Florentino Fdez-Riverola

Florentino Fdez-Riverola
University of Vigo | UVIGO · Department of Computer Sciences

PhD

About

428
Publications
39,802
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
5,129
Citations
Introduction
Professor Fdez-Riverola holds a Technical Engineering Degree in Computer Management by the University of Vigo, Spain (1994) and a Engineering Degree in Computer Science by the University of Oviedo, Spain (1999). Founding member (2001) and actual Coordinator of the SING research group (http://sing-group.org), he obtained his Ph.D. in Computer Science by the University of Vigo (2002), being honoured with the Extraordinary Doctoral Thesis prize.

Publications

Publications (428)
Article
Full-text available
This work presents an exploratory study that retrieves, processes, and analyses Twitter data to gain insights about the relevance and perceptions of the wine industry in the Douro Portuguese region (including Porto and Douro wines), as well as other regions in the country. The main techniques and algorithms used in our work belong to the families o...
Article
Sepsis is a major public health problem and a leading cause of death in the world, where delay in the beginning of treatment, along with clinical guidelines non-adherence have been proved to be associated with higher mortality. Machine Learning is increasingly being adopted in developing innovative Clinical Decision Support Systems in many areas of...
Article
Discover relevant biomedical interactions in the literature is crucial for enhancing biology research. This curation process has an essential role in studying the different processes and interactions reported that affect the biological process (e.g., genome, metabolome, and transcriptome). In this sense, the objective of this work is twofold: reduc...
Book
This book features novel research papers spanning many different subfields in bioinformatics and computational biology, presenting the latest research on the practical applications to promote fruitful interactions between young researchers in different areas related to the field. Clearly, biology is increasingly becoming a science of information, r...
Article
Full-text available
Convolutional neural networks have pushed forward image analysis research and computer vision over the last decade, constituting a state-of-the-art approach in object detection today. The design of increasingly deeper and wider architectures has made it possible to achieve unprecedented levels of detection accuracy, albeit at the cost of both a dra...
Article
The increasing number of scientific research documents published keeps growing at an unprecedented rate, making it increasingly difficult to access practical information within a target domain. This situation is motivating a growing interest in applying text mining techniques for the automatic processing of text resources to structure the informati...
Article
Full-text available
Ambient Intelligence (AmI) encompasses technological infrastructures capable of sensing data from environments and extracting high-level knowledge to detect or recognize users’ features and actions, as well as entities or events in their surroundings. Visual perception, particularly object detection, has become one of the most relevant enabling fac...
Article
Full-text available
Colorectal cancer is a major health problem, where advances towards computer-aided diagnosis (CAD) systems to assist the endoscopist can be a promising path to improvement. Here, a deep learning model for real-time polyp detection based on a pre-trained YOLOv3 (You Only Look Once) architecture and complemented with a post-processing step based on a...
Article
Big data importance and potential are becoming more and more relevant nowadays, enhanced by the explosive growth of information volume that is being generated on the Internet in the last years. In this sense, many experts agree that social media networks are one of the internet areas with higher growth in recent years and one of the fields that are...
Article
Full-text available
In recent years, natural thermal mineral waters have been gaining the special attention of the scientific community, namely in the prevention and treatment of some diseases, due to the microbial properties that exist in these habitats. The aim of this work was to characterize the physicochemical composition and the microbial taxonomic communities p...
Article
The identification of clinically relevant bacterial amino acid changes can be performed using different methods aimed at the identification of genes showing positively selected amino acid sites (PSS). Nevertheless, such analyses are time consuming, and the frequency of genes showing evidence for PSS can be low. Therefore, the development of a pipel...
Chapter
Social Media have changed the conditions and rules of Social Networking (SNet) where it comes from people intermingling with each other, i.e., SNet is to be understood as a process that works on the principle of many-to-many; any individual can create and share content. It is intended to explore explore the complex dynamics between SNet, Logic Prog...
Chapter
The identification in bacteria, of the set of genes and amino acid positions showing evidence for positive selection, can give insight, among others, on which genes and amino acid positions are responsible for modulating the host immune response. However, such analyses are time consuming, and the frequency of genes showing evidence for positively s...
