Carlos Rodríguez-Caso

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BACKGROUND Two genes are called synthetic lethal (SL) if mutation of either alone is not lethal, but mutation of both leads to death or a significant decrease in organism's fitness. The detection of SL gene pairs constitutes a promising alternative for anti-cancer therapy. As cancer cells exhibit a large number of mutations, the identification of these(More)
Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and their target genes. The large size of these webs and their entangled nature make it difficult to achieve a global view of(More)
In this paper we explore the concept of hierarchy as a quantifiable descriptor of ordered structures, departing from the definition of three conditions to be satisfied for a hierarchical structure: order, predictability, and pyramidal structure. According to these principles, we define a hierarchical index taking concepts from graph and information theory.(More)
The search for a systems-level picture of metabolism as a web of molecular interactions provides a paradigmatic example of how the methods used to characterize a system can bias the interpretation of its functional meaning. Metabolic maps have been analyzed using novel techniques from network theory, revealing some non-trivial, functionally relevant(More)
Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses-the so-called transfer function-and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel(More)
The feed-forward relationship naturally observed in time-dependent processes and in a diverse number of real systems-such as some food webs and electronic and neural wiring-can be described in terms of the so-called directed acyclic graphs (DAGs). An important ingredient of the analysis of such networks is a proper comparison of their observed architecture(More)
Genomic instability is considered by many authors the key engine of tumorigenesis. However, mounting evidence indicates that a small population of drug resistant cancer cells can also be a key component of tumor progression. Such cancer stem cells would define a compartment effectively acting as the source of most tumor cells. Here we study the interplay(More)
H(3) autoreceptors provide feedback control of neurotransmitter synthesis in histaminergic neurons, but the transduction pathways involved are poorly understood. In rat brain cortical slices, histamine synthesis can be stimulated by depolarization and inhibited by H(3) agonists. We show that histamine synthesis stimulation by depolarization with 30 mM K(+)(More)
In this paper we present a Semantic Web application (http://, which is based on a Semantic Web infrastructure (NEMESIS). This application is a Semantic Web graphical tool used for analyzing transcription factor databases. NEMESIS not only solves several problems of the Semantic Web but is also a generic infrastructure for the(More)
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