15 results for "Roderic Guigó"
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Relaxation of Selective Constraints Causes Independent Selenoprotein Extinction in Insect Genomes
Background: Selenoproteins are a diverse family of proteins notable for the presence of the 21st amino acid, selenocysteine. Until very recently, all metazoan genomes investigated encoded selenoproteins, and these proteins had therefore been believed to be essential for animal life. Challenging…
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A General Definition and Nomenclature for Alternative Splicing Events
Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature…
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Computational identification of the selenocysteine tRNA (tRNA Sec ) in genomes
Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA…
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Overcoming the widespread flaws in the annotation of vertebrate selenoprotein genes in public databases
Genome annotations provide the essential framework for genomic analyses, capturing our current knowledge of gene structure and function as inferred from computational predictions and experimental evidence. Even as automated annotation pipelines become more sophisticated, their accuracy in…
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Transcription Factor Map Alignment of Promoter Regions
We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed genes do not show discernible sequence conservation. In our approach…
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ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization
We present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments, a feature unique to this software…
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PyHIST: A Histological Image Segmentation Tool
The development of increasingly sophisticated methods to acquire high-resolution images has led to the generation of large collections of biomedical imaging data, including images of tissues and organs. Many of the current machine learning methods that aim to extract biological knowledge from…
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Day-night and seasonal variation of human gene expression across tissues
Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate transcriptomic changes associated with those cycles across multiple tissues…
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Fast Computation and Applications of Genome Mappability
We present a fast mapping-based algorithm to compute the mappability of each region of a reference genome up to a specified number of mismatches. Knowing the mappability of a genome is crucial for the interpretation of massively parallel sequencing experiments. We investigate the properties of the…
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bsAS , an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage
Natural Antisense Transcripts (NATs) are long non-coding RNAs (lncRNAs) that overlap coding genes in the opposite strand. NATs roles have been related to gene regulation through different mechanisms, including post-transcriptional RNA processing. With the aim to identify NATs with potential…
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Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells
The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using…
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The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We…
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Interplay between BRCA1 and RHAMM Regulates Epithelial Apicobasal Polarization and May Influence Risk of Breast Cancer
Genetic analysis identifies the HMMR gene as a modifier of the breast cancer risk associated with BRCA1 gene mutation, while cell biological analysis of the protein product suggests a function in regulating development of the mammary gland. Differentiated mammary epithelium shows apicobasal…