The influence of human genetic variation on Epstein–Barr virus sequence diversity

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Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

Infectious agents contribute significantly to the global burden of diseases through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Traditional cell cultures have long been fundamental to biological research, offering an alternative to animal models burdened by ethical constraints and procedural intricacies, often lacking relevance to human physiology and disease. Moreover, their inabi ...

Aerosol transmission remains a major challenge for control of respiratory viruses, particularly those causing recurrent epidemics, like influenza A virus (IAV). These viruses are rarely expelled alone, but instead are embedded in a consortium of microorgan ...

Inflammation stands as a dynamic and intricate biological process, promoting vital defence mechanisms against harmful stimuli, including infections and injuries, to drive pathogen clearance and healing. On one hand, these responses can manifest acutely and ...

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

Hosts and pathogens are involved in a long-standing evolutionary arms race characterized by successive rounds of evolution. Specifically, while hosts evolve resistance against infections, pathogens adapt to re-establish virulence. Since the signatures of t ...

The influence of human genetic variation on Epstein–Barr virus sequence diversity

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Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Accessible and highly observable gastrointestinal organoid model systems for studying host-pathogen interactions

Stability of influenza A virus in droplets and aerosols is heightened by the presence of commensal respiratory bacteria

Exploring the role of cGAS-STING-mediated inflammation in age-associated neurodegeneration and antitumor immunity

Multimodal transcriptomic atlases of mouse spinal cord injury

Statistical learning quantifies transposable element-mediated cis-regulation

Host-Pathogen Interactions Through the Genomic Lens