Chapter
Concerning the field of Health Sciences, one of the trends with the greatest impact today is related to the feeding and consumption of foods intended for chronic patients with a nutritional association. According to this, the gluten-free diet is one of the diets with a today’s fastest-growing due to their health therapy associations for different d...
Chapter
In this work, different social data mining approaches are used to characterize the user churning and social traits of the Bioinformatics community over the first ten years of Stack Overflow. The proposed workflow consists of a four-step procedure that allows the characterization of users based on the social exchange exhibited by the Bioinformatics...
Book
This book highlights the latest research on practical applications of computational biology and bioinformatics, and addresses emerging experimental and sequencing techniques that are posing new challenges for bioinformatics and computational biology. Successfully applying these techniques calls for new algorithms and approaches from fields such as...
Article
SEDA (SEquence DAtaset builder) is a multiplatform desktop application for the manipulation of FASTA files containing DNA or protein sequences. The convenient graphical user interface gives access to a collection of simple (filtering, sorting, or file reformatting, among others) and advanced (BLAST searching, protein domain annotation, gene annotat...
Article
Full-text available
A better understanding of the response against Tuberculosis (TB) infection is required to accurately identify the individuals with an active or a latent TB infection (LTBI) and also those LTBI patients at higher risk of developing active TB. In this work, we have used the information obtained from studying the gene expression profile of active TB p...
Article
Full-text available
This work supports the massive presence of potential immunomodulatory peptides in the human gut metaproteome. These peptides were identified through the MAHMI database as potentially anti-inflammatory, and sixteen of them synthesized for characterize their mechanism of action. From them, peptide HM14 was encrypted in an extracellular protein produc...
Article
Full-text available
Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and...
Article
Full-text available
Deep Learning (DL) has attracted a lot of attention in the field of medical image analysis because of its higher performance in image classification when compared to previous state-of-the-art techniques. In addition, a recent meta-analysis found that the diagnostic performance of DL models is equivalent to that of health-care professionals. In this...
Article
This work introduces HaemoKBS, a novel Haemovigilance decision support system for adverse reactions in blood recipients. Machine learning inference and rule-based reasoning were applied to build the underlying decision support models, namely to automatically extract evidence from different types of data included in hospital notifications and incorp...
Article
Sepsis is a major public health problem and a leading cause of death in the world, where delay in the beginning of treatment, along with clinical guidelines non-adherence have been proved to be associated with higher mortality. Machine Learning is increasingly being adopted in developing innovative Clinical Decision Support Systems in many areas of...
Article
The human body immune system, metabolism and homeostasis are affected by microbes. Dysbiosis occurs when the homeostatic equilibrium is disrupted due to an alteration in the normal microbiota of the intestine. Dysbiosis can cause cancer, and also affect a patient’s ability to respond to treatment. Metataxonomics seeks to identify the bacteria prese...
Article
In recent years, the number of active users in social media has grown exponentially. Despite the thematic diversity of the messages, social media have become an important vehicle to disseminate health information as well as to gather insights about patients’ experiences and emotional intelligence. Therefore, the present work proposes a new methodol...
Article
Glycoside hydrolases are responsible for the enzymatic deconstruction of complex carbohydrates. This work introduces a new method to predict glycolytic abilities in sequenced genomes and thus, gain a better understanding of how to target specific carbohydrates and identify potentially interesting sources of specialised enzymes. Sequence alignment e...
Chapter
A large amount of viral nucleotide sequences is available in databases that can be used to identify positively selected amino acid sites, and thus make inferences on which sites are important for immune system escape and adaptation to their host. Nevertheless, the software pipelines needed to analyse such large datasets usually imply long running t...
Chapter
Microbes are found all over the human body and they have a direct impact on the immune system, metabolism and homeostasis. The homeostatic balance of the intestinal microflora can be broken under certain conditions, a situation known as dysbiosis, which can lead to disease, including certain types of cancer, or even affect a patient response to a t...
