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Article
Open AccessIdentification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities
The identification of ligand binding sites is a key task in the annotation of proteins with known structure but uncharacterized function. Here we describe a knowledge-based method exploiting the observation th...
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Article
Open AccessAlternative splicing tends to avoid partial removals of protein-protein interaction sites
Anecdotal evidence of the involvement of alternative splicing (AS) in the regulation of protein-protein interactions has been reported by several studies. AS events have been shown to significantly occur in re...
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Article
Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis
Global transcriptional and epigenomic analyses in diverse cell types reveal that the primary action of Myc is to up- and downregulate transcription of distinct groups of genes, rather than to amplify transcrip...
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Article
Open AccessmethylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data
Numerous methods are available to profile several epigenetic marks, providing data with different genome coverage and resolution. Large epigenomic datasets are then generated, and often combined with other hig...
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Article
Open AccessAn enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo
Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia disorders. Here, we identify an evoluti...
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Article
Open AccessHominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients
Speciation is associated with substantial rewiring of the regulatory circuitry underlying the expression of genes. Determining which changes are relevant and underlie the emergence of the human brain or its un...
