57 hasil untuk "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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Correction: Relaxation of Selective Constraints Causes Independent Selenoprotein Extinction in Insect Genomes.
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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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Ten Simple Rules on How to Organize a Scientific Retreat.
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Computational identification of the selenocysteine tRNA (tRNASec) 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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The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues
Abstract Background Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few…
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A fast non-parametric test of association for multiple traits
Abstract The increasing availability of multidimensional phenotypic data in large cohorts of genotyped individuals requires efficient methods to identify genetic effects on multiple traits. Permutational multivariate analysis of variance (PERMANOVA) offers a powerful non-parametric approach…
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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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Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome
The profiling of genetic variants affecting splicing can give insight into disease mechanisms. Here, the authors develop a pipeline for discovery of variants affecting splicing (sQTLs) and with application to the GTEx dataset they generate a catalog of human sQTLs.