Related papers: Prediction and replication from case-control seque…
Gene/pathway-based methods are drawing significant attention due to their usefulness in detecting rare and common variants that affect disease susceptibility. The biological mechanism of drug responses indicates that a gene-based analysis…
In sexual population, recombination reshuffles genetic variation and produces novel combinations of existing alleles, while selection amplifies the fittest genotypes in the population. If recombination is more rapid than selection,…
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations, and to look for genomic regions with…
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…
Meta-analysis of multiple genome-wide association studies (GWAS) is effective for detecting single or multi marker associations with complex traits. We develop a flexible procedure ("STAMP") based on mixture models to perform region based…
We analyze dynamic random network models where younger vertices connect to older ones with probabilities proportional to their degrees as well as a propensity kernel governed by their attribute types. Using stochastic approximation…
Nested case-control (NCC) is a sampling method widely used for developing and evaluating risk models with expensive biomarkers on large prospective cohort studies. The biomarker values are typically obtained on a sub-cohort, consisting of…
Anomaly detection aims to separate anomalies from normal samples, and the pretrained network is promising for anomaly detection. However, adapting the pretrained features would be confronted with the risk of pattern collapse when finetuning…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
RNA-sequencing has revolutionized biomedical research and, in particular, our ability to study gene alternative splicing. The problem has important implications for human health, as alternative splicing may be involved in malfunctions at…
Large populations may contain numerous simultaneously segregating polymorphisms subject to natural selection. Since selection acts on individuals whose fitness depends on many loci, different loci affect each other's dynamics. This leads to…
The genetic etiologies of common diseases are highly complex and heterogeneous. Classic statistical methods, such as linear regression, have successfully identified numerous genetic variants associated with complex diseases. Nonetheless,…
In addition to variation in terms of single nucleotide polymorphisms (SNPs), whole regions ranging from several kilobases up to a megabase in length differ in copy number among individuals. These differences are referred to as Copy Number…
Neural approaches to sequence labeling often use a Conditional Random Field (CRF) to model their output dependencies, while Recurrent Neural Networks (RNN) are used for the same purpose in other tasks. We set out to establish RNNs as an…
Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…
Contrastive dimension reduction methods have been developed for case-control study data to identify variation that is enriched in the foreground (case) data X relative to the background (control) data Y. Here, we develop contrastive…
Next-generation sequencing technology enables routine detection of bacterial pathogens for clinical diagnostics and genetic research. Whole genome sequencing has been of importance in the epidemiologic analysis of bacterial pathogens.…
A mechanism of sympatric speciation is presented based on the interaction-induced developmental plasticity of phenotypes. First, phenotypes of individuals with identical genotypes split into a few groups, according to instability in the…
We study the identification of causal effects in the presence of different types of constraints (e.g., logical constraints) in addition to the causal graph. These constraints impose restrictions on the models (parameterizations) induced by…
Millions of patients suffer from rare diseases around the world. However, the samples of rare diseases are much smaller than those of common diseases. In addition, due to the sensitivity of medical data, hospitals are usually reluctant to…