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Biomedical subjects

Oswaldo Trelles

Publications and source records attributed to Oswaldo Trelles.

7 recordsLinked to original sources
PubMed2006

A new user-friendly software platform for systematic classification of skin lesions to aid in their diagnosis and prognosis.

BACKGROUND AND AIMS: The field of much less invasive nonablative aesthetic surgery continues to grow, but consistent and truly objective evaluation of the sometimes comparatively small improvements in the treated skin remains a problem for both clinicians and patients. In this work, we present the development of a generic, modular and expandable platform to allow user-friendly image manipulation, sampling extraction and computer-assisted evaluation of tissue features in the dermatological/aesthetic field of clinical medicine. MATERIALS AND METHODS: The unique characteristic of the platform is the modular extension of the algorithm gallery by the use of extended value added services, which enables the easy incorporation of new image processing procedures to customise the gallery for specific concerns. A novel algorithm to evaluate skin wrinkles is also presented as a demonstration of this integration process. The software platform is designed to evaluate image-tissue indices and to identify individual or combined descriptors which will more accurately represent differences in skin quality. It is based on a set of indices correlating clinical expert and computer classifications, which build up a constantly expanding tissue catalogue. By means of this catalogue, the different tissue qualities of photographic samples can be assessed according to the different positions of the samples in the catalogue. CONCLUSIONS: This new platform can be used to generate sensitive and objective comparative measurement not only for diagnostic reports on the pre-treatment condition of samples but also for demonstrating the improvement and efficacy of the prescribed treatment to both the clinician and colleagues and the patient, thereby helping to increase the patient satisfaction index.

Algorithms↗
PubMed2006

Integrated analysis of gene expression by Association Rules Discovery.

BACKGROUND: Microarray technology is generating huge amounts of data about the expression level of thousands of genes, or even whole genomes, across different experimental conditions. To extract biological knowledge, and to fully understand such datasets, it is essential to include external biological information about genes and gene products to the analysis of expression data. However, most of the current approaches to analyze microarray datasets are mainly focused on the analysis of experimental data, and external biological information is incorporated as a posterior process. RESULTS: In this study we present a method for the integrative analysis of microarray data based on the Association Rules Discovery data mining technique. The approach integrates gene annotations and expression data to discover intrinsic associations among both data sources based on co-occurrence patterns. We applied the proposed methodology to the analysis of gene expression datasets in which genes were annotated with metabolic pathways, transcriptional regulators and Gene Ontology categories. Automatically extracted associations revealed significant relationships among these gene attributes and expression patterns, where many of them are clearly supported by recently reported work. CONCLUSION: The integration of external biological information and gene expression data can provide insights about the biological processes associated to gene expression programs. In this paper we show that the proposed methodology is able to integrate multiple gene annotations and expression data in the same analytic framework and extract meaningful associations among heterogeneous sources of data. An implementation of the method is included in the Engene software package.

Algorithms↗
PubMed2005

Intelligent client for integrating bioinformatics services.

MOTIVATION: In addition to existing bioinformatics software, a lot of new tools are being developed world wide to supply services for an ever growing, widely dispersed and heterogeneous collection of biological data. The integration of these resources under a common platform is a challenging task. To this end, several groups are developing integration technologies, in which services are usually registered in some sort of catalogue to allow novel discovering and accessing mechanisms to be implemented. However, each service demands specific interfaces to accommodate their parameters and it is a complicated task linking the different service inputs and outputs to solve a biological problem. RESULTS: In this work we address the design and implementation of a versatile web client to access BioMOBY compatible services (a system by which a client can interact with multiple sources of biological data regardless of the underlying format or schema) using the service description stored in the BioMOBY catalogue. The automatic interface generator significantly reduces developing time and produces uniform service access mechanisms. The design and proof of concept (for such a client) including the generic interface generator have been developed and implemented in the National Institute for Bioinformatics in Spain. AVAILABILITY: The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ

Automation↗
PubMed2004

Saturation and quantization reduction in microarray experiments using two scans at different sensitivities.

We present a mathematical model to extend the dynamic range of gene expression data measured by laser scanners. The strategy is based on the rather simple but novel idea of producing two images with different scanner sensitivities, obtaining two different sets of expression values: the first is a low-sensitivity measure to obtain high expression values which would be saturated in a high-sensitivity measure; the second, by the converse strategy, obtains additional information about the low-expression levels. Two mathematical models based on linear and gamma curves are presented for relating the two measurements to each other and producing a coherent and extended range of values. The procedure minimizes the quantization relative error and avoids the collateral effects of saturation. Since most of the current scanner devices are able to adjust the saturation level, the strategy can be considered as a universal solution, and not dependent on the image processing software used for reading the DNA chip. Various tests have been performed, on both proprietary and public domain data sets, showing a reduction of the saturation and quantization effects, not achievable by other methods, with a more complete description of gene-expression data and with a reasonable computational complexity.

Journal Article↗
PubMed2003

PreP: gene expression data pre-processing.

UNLABELLED: PreP is a versatile, powerful, standalone application that aims at pre-processing gene expression data. AVAILABILITY: Documentation and executable file for MS-Windows are available at http://chirimoyo.ac.uma.es/bitlab/services/index.htm

Algorithms↗
PubMed2003

MicroPreP: a cDNA microarray data pre-processing framework.

The user-friendly MicroPreP framework was developed to transform raw intensity data from cDNA microarrays into high-quality data. The main features of this software are: LOWESS normalisation; merging of DNA microarray data from changing slide versions; outlier detection; and slide quality assessment.

Algorithms↗