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Heterogeneous treatment effects (HTE) based on patients' genetic or clinical factors are of significant interest to precision medicine. Simultaneously modeling HTE and corresponding main effects for randomized clinical trials with…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Being able to design genetic regulatory networks (GRNs) to achieve a desired cellular function is one of the main goals of synthetic biology. However, determining minimal GRNs that produce desired time-series behaviors is non-trivial. In…
The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…
Substantial progress has been made in identifying single genetic variants predisposing to common complex diseases. Nonetheless, the genetic etiology of human diseases remains largely unknown. Human complex diseases are likely influenced by…
Gene-based testing is a commonly employed strategy in many genetic association studies. Gene-trait associations can be complex due to underlying population heterogeneity, gene-environment interactions, and various other reasons. Existing…
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…
As a discrete approach to genetic regulatory networks, Boolean models provide an essential qualitative description of the structure of interactions among genes and proteins. Boolean models generally assume only two possible states…
Background: State-of-the art selection methods fail to identify weak but cumulative effects of features found in many high-dimensional omics datasets. Nevertheless, these features play an important role in certain diseases. Results: We…
Converging evidence suggests that common complex diseases with the same or similar clinical manifestations could have different underlying genetic etiologies. While current research interests have shifted toward uncovering rare variants and…
Genome-wide association studies(GWAS) have proven to be highly useful in revealing the genetic basis of complex diseases. At present, most GWAS are studies of a particular single disease diagnosis against controls. However, in practice, an…
Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6),…
For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each gene) and structure (order…
Genomic instability, the propensity of aberrations in chromosomes, plays a critical role in the development of many diseases. High throughput genotyping experiments have been performed to study genomic instability in diseases. The output of…
The value of research containing novel combinations of molecules can be seen in many innovative and award-winning research programs. Despite calls to use innovative approaches to address common diseases, an increasing majority of research…
Epistasis (gene-gene interaction) is crucial to predicting genetic disease. Our work tackles the computational challenges faced by previous works in epistasis detection by modeling it as a one-step Markov Decision Process where the state is…
A great deal of effort has been devoted to discovering a particular genetic disorder, but its classification across a broad spectrum of disorder classes and types remains elusive. Early diagnosis of genetic disorders enables timely…
Understanding the molecular-level mechanisms underpinning Alzheimer's disease (AD) by studying crucial genes associated with the disease remains a challenge. Alzheimer's, being a multifactorial disease, requires understanding the gene-gene…
Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…
Diabetes is currently one of the most common, dangerous, and costly diseases in the world that is caused by an increase in blood sugar or a decrease in insulin in the body. Diabetes can have detrimental effects on people's health if…