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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... -
Biodiversity-function relationships in methanogenic communities
Methanogenic communities play a crucial role in carbon cycling and biotechnology (anaerobic digestion), but our understanding of how their diversity, or composition in general,... -
SPECTRE: a suite of phylogenetic tools for reticulate evolution
Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks,... -
The ash dieback invasion of Europe was founded by two genetically divergent i...
Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen... -
GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl...
Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological,... -
Interplay of cis and trans mechanisms driving transcription factor binding an...
Noncoding regulatory variants play a central role in the genetics of human diseases and in evolution. Here we measure allele-specific transcription factor binding occupancy of... -
Sex-specific changes in the aphid DNA methylation landscape
Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome... -
A transatlantic perspective on 20 emerging issues in biological engineering
Advances in biological engineering are likely to have substantial impacts on global society. To explore these potential impacts we ran a horizon scanning exercise to capture a... -
The Galaxy platform for accessible, reproducible and collaborative biomedical...
Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists... -
Semi-quantitative characterisation of mixed pollen samples using MinION seque...
The ability to identify and quantify the constituent plant species that make up a mixed-species sample of pollen has important applications in ecology, conservation, and... -
VERNALIZATION1 controls developmental responses of winter wheat under high am...
Low temperatures are required to regulate the transition from vegetative to reproductive growth via a pathway called vernalization. In wheat, vernalization predominantly... -
Defining Cell Identity with Single-Cell Omics
Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological... -
What We Learned From Big Data for Autophagy Research
Autophagy is the process by which cytoplasmic components are sequestered in autophagosomal vesicles and delivered to the lysosome for degradation. Defective autophagy has been... -
Plant genetic resources for food and agriculture: opportunities and challenge...
Over the last decade, there has been an ongoing revolution in the exploration, manipulation and synthesis of biological systems, through the development of new technologies that... -
Primula vulgaris (primrose) genome assembly, annotation and gene expression, ...
Primula vulgaris (primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded... -
Harnessing genetic potential of wheat germplasm banks through impact-oriented...
The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with... -
Finding a partner in the ocean: molecular and evolutionary bases of the respo...
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process...
