Alfonso E. Romero

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The evolutionarily conserved mitogen-activated protein kinase (MAPK) signaling network comprises connected protein kinases arranged in MAPK modules. In this Opinion article, we analyze MAPK signaling components in evolutionarily representative species of the plant lineage and in Naegleria gruberi, a member of an early diverging eukaryotic clade. In(More)
A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for(More)
This paper describes our participation in the BioASQ semantic indexing challenge with two hierarchical text categorization systems. Both systems originated from previous research in thesaurus topic assignment applied on small domains from the legal document management field. One of the described systems employs a classical top-down approach based on a(More)
This paper exposes the results of our participation in the Document Mining track at INEX’07. We have focused on the task of classification of XML documents. Our approach to deal with structured document representations uses classification methods for plain text, applied to flattened versions of the documents, where some of their structural properties have(More)
We propose a method which, given a document to be classified, automatically generates an ordered set of appropriate descriptors extracted from a thesaurus. The method creates a Bayesian network to model the thesaurus and uses probabilistic inference to select the set of descriptors having high posterior probability of being relevant given the available(More)
In this paper we propose a new method for link-based classification using Bayesian networks. It can be used in combination with any content only probabilistic classsifier, so it can be useful in combination with several different classifiers. We also report the results obtained of its application to the XML Document Mining Track of INEX’08.
A new algorithm and Web server, mutation3D (, proposes driver genes in cancer by identifying clusters of amino acid substitutions within tertiary protein structures. We demonstrate the feasibility of using a 3D clustering approach to implicate proteins in cancer based on explorations of single proteins using the mutation3D Web(More)
We present a knowledge representation framework that allows an agent situated in an environment to recognise complex activities, reason about their progress and take action to avoid or support their successful completion. Activities are understood as parameterised templates whose parameters consist of a unique name labelling the activity to be recognised, a(More)
Diabetes is both heavily affected by the patients' lifestyle, and it affects their lifestyle. Most diabetic patients can manage the disease without technological assistance, so we should not burden them with technology unnecessarily, but lifestyle-monitoring technology can still be beneficial both for patients and their physicians. Because of that we(More)
In this paper, we propose the V-index (or, Virtuosity index) as a novel metric to assess the scientific virtuosity of academics. This index can be applied to researchers and journals as well. In particular, we show that the V-index fills the gap of h-index and similar metrics in considering the self-citations of authors or journals. The paper provides with(More)