Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses

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Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

Regulatory elements, such as enhancers and silencers, control transcription by establishing physical proximity to target gene promoters. Neurons in flies and mammals exhibit long-range three-dimensional genome contacts, proposed to connect genes with dista ...

Objectives: The risk of diabetes mellitus (DM) is increased in people with HIV. Chronic inflammation contributes to DM risk. High leukocytes are associated with DM in the general population, but in people with HIV, evidence of a leukocyte-DM association is ...

5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention an ...

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 ...

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 ...

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 ...

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 ...

Many enhancers control gene expression by assembling regulatory factor clusters, also referred to as condensates. This process is vital for facilitating enhancer communication and establishing cellular identity. However, how DNA sequence and transcription ...

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 ...

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 ...

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fus ...

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 ...

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 ...

Two fundamental properties of embryonic stem cells (ESCs) are their ability to self-renew and differentiate into all somatic cell types. Maintenance of their identity faces major challenges when transitioning through mitosis, as most DNA-binding proteins a ...

The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions remains unknown. Here, we employed reverse genetics to inv ...

An individual polygenic risk score was associated with osteoporosis in people living with HIV. The genetic effect was robust, as it persisted after multivariable adjustment for established traditional and HIV-related osteoporosis risk factors, including te ...

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses

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Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

A boundary-defining protein facilitates megabase-scale regulatory chromosomal loop formation in Drosophila neurons

Leukocyte Count and New-onset Diabetes Mellitus in People with Hiv: a Longitudinal Study

DNA methylation enables recurrent endogenization of giant viruses in an animal relative

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

The dynamic genetic determinants of increased transcriptional divergence in spermatids

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

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

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

Context transcription factors establish cooperative environments and mediate enhancer communication

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

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

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Stimulus-responsive assembly of nonviral nucleocapsids

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

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

Deciphering the molecular events leading to the global restoration of the chromatin landscape during mitotic exit

Influence of Amino Acid Substitutions in Capsid Proteins of Coxsackievirus B5 on Free Chlorine and Thermal Inactivation

Association of a Polygenic Risk Score With Osteoporosis in People Living With HIV: The Swiss HIV Cohort Study

Modeling, analysis, and design of complex biological networks