Marcelo Bento Soares

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MOTIVATION High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated(More)
This paper describes the UIcluster software tool, which partitions expressed sequence tag (EST) sequences and other genetic sequences into " clusters " based on sequence similarity. Ideally, each cluster will contain sequences that all represent the same gene. UIcluster has been developed over the course of 4 years to solve this problem efficiently and(More)
From early in limb development the transcription factor Gli3 acts to define boundaries of gene expression along the anterior-posterior (AP) axis, establishing asymmetric patterns required to provide positional information. As limb development proceeds, posterior mesenchyme expression of Sonic hedgehog (Shh) regulates Gli3 transcription and(More)
Microarray technology allows the monitoring of expression levels of thousands of genes simultaneously. A semiparametric location and scale model is proposed to model gene expression levels for normalization and significance analysis purposes. Robust estimation based on weighted least absolute deviation regression and significance analysis based on the(More)
Microarray analysis is a technology for monitoring gene expression levels on a large scale and has been widely used in functional genomics. A challenging issue in the analysis of microarray data is normalization. A proper normalization procedure ensures that the intensity ratios provide meaningful measures of relative expression levels. There are two(More)
We propose an innovative, integrated, cost-effective health system to combat major non-communicable diseases (NCDs), including cardiovascular, chronic respiratory, metabolic, rheumatologic and neurologic disorders and cancers, which together are the predominant health problem of the 21st century. This proposed holistic strategy involves comprehensive(More)
BACKGROUND Between embryonic day 12 and postnatal day 21, six major neuronal and one glia cell type are generated from multipotential progenitors in a characteristic sequence during mouse retina development. We investigated expression patterns of retina transcripts during the major embryonic and postnatal developmental stages to provide a systematic view of(More)
MOTIVATION In gene discovery projects based on EST sequencing, effective post-sequencing identification methods are important in determining tissue sources of ESTs within pooled cDNA libraries. In the past, such identification efforts have been characterized by higher than necessary failure rates due to the presence of errors within the subsequence(More)
BACKGROUND Normalization is a basic step in microarray data analysis. A proper normalization procedure ensures that the intensity ratios provide meaningful measures of relative expression values. METHODS We propose a robust semiparametric method in a two-way semi-linear model (TW-SLM) for normalization of cDNA microarray data. This method does not make(More)
The identification of molecular signatures predictive of clinical behavior and outcome in brain tumors has been the focus of many studies in the recent years. Despite the wealth of data that are available in the public domain on alterations in the genome, epigenome and transcriptome of brain tumors, the underlying molecular mechanisms leading to tumor(More)