Víctor Maojo

Universidad Politécnica de Madrid | UPM · Biomedical Informatics Group

Background and objective: Nanoparticles present properties that can be applied to a wide range of fields such as biomedicine, electronics or optics. The type of properties depends on several characteristics, being some of them related with the particle structure. A proper characterization of nanoparticles is crucial since it could affect their app...

Drug discovery aims at finding new compounds with specific chemical properties for the treatment of diseases. In the last years, the approach used in this search presents an important component in computer science with the skyrocketing of machine learning techniques due to its democratization. With the objectives set by the Precision Medicine initi...

The integration of genetic information in current clinical routine has raised a need for tools to exploit family genetic knowledge. On the clinical side, an application for managing and visualizing pedigree diagrams could provide genetics specialists with an integrated environment with potential positive impact on their current practice. This artic...

This study presents the impact of carbon nanotubes (CNTs) on mitochondrial oxygen mass flux (Jm) under three experimental conditions. New experimental results and a new methodology are reported for the first time and they are based on CNT Raman spectra star graph transform (spectral moments) and perturbation theory. The experimental measures of Jm...

Introduction: The introduction of omics data and advances in technologies involved in clinical treatment has led to a broad range of approaches to represent clinical information. Within this context, patient stratification across health institutions due to omic profiling presents a complex scenario to carry out multi-center clinical trials. Metho...

Background: Medical informatics, or biomedical and health informatics (BMHI), has become an established scientific discipline. In all such disciplines there is a certain inertia to persist in focusing on well-established research areas and to hold on to well-known research methodologies rather than adopting new ones, which may be more appropriate....

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "The New Role of Biomedical Informatics in the Age of Digital Medicine" written by Fernando J. Martin-Sanchez and Guillermo H. Lopez-Campos [1]. It is introduced by an editorial. This article contains the combined commentaries invited to independe...

Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements—e.g. genes, compounds, pathways—that lead to interesting correlations. Normally, they must refer to additional public databases in order to enrich the...

Background: Clinical Trials (CTs) are essential for bridging the gap between experimental research on new drugs and their clinical application. Just like CTs for traditional drugs and biologics have helped accelerate the translation of biomedical findings into medical practice, CTs for nanodrugs and nanodevices could advance novel nanomaterials as...

Recent commentaries have proposed the advantages of using open exchange of data and informatics resources for improving health-related policies and patient care in Africa. Yet, in many African regions, both private medical and public health information systems are still unaffordable. Open exchange over the social Web 2.0 could encourage more altrui...

Unlabelled: The shape of nanoparticles and nanomaterials is a fundamental characteristic that has been shown to influence a number of their properties and effects, particularly for nanomedical applications. The information related with this feature of nanoparticles and nanomaterials is, therefore, crucial to exploit and foster in existing and futu...

Health care and information technology in health care is advancing at tremendous speed. We analysed whether the prognoses by Haux et al. - first presented in 2000 and published in 2002 [1] - have been fulfilled in 2013 and which might be the reasons for match or mismatch. Twenty international experts in biomedical and health informatics met in May...

More than 10 years ago Haux et al. tried to answer the question how health care provision will look like in the year 2013. A follow-up workshop was held in Braunschweig, Germany, for 2 days in May, 2013, with 20 invited international experts in biomedical and health informatics. Among other things it had the objectives to discuss the suggested goal...

The Institute of Tropical Medicine in Antwerp hereby presents the results of two pilot distance learning training programmes, developed under the umbrella of the AFRICA BUILD project (FP7). The two courses focused on evidence-based medicine (EBM): with the aim of enhancing research and education, via novel approaches and to identify research needs...

Introduction: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". Background: The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While sev...

AFRICA BUILD is a Coordination Action to support the development of centers of excellence in health care, education and health research in African countries, thanks to Information Technology. This project, developed under the 7th European Framework Programme, consists of seven Work Packages (WPs). The Institute of Tropical Medicine in Antwerp is in...

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al....

Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and s...

Current research in oncology, require the involvement of several institutions participating in clinical trials. Heterogeneities of data formats and models require advanced methods to achieve semantic interoperability and provide sustainable solutions. In this field, the EU funded INTEGRATE project aims to develop the basic knowledge to allow data s...

RDF has established in the last years as the language for describing, publishing and sharing biomedical resources. Following this trend, a great amount of RDF-based data sources, as well as ontologies, have appeared. Using a common language as RDF has provided a unified syntactic for sharing resources, but the semantics remain as the main cause of...

Breast cancer clinical trial researchers have to handle heterogeneous data coming from different data sources, overloading biomedical researchers when they need to query data for retrospective analysis. This paper presents the Common Data Model (CDM) proposed within the INTEGRATE EU project to homogenize data coming from different clinical partners...

Current post-genomic clinical trials in cancer involve the collaboration of several institutions. Multi-centric retrospective analysis requires advanced methods to ensure semantic interoperability. In this scenario, the objective of the EU funded INTEGRATE project, is to provide an infrastructure to share knowledge and data in post-genomic breast c...

Traditionally, participation of African researchers in top Biomedical Informatics (BMI) scientific journals and conferences has been scarce. Looking beyond these numbers, an educational goal should be to improve overall research and, therefore, to increase the number of scientists/authors able to produce and publish high quality research. In such s...

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-...

"Once upon a time, several engineers, biologists and clinicians realized that a lot of information in biomedicine was partitioned into 'silos' that do not intercommunicate. These silos were a side effect of the existence of different disciplines required to, for example, develop new drugs. The engineers decided to dispose of the silos, and to put t...

Education and research are two fundamental pillars to ensure progress. Without an appropriate education, quality research is not feasible. In the case of developing countries, these issues become more challenging since literacy and access to information are still unsolved. In this regard, numerous initiatives around the world have been launched for...

This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to exe...

Friedman's article ‘What informatics is and isn't’,1 presents a necessary and timely analysis of the field of informatics. After defining some of its characteristics, training needs and also examples of what it isn't, the author re-introduces what he has called ‘the fundamental theorem of informatics’1—originally formulated for biomedical informati...

The Human Genome Project and the explosion of high-throughput data have transformed the areas of molecular and personalized medicine, which are producing a wide range of studies and experimental results and providing new insights for developing medical applications. Research in many interdisciplinary fields is resulting in data repositories and com...

Nanoinformatics is an emerging research field that uses informatics techniques to collect, process, store, and retrieve data, information, and knowledge on nanoparticles, nanomaterials, and nanodevices and their potential applications in health care. In this paper, we have focused on the solutions that nanoinformatics can provide to facilitate nano...

AFRICA BUILD is a Coordination Action to support the development of centers of excellence in health care, education and health research in African countries, thanks to Information Technology. This project, developed under the 7th European Framework Programme, consists of seven Work Packages (WPs). The Institute of Tropical Medicine in Antwerp is in...

The AFRICA BUILD project aims to develop and support health care, education and research centres in Africa through Information and Communication Technologies. One of the main outputs of the project is a collaborative platform which integrates a myriad of research and learning resources. This article presents the first prototype of this platform: th...

Information and Communication Technologies has led to a biomedical data explosion. A proportional growth has been produced regarding the amount of scientific literature, but information retrieval methods did not follow the same pattern. By using specialized clinical search engines such as PubMed, Medscape and Cochrane, biomedical publications has b...

Over the past years, the number of available informatics resources in medicine has grown exponentially. While specific inventories of such resources have already begun to be developed for Bioinformatics (BI), comparable inventories are as yet not available for the Medical Informatics (MI) field, so that locating and accessing them currently remains...

Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous informatio...

Low resources in many African locations do not allow many African scientists and physicians to access the latest advances in technology. This deficiency hinders the daily life of African professionals that often cannot afford, for instance, the cost of internet fees or software licenses. The AFRICA BUILD project, funded by the European Commission a...

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also off...

Over the last few decades, the ever-increasing output of scientific publications has led to new challenges to keep up to date with the literature. In the biomedical area, this growth has introduced new requirements for professionals, e.g., physicians, who have to locate the exact papers that they need for their clinical and research work amongst a...

Biomedical Informatics (BMI) is a broad discipline, having evolved from both Medical Informatics (MI) and Bioinformatics (BI). An analysis of publications in the fieldshould provide an indication about the geographic distribution of BMI research contributions and possible lessons for the future, both for research and professional practice. In part...

In the past decade, Medical Informatics (MI) and Bioinformatics (BI) have converged towards a new discipline, called Biomedical Informatics (BMI) bridging informatics methods across the spectrum from genomic research to personalized medicine and global healthcare. This convergence still raises challenging research questions which are being addresse...

Biomedical informatics is a broad discipline that borrows many methods and techniques from other disciplines. To reflect a) on the character of biomedical informatics and to determine whether it is multi-disciplinary or inter-disciplinary; b) on the question whether biomedical informatics is more than the sum of its supporting disciplines and c) on...

In this chapter we introduce a new informatics field called “Nanoinformatics” based on our own research and on consensus work carried out under the auspices of the US National Cancer Institute (NCI) and the European Commission (EC). Nanoinformatics can be defined as the “use of informatics techniques for analyzing and processing information about t...

Biomedical ontologies have been very successful in structuring knowledge for many different applications, receiving widespread praise for their utility and potential. Yet, the role of computational ontologies in scientific research, as opposed to knowledge management applications, has not been extensively discussed. We aim to stimulate further disc...

Managing large medical image collections is an increasingly demanding important issue in many hospitals and other medical settings. A huge amount of this information is daily generated, which requires robust and agile systems. In this paper we present a distributed multi-agent system capable of managing very large medical image datasets. In this ap...

