S. D. de Souza

Publications107
h-index33
Citations4,116
Highly Influential Citations133
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An anatomy of normal and malignant gene expression
A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP)… Expand
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Shotgun sequencing of the human transcriptome with ORF expressed sequence tags.
TLDR
Theoretical considerations predict that amplification of expressed gene transcripts by reverse transcription-PCR using arbitrarily chosen primers will result in the preferential amplification of the central portion of the transcript. Expand
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Detection and evaluation of intron retention events in the human transcriptome.
Alternative splicing is a very frequent phenomenon in the human transcriptome. There are four major types of alternative splicing: exon skipping, alternative 3' splice site, alternative 5' splice… Expand
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Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins.
We present evidence that a well defined subset of intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to… Expand
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Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this… Expand
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Origin of genes.
We discuss two tests of the hypothesis that the first genes were assembled from exons. The hypothesis of exon shuffling in the progenote predicts that intron phases will be correlated so that exons… Expand
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Sequence features responsible for intron retention in human
BackgroundOne of the least common types of alternative splicing is the complete retention of an intron in a mature transcript. Intron retention (IR) is believed to be the result of intron, rather… Expand
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Evolution of the intron-exon structure of eukaryotic genes.
The origin and evolution of intron-exon structures continue to be controversial topics. Two alternative theories, the 'exon theory of genes' and the 'insertional theory of introns', debate the… Expand
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Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor.
Since most of the examples of "exon shuffling" are between vertebrate genes, the view is often expressed that exon shuffling is limited to the evolutionarily recent lineage of vertebrates. Although… Expand
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Sense-antisense pairs in mammals: functional and evolutionary considerations
BackgroundA significant number of genes in mammalian genomes are being found to have natural antisense transcripts (NATs). These sense-antisense (S-AS) pairs are believed to be involved in several… Expand
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