Article
Full-text available
Background: L-ascorbate (Vitamin C) is an important antioxidant and co-factor in eukaryotic cells, and in mammals it is indispensable for brain development and cognitive function. Vertebrates usually become L-ascorbate auxothrophs when the last enzyme of the synthetic pathway, an L-gulonolactone oxidase (GULO), is lost. Since Protostomes were unti...
Article
Today, Social Media is a key information source for a wide range of domains as a means to gain a better understanding of information flows and user communities. This work introduces a methodology combining machine learning and graph mining approaches to address relevant aspects of quality of service and user intrinsic motivation from the user’s per...
Article
Full-text available
Lactobacillus genus includes both probiotic and representative strains of the human gut microbiota. Independent studies have reported on the anti-inflammatory properties of different Lactobacillus strains, although we are far from understanding the underlying molecular interplay. In this work we show that a daily administration of Lactobacillus aci...
Article
Full-text available
Background: Wild-type (wt) polyglutamine (polyQ) regions are implicated in stabilization of protein-protein interactions (PPI). Pathological polyQ expansion, such as that in human Ataxin-1 (ATXN1), that causes spinocerebellar ataxia type 1 (SCA1), results in abnormal PPI. For ATXN1 a larger number of interactors has been reported for the expanded...
Article
Full-text available
Hospital-acquired Infections (HAIs) surveillance, defined as the systematic collection of data related to a certain health event, is considered an essential dimension for a prevention HAI program to be effective. In recent years, new automated HAI surveillance methods have emerged with the wide adoption of electronic health records (EHR). Here we p...
Article
Full-text available
Non-self gametophytic self-incompatibility (GSI) recognition system is characterized by the presence of multiple F-box genes tandemly located in the S-locus, that regulate pollen specificity. This reproductive barrier is present in Solanaceae, Plantaginacea and Maleae (Rosaceae), but only in Petunia functional assays have been performed to get insi...
Book
Next-generation sequencing technologies, together with other emerging and quite diverse experimental techniques, are evolving rapidly, creating numerous types of omics data. These are creating new challenges for the expanding fields of bioinformatics and computational biology, which seek to analyze, process, integrate, and extract meaningful knowle...
Article
Full-text available
Background: Shared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such tasks relied on the comparison of automatically generated results against a so-called Gold Standard dataset of manually labelled t...
Article
Internet, in general, and the WWW, in particular, have become an immediate, practical means of introducing software tools and resources, and most importantly, a key vehicle to attract the attention of the potential users. In this scenario, content organization as well as different development practices may affect the online visibility of the target...
Article
This work reports on a large-scale potential neuropeptide activity screening in human gut microbiomes deposited in public databases. In our experimental approach, the sequences of the bioactive peptides collected in the MAHMI database, mainly predicted as immunomodulatory or antitumoral, were crossed with those of the neuroactive/digestive peptides...
Article
Full-text available
This work presents a novel in silico approach to the prediction and characterization of the glycolytic capacities of the beneficial intestinal bacterium Faecalibacterium prausnitzii. Available F. prausnitzii genomes were explored taking the glycolytic capacities of F. prausnitzii SL3/3 and F. prausnitzii L2-6 as reference. The comparison of the gen...
Data
Extended analysis of the homology among F. prausntizii strains.
Data
List of SEED URLs shown for the gene neighbourhood.
Data
List of the amino acid sequences of the glycoside hydrolases in two fasta files fpa.fasta (corresponds to F. prausnitzii SL3/3) and fpr.fasta (corresponds to F. prausntizii L2-6).
Data
Graphic representation of the clusters and the Davis-Boulding index.
Data
Differents examples of gene neighbourhoods related to glycoside hydrolase activities en F. prausnitzii.
Article
Motivation: Single cells often show stochastic behaviour and variations in the physiological state of individual cells affect the behaviour observed in cell populations. This may be partially explained by variations in the concentration and spatial location of molecules within and in the vicinity of each cell. Methods: This paper introduces an a...
Article
Nowadays, bioinformatics is one of the most important areas in modern biology and the creation of high-quality scientific software supporting this recent research area is one of the core activities of many researchers. In this context, high-quality sequence datasets are needed to perform inferences on the evolution of species, genes, and gene famil...
