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A genomics approach reveals insights into the importance of gene losses for mammalian adaptations
Identifying the genomic changes that underlie phenotypic adaptations is a key challenge in evolutionary biology and genomics. Loss of protein-coding genes is one type of genomic change with theExpand
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Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome.
The use of alternative translation initiation sites enables production of more than one protein from a single gene, thereby expanding the cellular proteome. Although several such examples have beenExpand
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Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish
The killifish Nothobranchius furzeri is the shortest-lived vertebrate that can be bred in the laboratory. Its rapid growth, early sexual maturation, fast aging, and arrested embryonic developmentExpand
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Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation
Abstract Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from oneExpand
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Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations
Several genes lost in the ancestors of whales and dolphins likely contributed to adapting to a fully aquatic environment. The transition from land to water in whales and dolphins (cetaceans) wasExpand
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Loss of Enzymes in the Bile Acid Synthesis Pathway Explains Differences in Bile Composition among Mammals
Abstract Bile acids are important for absorbing nutrients. Most mammals produce cholic and chenodeoxycholic bile acids. Here, we investigated genes in the bile acid synthesis pathway in four mammalsExpand
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A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.
Bacterial genome annotations contain a number of coding sequences (CDSs) that, in spite of reading frame disruptions, encode a single continuous polypeptide. Such disruptions have different origins:Expand
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SubCellProt: Predicting Protein Subcellular Localization Using Machine Learning Approaches
We present two machine learning approaches for prediction of the subcellular localization of a protein from the primary sequence information. Expand
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Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators
Significance Perturbation of transcription register by RNA polymerase, transcription slippage, is used to yield additional protein products. Known functionally important cases involve a small numberExpand
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Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores
Significance Mammals repeatedly adapted to specialized diets, including plant-based diets for herbivores and meat- or insect-based diets for carnivores. Apart from consuming diets with differentExpand
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