- http://vis.usal.es/rodrigo
Rodrigo Santamaria
University of Salamanca, Computer Science and Automation, Faculty Member
- I received the M.S. degree in Computer Science from the University of Salamanca, Spain. In 2009, I received my PhD de... moreI received the M.S. degree in Computer Science from the University of Salamanca, Spain.
In 2009, I received my PhD degree in Computer Science with my work on biclustering analysis of gene expression data and its visualization.
Nowadays, my research interests are bioinformatics, data mining, information visualization and visual analytics.edit
Research Interests:
Research Interests:
Motivation: Systems biology demands the use of several point of views to get a more comprehensive understanding of biological problems. This usually leads to take into account different data regarding the problem at hand, but it also has... more
Motivation: Systems biology demands the use of several point of views to get a more comprehensive understanding of biological problems. This usually leads to take into account different data regarding the problem at hand, but it also has to do with using different perspectives of the same data. This multifaceted aspect of systems biology often requires the use of several tools, and it is often hard to get a seamless integration of all of them, which would help the analyst to have an interactive discourse with the data. Results: Focusing on expression profiling, BicOverlapper 2.0 visualizes the most relevant aspects of the analysis, including expression data, profiling analysis results and functional annotation. It also integrates several state-of-the-art numerical methods, such as differential expression analysis, gene set enrichment or biclustering. Availability and implementation: BicOverlapper 2.0 is available at:
Research Interests:
Autophagy is a key degradative pathway coordinated by external cues, including starvation, oxidative stress, or pathogen detection. Rare are the molecules known to contribute mechanistically to the regulation of autophagy and expressed... more
Autophagy is a key degradative pathway coordinated by external cues, including starvation, oxidative stress, or pathogen detection. Rare are the molecules known to contribute mechanistically to the regulation of autophagy and expressed speci cally in particular environmental contexts or in distinct cell types. Here, we unravel the role of RUN and FYVE domain–containing protein 4 (RUFY4) as a positive molecular regulator of macroautophagy in primary dendritic cells (DCs). We show that exposure to interleukin-4 (IL-4) during DC differentiation enhances autophagy ux through mTORC1 regulation and RUFY4 induction, which in turn actively promote LC3 degradation, Syntaxin 17– positive autophagosome formation, and lysosome tethering. Enhanced autophagy boosts endogenous antigen pre- sentation by MHC II and allows host control of Brucella abortus replication in IL-4–treated DCs and in RUFY4-expressing cells. RUFY4 is therefore the rst molecule characterized to date that promotes autophagy and in uences endosome dynamics in a subset of immune cells.
Research Interests:
Abstract Motivation: Several techniques analyze gene expression data from the point of view of biological ontologies. These methods focus on statistical and numerical analyses, but there is an additional need for fast, global and... more
Abstract Motivation: Several techniques analyze gene expression data from the point of view of biological ontologies. These methods focus on statistical and numerical analyses, but there is an additional need for fast, global and interactive visualizations of gene expression data in the context of biological ontologies. Results: Voronto addresses these needs with an easy to use integration of custom gene expression data with custom or public ontologies.
Background Organisms use highly accurate molecular processes to transcribe their genes and a variety of mRNA quality control and ribosome proofreading mechanisms to maintain intact the fidelity of genetic information flow. Despite this,... more
Background Organisms use highly accurate molecular processes to transcribe their genes and a variety of mRNA quality control and ribosome proofreading mechanisms to maintain intact the fidelity of genetic information flow. Despite this, low level gene translational errors induced by mutations and environmental factors cause neurodegeneration and premature death in mice and mitochondrial disorders in humans.
Abstract. A gamma spectrometer with HPGe detector of 50% relative efficiency and 1 cps total background has been dedicated to the measurement of an intertidal sediment core from a coastal environment at the Ría de Vigo (Spain). The area... more
Abstract. A gamma spectrometer with HPGe detector of 50% relative efficiency and 1 cps total background has been dedicated to the measurement of an intertidal sediment core from a coastal environment at the Ría de Vigo (Spain). The area is affected by lead pollution and the source identification needs of a precise dating of the sediment core.
The Bicluster Overlapper has been tested for the platforms in Table 1.1. Developed in Java, it is expected to work under other Operating Systems that support the required JRE version and with enough disk and RAM, but we cannot assure it.... more
The Bicluster Overlapper has been tested for the platforms in Table 1.1. Developed in Java, it is expected to work under other Operating Systems that support the required JRE version and with enough disk and RAM, but we cannot assure it. For any problem, please contact us at rodri@ usal. es providing the details of your problem running BicOverlapper, along with your platform characteristics.
ABSTRACT The presented work aims to identify interesting relationships between persons involved in the movie world. The tool integrates different visualization techniques: parallel coordinates, scatterplots, treemaps, word clouds and... more
ABSTRACT The presented work aims to identify interesting relationships between persons involved in the movie world. The tool integrates different visualization techniques: parallel coordinates, scatterplots, treemaps, word clouds and graph networks, along with textual information and searchs. The visualizations are interconnected and allow overlapping through different data selections to quickly extract data analysis.
Introducción Son muchos los estudios ambientales que requieren de la medida de radionúclidos naturales como 210Pb, 226Ra, 228Th, 230Th, 232Th, 235U y 238U. Por formar parte del fondo natural, todos ellos contribuyen a la dosis a la que la... more
Introducción Son muchos los estudios ambientales que requieren de la medida de radionúclidos naturales como 210Pb, 226Ra, 228Th, 230Th, 232Th, 235U y 238U. Por formar parte del fondo natural, todos ellos contribuyen a la dosis a la que la población está expuesta1, por lo tanto, una alteración de las concentraciones en las que se encuentran en la naturaleza debe ser vigilada.
This version of BicOverlapper integrates biclustering analysis of microarrays and requests for gene information, by means of the statistical package R and Bio-Conductor. Therefore, in order to load and analyze gene expression matrices, R... more
This version of BicOverlapper integrates biclustering analysis of microarrays and requests for gene information, by means of the statistical package R and Bio-Conductor. Therefore, in order to load and analyze gene expression matrices, R 2.8 or higher must be installed, with the following requirements: