Related papers: Replicability analysis for genome-wide association…
Over the past few years, deep learning methods have been applied for a wide range of Software Engineering (SE) tasks, including in particular for the important task of automatically predicting and localizing faults in software. With the…
With advancement of medicine, alternative exposures or interventions are emerging with respect to a common outcome, and there are needs to formally test the difference in the associations of multiple exposures. We propose a duplication…
Reproducibility is an important task in scientific research. It is crucial for researchers to compare newly developed systems with the state-of-the-art to assess whether they made a breakthrough. However previous works may not be…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
We devise survey-weighted pseudo posterior distribution estimators under two-stage informative sampling of both primary clusters and secondary nested units for a one-way analysis of variance (ANOVA) population generating model as a simple…
We discuss replica analytic continuation using several simple models in order to prove mathematically the validity of replica analysis, which is used in a wide range of fields related to large scale complex systems. While replica analysis…
When testing for replication of results from a primary study with two-sided hypotheses in a follow-up study, we are usually interested in discovering the features with discoveries in the same direction in the two studies. The direction of…
Although prospective logistic regression is the standard method of analysis for case-control data, it has been recently noted that in genetic epidemiologic studies one can use the ``retrospective'' likelihood to gain major power by…
The development of next generation sequencing (NGS) technology and genotype imputation methods enabled researchers to measure both common and rare variants in genome-wide association studies (GWAS). Statistical methods have been proposed to…
Common complex diseases are likely influenced by the interplay of hundreds, or even thousands, of genetic variants. Converging evidence shows that genetic variants with low marginal effects (LME) play an important role in disease…
Many published research results are false, and controversy continues over the roles of replication and publication policy in improving the reliability of research. Addressing these problems is frustrated by the lack of a formal framework…
Directional replicability addresses the question of whether an effect studied across $n$ independent studies is present with the same direction in at least $r$ of them, for $r \geq 2$. When the expected direction of the effect is not…
Statistically resolving the underlying haplotype pair for a genotype measurement is an important intermediate step in gene mapping studies, and has received much attention recently. Consequently, a variety of methods for this problem have…
The aim of this paper is to propose a novel estimation method of using genetic-predicted observations to estimate trans-ancestry genetic correlations, which describes how genetic architecture of complex traits varies among populations, in…
Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying…
With advancements in next generation sequencing technology, a massive amount of sequencing data are generated, offering a great opportunity to comprehensively investigate the role of rare variants in the genetic etiology of complex…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
Diabetes, particularly Type 2 diabetes (T2D), poses a substantial global health burden, compounded by its associated complications such as cardiovascular diseases, kidney failure, and vision impairment. Early detection of T2D is critical…
Being able to duplicate published research results is an important process of conducting research whether to build upon these findings or to compare with them. This process is called "replicability" when using the original authors'…
Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly…