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

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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 ...

Sharing data across institutions for genome-wide association studies (GWAS) would enhance the discovery of genetic variation linked to health and disease1,2. However, existing data-sharing regulations limit the scope of such collaborations3. Although crypt ...

Motivation Many machine learning (ML) models developed to classify phenotype from gene expression data provide interpretations for their decisions, with the aim of understanding biological processes. For many models, including neural networks, interpretati ...

In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependent antagonism. Using single-cell live imaging and isotopi ...

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 ...

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 ...

One of the main challenges in coral reef conservation and restoration is the identification of coral populations resilient under global warming. Seascape genomics is a powerful tool to uncover genetic markers potentially involved in heat tolerance among la ...

Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address thes ...

The present invention provides a method for preparing a sequencing library from a ribonucleic acid (RNA) sample. ...

Although cardinal cortical interneuron identity is established upon cell-cycle exit, it remains unclear whether specific interneuron subtypes are pre-established, and if so, how their identity is maintained prior to circuit integration. We conditionally re ...

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent per ...

SARS-CoV-2 infected a large fraction of humans in the past 2 years. The clinical presentation of acute infection varies greatly between individuals, ranging from asymptomatic or mild to life-threatening COVID-19 pneumonia with multi-organ complications. De ...

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...

NOTCH1 is a well-established lineage specifier for T cells and among the most frequently mutated genes throughout all subclasses of T cell acute lymphoblastic leukemia (T-ALL). How oncogenic NOTCH1 signaling launches a leukemia-prone chromatin landscape du ...

Infectious diseases are particularly challenging for genome-wide association studies (GWAS) because genetic effects from two organisms (pathogen and host) can influence a trait. Traditional GWAS assume individual samples are independent observations. Howev ...

The transcription factor network required for primordial germ cell (PGC) specification is known to diverge in mammals. Here the authors show that hominidae-specific transposable element (TE) LTR5Hs becomes transcriptionally active during PGC specification, ...

The invention relates to methods for the preparation of method of preparation of cDNA library based on one or many RNA samples useful for efficient RNA sequencing and uses thereof. The invention further relates to related tools and kits useful in said meth ...

Biologically inspired solid-state nanopores are artificial openings or apertures in thin membranes similar to natural protein ion channels in a lipid bilayer of cell membranes. In solid-state nanopores, a thin insulating membrane with single or multiple po ...

Background: Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinica ...

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

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Secure and federated genome-wide association studies for biobank-scale datasets

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

Context transcription factors establish cooperative environments and mediate enhancer communication

Climate adaptive loci revealed by seascape genomics correlate with phenotypic variation in heat tolerance of the coral Acropora millepora

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Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits

Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections

Method of preparation of cdna library useful for efficient mrna sequencing and uses thereof

2D MoS2 Nanopores: Wafer-scale Fabrication and Monolayer Stability for Long-term Single-Molecule Sensing

Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples