Tomás Norambuena

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The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating organisms. To study the basic principles of bacterial proteome organization, we used tandem affinity purification-mass spectrometry (TAP-MS) in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble protein complexes, of which the(More)
As in many different areas of science and technology, most important problems in bioinformatics rely on the proper development and assessment of binary classifiers. A generalized assessment of the performance of binary classifiers is typically carried out through the analysis of their receiver operating characteristic (ROC) curves. The area under the ROC(More)
The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This(More)
Currently, about 20 crystal structures per day are released and deposited in the Protein Data Bank. A significant fraction of these structures is produced by research groups associated with the structural genomics consortium. The biological function of many of these proteins is generally unknown or not validated by experiment. Therefore, a growing need for(More)
MOTIVATION Over the recent years, the vision that RNA simply serves as information transfer molecule has dramatically changed. The study of the sequence/structure/function relationships in RNA is becoming more important. As a direct consequence, the total number of experimentally solved RNA structures has dramatically increased and new computer tools for(More)
Transposable elements comprise a large proportion of animal genomes. Transposons can have detrimental effects on genome stability but also offer positive roles for genome evolution and gene expression regulation. Proper balance of the positive and deleterious effects of transposons is crucial for cell homeostasis and requires a mechanism that tightly(More)
An accurate and robust large-scale melting temperature prediction server for short DNA sequences is dispatched. The server calculates a consensus melting temperature value using the nearest-neighbor model based on three independent thermodynamic data tables. The consensus method gives an accurate prediction of melting temperature, as it has been recently(More)
SUMMARY The understanding of the biological role of RNA molecules has changed. Although it is widely accepted that RNAs play important regulatory roles without necessarily coding for proteins, the functions of many of these non-coding RNAs are unknown. Thus, determining or modeling the 3D structure of RNA molecules as well as assessing their accuracy and(More)
We describe a web server for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE). The core of the server relies on a database of genomic virtual tags built by a recently described method that attempts to reduce the amount of ambiguous assignments for those tags that are not unique in the genome. The method provides a(More)
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