transcription factor interactions by positional and protein-protein interaction information
Inferring the mechanisms that drive transcriptional regulation is of great interest to biologists. Generally, methods that predict physical interactions between transcription factors (TFs) based on positional ...
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Article
Open AccessSpatial patterns of CTCF sites define the anatomy of TADs and their boundaries
Topologically associating domains (TADs) are genomic regions of self-interaction. Additionally, it is known that TAD boundaries are enriched in CTCF binding sites. In turn, CTCF sites are known to be asymmetri...
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Article
Open AccessTopology comparison of Twitter diffusion networks effectively reveals misleading information
In recent years, malicious information had an explosive growth in social media, with serious social and political backlashes. Recent important studies, featuring large-scale analyses, have produced deeper know...
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Chapter and Conference Paper
Designing and Evaluating Deep Learning Models for Cancer Detection on Gene Expression Data
Transcription profiling enables researchers to understand the activity of the genes in various experimental conditions; in human genomics, abnormal gene expression is typically correlated with clinical conditi...
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Chapter and Conference Paper
Empowering Virus Sequence Research Through Conceptual Modeling
The pandemic outbreak of the coronavirus disease has attracted attention towards the genetic mechanisms of viruses. We hereby present the Viral Conceptual Model (VCM), centered on the virus sequence and descri...