Specialized search engines such as PubMed, MedScape or Cochrane have increased dramatically the visibility of biomedical scientific results. These web-based tools allow physicians to access scientific papers instantly. However, this decisive improvement had not a proportional impact in clinical practice due to the lack of advanced search methods. E...

The post-genomic era, beginning at the end of the Human Genome Project, has led to new needs and challenges in the management of clinical and -omics data. One of the main issues in this new context for biomedical data management is the integration of heterogeneous sources, enabling access to different, remote biological data sources and the interpr...

PubDNA Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features (i) searching...

PubDNA Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features (i) searching...

Nanomedicine and nanoinformatics are novel disciplines facing substantial challenges. Since nanomedicine involves complex and massive data analysis and management, a new discipline named nanoinformatics is now emerging to provide the vision and the informatics methods and tools needed for such purposes. Methods from biomedi-cal informatics may prov...

The goal of image segmentation is to partition an input image into a set of regions. In mathematical morphology, the reconstruction of images from markers has proven to be useful in morphological filtering and image segmentation. The utilization of a criterion in the problem of the image reconstruction from an image marker has been partially treate...

Dictionary of problem English words. list of English dictionary words belonging to ∑+ used by the expert system for sequence refinement.

List of problem affixes. list of problem affixes used by the expert system for sequence refinement.

Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is beco...

In this paper we present a knowledge engineering approach to automatically recognize and extract genetic sequences from scientific articles. To carry out this task, we use a preliminary recognizer based on a finite state machine to extract all candidate DNA/RNA sequences. The latter are then fed into a knowledge-based system that automatically disc...

The development of high-throughput techniques for analyzing cell components has provided vast amounts of data in recent years. This development of gene-sequencing methods was followed by advances in techniques for analyzing and managing data from transcriptomes, proteomes, and other omics data. The so-called omics revolution has led to the developm...

Managing large image collections has become an important issue for information companies and institutions. We present a cloud computing service and its application for the storage and analysis of very-large images. This service has been implemented using multiple distributed and collaborative agents. For image storage and analysis, a regionoriented...

Five decades of research and practical application of computers in biomedicine has given rise to the discipline of medical informatics, which has made many advances in genomic and translational medicine possible. Developments in nanotechnology are opening up the prospects for nanomedicine and regenerative medicine where informatics and DNA computin...

Bringing together structured and text-based sources is an exciting challenge for biomedical informaticians, since most relevant biomedical sources belong to one of these categories. In this paper we evaluate the feasibility of integrating relational and text-based biomedical sources using: i) an original logical schema acquisition method for textua...

PubMed identifiers list. This file contains the list of the 392 PubMed identifiers selected to create the test set.

The rapid evolution of Internet technologies and the collaborative approaches that dominate the field have stimulated the development of numerous bioinformatics resources. To address this new framework, several initiatives have tried to organize these services and resources. In this paper, we present the BioInformatics Resource Inventory (BIRI), a...

To analyze the role that biomedical informatics could play in the application of the NBIC Converging Technologies in the medical field and raise awareness of these new areas throughout the Biomedical Informatics community. Review of the literature and analysis of the reference documents in this domain from the biomedical informatics perspective. De...

Over the last years, collaborative research has been continuously growing in many scientific areas such as biomedicine. However, traditional Knowledge Discovery in Databases (KDD) processes generally adopt centralized approaches that do not fully address many research needs in these distributed environments. This paper presents a method to improve...

Nanomedicine and nanoinformatics are emerging disciplines with substantial challenges ahead. For instance, nanomedicine involves complex and massive data analysis. Nanoinformatics could expand previous experiences in Biomedical Informatics with new features required to study different scientific biological and physical characteristics at a differen...

Over the last decades Nanotechnology has promised to advance science and technology in many areas. Within medicine, Nanomedicine promises to deliver new methods for diagnosis, prognosis and therapy. As the amount of available information is rapidly growing, new Biomedical Informatics approaches have to be developed to satisfy the increasing demand...

Having all been involved in proposal evaluation, we believe the studies indicate that a text matching analysis of research proposals could reduce plagiarism in subsequent publications. For instance, when European Commission evaluators have met in the past to evaluate research proposals, they received printed copies which had to be returned before t...

This paper studies connectivity aspects that arise in image operators that process connected components. The focus is on morphological image analysis (i.e., on increasing image operators) and, in particular, on a robustness property satisfied by certain morphological filters that is denominated the strong property. The behavior of alternated compos...

Nanomedicine is an emerging discipline aimed to applying recent developments in nanotechnology to the medical domain. In recent years, there has been an exponential growth of the number of available nanomedical resources. The latter are aimed to different tasks and include databases, nanosensors, implantable materials, etc. This leads to the necess...