Related papers: BOOST: A fast approach to detecting gene-gene inte…
The description of gene interactions that constantly occur in the cellular environment is an extremely challenging task due to an immense number of degrees of freedom and incomplete knowledge about microscopic details. Hence, a…
Identification of disease genes, which are a set of genes associated with a disease, plays an important role in understanding and curing diseases. In this paper, we present a biomedical knowledge graph designed specifically for this…
This paper proposes Genetic Algorithm with Border Trades (GAB), a novel modification of the standard genetic algorithm that enhances exploration by incorporating new chromosome patterns in the breeding process. This approach significantly…
The advent of high--throughput transcription profiling technologies has enabled identification of genes and pathways associated with disease, providing new avenues for precision medicine. A key challenge is to analyze this data in the…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Collection of genotype data in case-control genetic association studies may often be incomplete for reasons related to genes themselves. This non-ignorable missingness structure, if not appropriately accounted for, can result in…
Diabetes is a global health burden, and early detection is critical for timely intervention. This study explores a non-invasive, data-driven framework to identify individuals at risk of diabetes using Volatile Organic Compounds (VOCs) and…
Background: Large-scale biological jobs on high-performance computing systems require manual intervention if one or more computing cores on which they execute fail. This places not only a cost on the maintenance of the job, but also a cost…
As data collections become larger, exploratory regression analysis becomes more important but more challenging. When observations are hierarchically clustered the problem is even more challenging because model selection with mixed effect…
Prediction of new drug-target interactions is extremely important as it can lead the researchers to find new uses for old drugs and to realize the therapeutic profiles or side effects thereof. However, experimental prediction of drug-target…
Motivated by the important problem of detecting association between genetic markers and binary traits in genome-wide association studies, we present a novel Bayesian model that establishes a hierarchy between markers and genes by defining…
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…
Early detection of chronic diseases is beneficial to healthcare by providing a golden opportunity for timely interventions. Although numerous prior studies have successfully used machine learning (ML) models for disease diagnoses, they…
One of the focus areas of modern scientific research is to reveal mysteries related to genes and their interactions. The dynamic interactions between genes can be encoded into a gene regulatory network (GRN), which can be used to gain…
Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many…
Genotype-by-Environment (GxE) interactions influence the performance of genotypes across diverse environments, reducing the predictability of phenotypes in target environments. In-depth analysis of GxE interactions facilitates the…
Motivation: Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regulatory landscapes…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…
Infections depend on interactions between pathogen and host proteins, but comprehensively mapping these interactions is challenging and labor intensive. Many biological networks have hierarchical, scale-free structure, so we developed a…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…