Article
Protein–protein interaction (PPI) data is essential to elucidate the complex molecular relationships in living systems, and thus understand the biological functions at cellular and systems levels. The complete map of PPIs that can occur in a living organism is called the interactome. For animals, PPI data is stored in multiple databases (e.g., BioG...
Article
Advances in the field of genome sequencing have enabled a comprehensive analysis and annotation of the dynamics of the protein inventory of cells. This has been proven particularly rewarding for microbial cells, for which the majority of proteins are already accessible to analysis through automatic metagenome annotation. The large-scale in silico s...
Article
Background: Transcriptomics profiling aims to identify and quantify all transcripts present within a cell type or tissue at a particular state, and thus provide information on the genes expressed in specific experimental settings, differentiation or disease conditions. RNA-Seq technology is becoming the standard approach for such studies, but avai...
Chapter
Biological processes are mediated by protein-protein interactions (PPI) that have been studied using different methodologies, and organized as centralized repositories - PPI databases. The data stored in the different PPI databases only overlaps partially. Moreover, some of the repositories are dedicated to a species or subset of species, not all h...
Chapter
The large scale genome datasets that are now available can provide unprecedented insight into the evolution of genes and gene families. Nevertheless, handling and transforming such datasets into the desired format for downstream analyses is often a difficult and time-consuming task for researchers without a background in informatics. Here, we prese...
Article
Useful insight into the evolution of genes and gene families can be provided by the analysis of all available genome datasets rather than just a few, which are usually those of model species. Handling and transforming such datasets into the desired format for downstream analyses is, however, often a difficult and time-consuming task for researchers...
Article
Background: Many bioinformatics pipelines are available nowadays to analyze transcriptomics data produced by high-throughput RNA sequencing. They implement different workflows that address several analysis tasks, supported by the use of third party programs. Nevertheless, a proper workflow definition for RNA-seq data analysis is still lacking. Obje...
Preprint
BACKGROUND Nowadays, the use of social media is part of daily life, with more and more people, including governments and Health organisations, using at least one platform regularly. Social media create the opportunity to interact among large groups of people that share the same interests and suffer the same afflictions. In particular, these channel...
Article
Background: Nowadays, the use of social media is part of daily life, with more and more people, including governments and health organizations, using at least one platform regularly. Social media enables users to interact among large groups of people that share the same interests and suffer the same afflictions. Notably, these channels promote the...
Article
Full-text available
Background The wide range of potential applications has made the Basic Local Alignment Search Tool (BLAST) a ubiquitous tool in the field of Molecular Biology. Within this context, it is increasingly appealing to embed BLAST services within larger Web applications. Results This work introduces BlasterJS viewer, a new JavaScript library for the lig...
Data
Comparison of BlasterJS to other BLAST data viewers. Notes for selected categories: Interface: General impression of the interface style. Interactive GUI = GUI as in contemporary user-friendly applications such as MS Word. Tabular = output is presented mostly as tables, possible with some limited interaction (sorting by table columns). Integrated B...
Article
Full-text available
Modern bioinformatics and computational biology are fields of study driven by the availability of effective software required for conducting appropriate research tasks. Apart from providing reliable and fast implementations of different data analysis algorithms, these software applications should also be clear and easy to use through proper user in...
Data
Complete list of GC4S components by package and type. Packages and components are listed alphabetically. (DOCX)
Article
Full-text available
A novel ecosystem to promote the physical, emotional and psychic health and well-being of the elderly is presented. Our proposal was designed to add several services developed to meet the needs of the senior population, namely services to improve social inclusion and increase contribution to society. Moreover, the solution monitors the vital signs...
Article
Experimental incapacity to track microbe–microbe interactions in structures like biofilms, and the complexity inherent to the mathematical modelling of those interactions, raises the need for feasible, alternative modelling approaches. This work proposes an agent-based representation of the diffusion of N-acyl homoserine lactones (AHL) in a multice...
Article
Full-text available
This work provides an overview and appraisal of the general evolution of IS/IT in haemovigilance, from which lessons can be learned for its future strategic management. An electronic survey was conducted among the members of the International Haemovigilance Network to compile information on the mechanisms implemented to gather, process, validate, a...