Computational analysis of ultraconserved non-coding DNA elements in vertebrate genomes

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

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 ...

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 ...

Plant cells harness osmotic pressures to stiffen their leaves through strong turgor pressures. Key to this osmosisdriven stiffening is the confinement of liquids within semipermeable membranes that can regulate the transport of water molecules and ions. In ...

Experimental measurements of the turbulence amplitude utilizing a short pulse reflectometry method are presented. Two discharges with shaped plasma possessing opposite signs of triangularity are considered and a higher turbulence amplitude is found in the ...

Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted ...

How to measure students' Computational Problem-Solving (CPS) competencies is an ongoing research topic. Prevalent approaches vary by measurement tools (e.g., interactive programming, multiple-choice tests, or programming-independent tests) and task types ( ...

Wastewater-based epidemiology offers a complementary approach to clinical case-based surveillance of emergent diseases and can help identify regions with infected people to prioritize clinical surveillance strategies. However, tracking emergent diseases in ...

Computational analysis of ultraconserved non-coding DNA elements in vertebrate genomes

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Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

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

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

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

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

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

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

The dynamic genetic determinants of increased transcriptional divergence in spermatids

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

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

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

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

Osmosis-driven stiffening of structured hydrogels

Validation of short-pulse reflectometry turbulence measurements with a synthetic diagnostic

Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures

A Comparative Analysis of Tools & Task Types for Measuring Computational Problem-Solving

Monitoring an Emergent Pathogen at Low Incidence in Wastewater Using qPCR: Mpox in Switzerland