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Genome sequencing of the staple food crop white Guinea yam enables the develo...
Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a... -
SalmoNet, an integrated network of ten Salmonella enterica strains reveals co...
Salmonella enterica is a prominent bacterial pathogen with implications on human and animal health. Salmonella serovars could be classified as gastro-intestinal or... -
Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Re...
Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In... -
Zinc finger nuclease-mediated precision genome editing of an endogenous gene ...
Sequence‐specific nucleases have been used to engineer targeted genome modifications in various plants. While targeted gene knockouts resulting in loss of function have been... -
Pathogenomic Analysis of Wheat Yellow Rust Lineages Detects Seasonal Variatio...
Recent disease outbreaks caused by (re-)emerging plant pathogens have been associated with expansions in pathogen geographic distribution and increased virulence. For example,... -
Systems-Level Feedbacks of NRF2 Controlling Autophagy upon Oxidative Stress R...
Although the primary role of autophagy-dependent cellular self-eating is cytoprotective upon various stress events (such as starvation, oxidative stress, and high temperatures),... -
Efficient and accurate detection of splice junctions from RNAseq with Portcullis
Next generation sequencing (NGS) technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression... -
Genomics of habitat choice and adaptive evolution in a deep-sea fish
Intraspecific diversity promotes evolutionary change, and when partitioned among geographic regions or habitats can form the basis for speciation. Marine species live in an... -
New approaches for assembly of short-read metagenomic data
In recent years, the use of longer-range read data combined with advances in assembly algorithms has stimulated big improvements in the contiguity and quality of genome... -
Identification of master regulators in goblet cells and Paneth cells using tr...
Dysfunction of intestinal epithelial cells is often associated with severe gut pathologies, such as inflammatory bowel disease (IBD). Although transcriptional signatures of... -
A critical comparison of technologies for a plant genome sequencing project
A high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow and expensive, whereas... -
Building a locally diploid genome and transcriptome of the diatom Fragilariop...
Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus -
Alpha-synuclein induces the unfolded protein response in Parkinson’s disease ...
The recent generation of induced pluripotent stem cells (iPSCs) from a patient with Parkinson’s disease (PD) resulting from triplication of the α-synuclein (SNCA) gene locus... -
A comprehensive genomic history of extinct and living elephants
Elephantids are the world’s most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2... -
Elucidating the genetic basis of biomass accumulation and radiation use effic...
One of the major challenges for plant scientists is increasing wheat (Triticum aestivum) yield potential (YP). A significant bottleneck for increasing YP is achieving increased... -
Practical Computational Reproducibility in the Life Sciences
AUTHOR CONTRIBUTIONS -
A quantitative model for characterizing the evolutionary history of mammalian...
Characterizing the evolutionary history of a gene’s expression profile is a critical component for understanding the relationship between genotype, expression, and phenotype.... -
Sixteen diverse laboratory mouse reference genomes define strain-specific hap...
We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and... -
Chromosome assembly of large and complex genomes using multiple references
Despite the rapid development of sequencing technologies, the assembly of mammalian-scale genomes into complete chromosomes remains one of the most challenging problems in... -
Genome variation and conserved regulation identify genomic regions responsibl...
The genomes of laboratory rat strains are characterised by a mosaic haplotype structure caused by their unique breeding history. These mosaic haplotypes have been recently...
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