Related papers: Comprehensive Detection of Genes Causing a Phenoty…
Identifying phenotype-associated genes is a common first step in polygenic risk score construction, enrichment testing, target prioritisation and variant interpretation, but relevant evidence is distributed across heterogeneous databases…
Studying phenotype-gene association can uncover mechanism of diseases and develop efficient treatments. In complex disease where multiple phenotypes are available and correlated, analyzing and interpreting associated genes for each…
Life science is entering a new era of petabyte-level sequencing data. Converting such big data to biological insights represents a huge challenge for computational analysis. To this end, we developed DeepMetabolism, a biology-guided deep…
Identifying phenotypes plays an important role in furthering our understanding of disease biology through practical applications within healthcare and the life sciences. The challenge of dealing with the complexities and noise within…
Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…
Background: A metabolic genotype comprises all chemical reactions an organism can catalyze via enzymes encoded in its genome. A genotype is viable in a given environment if it is capable of producing all biomass components the organism…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
This issue includes six articles that develop and apply statistical methods for the analysis of gene sequencing data of different types. The methods are tailored to the different data types and, in each case, lead to biological insights not…
Understanding how genes influence phenotype across species is a fundamental challenge in genetic engineering, which will facilitate advances in various fields such as crop breeding, conservation biology, and personalized medicine. However,…
To characterize natural selection, various analytical methods for detecting candidate genomic regions have been developed. We propose to perform genome-wide scans of natural selection using principal component analysis. We show that the…
Understanding how molecular changes caused by genetic variation drive disease risk is crucial for deciphering disease mechanisms. However, interpreting genome sequences is challenging because of the vast size of the human genome, and…
Identifying subtle phenotypic variations in cellular images is critical for advancing biological research and accelerating drug discovery. These variations are often masked by the inherent cellular heterogeneity, making it challenging to…
Decoding the genome confers the capability to predict characteristics of the organism(phenotype) from DNA (genotype). We describe the present status and future prospects of genomic prediction of complex traits in humans. Some highly…
Deep learning has been extensively researched in the analysis of pathology whole-slide images (WSIs). However, most existing methods are limited to providing prediction interpretability by locating the model's salient areas in a post-hoc…
The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing…
Many common diseases are highly polygenic, modulated by a large number genetic factors with small effects on susceptibility to disease. These small effects are difficult to map reliably in genetic association studies. To address this…
The genetic basis of multiple phenotypes such as gene expression, metabolite levels, or imaging features is often investigated by testing a large collection of hypotheses, probing the existence of association between each of the traits and…
Phenotypic variation is a hallmark of cellular physiology. Metabolic heterogeneity, in particular, underpins single-cell phenomena such as microbial drug tolerance and growth variability. Much research has focussed on transcriptomic and…
Three steps aid in the analysis of selection. First, describe phenotypes by their component causes. Components include genes, maternal effects, symbionts, and any other predictors of phenotype that are of interest. Second, describe fitness…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…