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Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…
The vast majority of connections between complex disease and common genetic variants were identified through meta-analysis, a powerful approach that enables large samples sizes while protecting against common artifacts due to population…
Chance constrained programming (CCP) refers to a type of optimization problem with uncertain constraints that are satisfied with at least a prescribed probability level. In this work, we study the sample average approximation (SAA) of…
The objective of a genome-wide association study (GWAS) is to associate subsequences of individuals' genomes to the observable characteristics called phenotypes (e.g., high blood pressure). Motivated by the GWAS problem, in this paper we…
Standing genetic variation provides a rich reservoir of potentially useful mutations facilitating the adaptation to novel environments. Experimental evolution studies have demonstrated that rapid and strong phenotypic responses to selection…
As large language models (LMs) advance, there is an increasing need to control their outputs to align with human values (e.g., detoxification) or desired attributes (e.g., personalization, topic). However, autoregressive models focus on…
Computer vision-based methods have valuable use cases in precision medicine, and recognizing facial phenotypes of genetic disorders is one of them. Many genetic disorders are known to affect faces' visual appearance and geometry. Automated…
Deep neural networks (DNN) have been used successfully in many scientific problems for their high prediction accuracy, but their application to genetic studies remains challenging due to their poor interpretability. In this paper, we…
Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…
This paper presents and compares alternative transfer learning methods that can increase the power of conditional testing via knockoffs by leveraging prior information in external data sets collected from different populations or measuring…
Given the lack of evidence for new particle discoveries at the Large Hadron Collider (LHC), it is critical to broaden the search program. A variety of model-independent searches have been proposed, adding sensitivity to unexpected signals.…
Historically, the majority of statistical association methods have been designed assuming availability of SNP-level information. However, modern genetic and sequencing data present new challenges to access and sharing of genotype-phenotype…
Recent advances in high-resolution sequencing have paved the way for population-scale analysis in single-cell RNA-sequencing (scRNA-seq) data. scRNA-seq data, in particular, have proven to be extremely powerful in profiling a variety of…
In the analysis of complex traits, genetic effects are frequently modelled as either fixed or random effects. Such assumptions serve as a foundation of defining heritability and relatedness using genome-wide single nucleotide polymorphism…
The prevalence of common chronic non-communicable diseases (CNCDs) far overshadows the prevalence of both monogenic and infectious diseases combined. All CNCDs, also called complex genetic diseases, have a heritable genetic component that…
The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the…
The SNPs (Single Nucleotide Polymorphisms) genotyping platforms are of great value for gene mapping of complex diseases. Nowadays, the high-density of these molecular markers enables studies of dependence patterns between loci over the…
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder (NDD) that is caused by genetic, epigenetic, and environmental factors. Recent advances in genomic analysis have uncovered numerous candidate genes with common…
Antibodies are capable of potently and specifically binding individual antigens and, in some cases, disrupting their functions. The key challenge in generating antibody-based inhibitors is the lack of fundamental information relating…
Motivation: Genome-wide association studies (GWASs), which assay more than a million single nucleotide polymorphisms (SNPs) in thousands of individuals, have been widely used to identify genetic risk variants for complex diseases. However,…