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Open AccessProteogenomics decodes the evolution of human ipsilateral breast cancer
Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and...
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Article
Open AccessHigh-throughput muscle fiber ty** from RNA sequencing data
Skeletal muscle fiber type distribution has implications for human health, muscle function, and performance. This knowledge has been gathered using labor-intensive and costly methodology that limited these stu...
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Open AccessGenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
Many wild species have suffered drastic population size declines over the past centuries, which have led to ‘genomic erosion’ processes characterized by reduced genetic diversity, increased inbreeding, and acc...
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Article
Open AccessContribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability
Despite the success of genome-wide association studies, much of the genetic contribution to complex traits remains unexplained. Here, we analyse high coverage whole-genome sequencing data, to evaluate the cont...
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Open AccessAuthor Correction: Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia
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Article
Open AccessGenomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions
Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made marine constructions and ships. Despite causing considerable ecologica...
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Open AccessGenome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion
Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is h...
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Open AccessIncreased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia
Despite considerable progress in schizophrenia genetics, most findings have been for large rare structural variants and common variants in well-imputed regions with few genes implicated from exome sequencing. ...
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Article
Open AccessThe genomic footprint of sexual conflict
Genes with sex-biased expression show a number of unique properties and this has been seen as evidence for conflicting selection pressures in males and females, forming a genetic ‘tug-of-war’ between the sexes...
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Article
Open AccessA major locus controls local adaptation and adaptive life history variation in a perennial plant
The initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth and have important fitness effects in perennial plants. Such adaptive life-history traits ...
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Article
Correction: Corrigendum: Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification
Nature 535, 294–298 (2016); doi:10.1038/nature18614 In the Author Information section of this Letter, LT571435 from the SRA was provided as the accession number for the PacBio whole-genome sequencing data. Imm...
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Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification
The zebrafish cloche gene is required for the formation of most endothelial and haematopoietic cells, however, it has been difficult to isolate; this study reveals that cloche encodes a PAS-domain-containing bHLH...
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Open AccessThe Chironomus tentans genome sequence and the organization of the Balbiani ring genes
The polytene nuclei of the dipteran Chironomus tentans (Ch. tentans) with their Balbiani ring (BR) genes constitute an exceptional model system for studies of the expression of endogenous eukaryotic genes. Here, ...
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Open AccessBESST - Efficient scaffolding of large fragmented assemblies
The use of short reads from High Throughput Sequencing (HTS) techniques is now commonplace in de novo assembly. Yet, obtaining contiguous assemblies from short reads is challenging, thus making scaffolding an imp...
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Open AccessEfficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools
Sampling genomes with Fosmid vectors and sequencing of pooled Fosmid libraries on the Illumina platform for massive parallel sequencing is a novel and promising approach to optimizing the trade-off between seq...
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Open AccessThe Norway spruce genome sequence and conifer genome evolution
Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the...
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Open AccessHierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing
Here we demonstrate the use of short-read massive sequencing systems to in effect achieve longer read lengths through hierarchical molecular tagging. We show how indexed and PCR-amplified targeted libraries ar...
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Open AccessA genome-wide study of recombination rate variation in Bartonella henselae
Rates of recombination vary by three orders of magnitude in bacteria but the reasons for this variation is unclear. We performed a genome-wide study of recombination rate variation among genes in the intracell...
