Rapid identification and interpretation of gene‐environment associations using the new R.SamBada landscape genomics pipeline

Chattez avec Graph Search

Posez n’importe quelle question sur les cours, conférences, exercices, recherches, actualités, etc. de l’EPFL ou essayez les exemples de questions ci-dessous.

AVERTISSEMENT : Le chatbot Graph n'est pas programmé pour fournir des réponses explicites ou catégoriques à vos questions. Il transforme plutôt vos questions en demandes API qui sont distribuées aux différents services informatiques officiellement administrés par l'EPFL. Son but est uniquement de collecter et de recommander des références pertinentes à des contenus que vous pouvez explorer pour vous aider à répondre à vos questions.

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 ...

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 ...

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 ...

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 ...

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 ...

Objectives The endosymbiosis with Symbiodiniaceae is key to the ecological success of reef-building corals. However, climate change is threatening to destabilize this symbiosis on a global scale. Most studies looking into the response of corals to heat str ...

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide ...

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 ...

Cells cope with and adapt to ever-changing environmental conditions. Sophisticated regulatory networks allow cells to adjust to these fluctuating environments. One such archetypal system is the Saccharomyces cerevisiae Pho regulon. When external inorganic ...

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 ...

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated ...

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACSDCE T and strain ACSTCE, were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirill ...

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

Zebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signa ...

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

2.5D Systems-on-Package (SoPs) are composed by several chiplets placed on an interposer. They are becoming increasingly popular as they enable easy integration of electronic components in the same package and high fabrication yields. Nevertheless, they int ...

Rapid identification and interpretation of gene‐environment associations using the new R.SamBada landscape genomics pipeline

Chattez avec Graph Search

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

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

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

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

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

Gene expression of Pocillopora damicornis coral larvae in response to acidification and ocean warming

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis

Statistical learning quantifies transposable element-mediated cis-regulation

Host-Pathogen Interactions Through the Genomic Lens

Perfect adaptation achieved by transport limitations governs the inorganic phosphate response in S. cerevisiae

Modeling, analysis, and design of complex biological networks

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil

Chromatin modules and their implication in genomic organization and gene regulation

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

REMOTE: Re-thinking Task Mapping on Wireless 2.5D Systems-on-Package for Hotspot Removal