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During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…
PURPOSE: The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools monitoring and prioritizing the literature to understand the clinical implications of the pathogenic genetic variants. We…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
Heterogeneity is a hallmark of complex diseases. Regression-based heterogeneity analysis, which is directly concerned with outcome-feature relationships, has led to a deeper understanding of disease biology. Such an analysis identifies the…
Repeating an imperfect biomarker test based on an initial result can introduce bias and influence misclassification risk. For example, in some blood donation settings, blood donors' hemoglobin is remeasured when the initial measurement…
Short-read DNA sequencing instruments can yield over 1e+12 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using…
Novel Magnetic Resonance (MR) imaging modalities can quantify hemodynamics but require long acquisition times, precluding its widespread use for early diagnosis of cardiovascular disease. To reduce the acquisition times, reconstruction…
Motivation: Biomarker discovery from high-dimensional data is a crucial problem with enormous applications in biology and medicine. It is also extremely challenging from a statistical viewpoint, but surprisingly few studies have…
We consider models for which it is important, early in processing, to estimate some variables with high precision, but perhaps at relatively low rates of recall. If some variables can be identified with near certainty, then they can be…
Biomedical data are widely accepted in developing prediction models for identifying a specific tumor, drug discovery and classification of human cancers. However, previous studies usually focused on different classifiers, and overlook the…
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…
Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, that can be applied to WGS data from one or more tumor samples to reconstruct complete genotypes of…
Whole genome sequencing (WGS) is quickly becoming the customary means for identification of antimicrobial resistance (AMR) due to its ability to obtain high resolution information about the genes and mechanisms that are causing resistance…
Despite the remarkable progress, weakly supervised segmentation approaches are still inferior to their fully supervised counterparts. We obverse the performance gap mainly comes from their limitation on learning to produce high-quality…
Assessing the statistical power to detect susceptibility variants plays a critical role in GWA studies both from the prospective and retrospective points of view. Power is empirically estimated by simulating phenotypes under a disease model…
Tumor cell populations can be thought of as being composed of homogeneous cell subpopulations, with each subpopulation being characterized by overlapping sets of single nucleotide variants (SNVs). Such subpopulations are known as subclones…
We develop several tools for the determination of sample size and design for MediCal audits. This audit setting involves a population of claims for reimbursement by a healthcare provider which need to be reviewed by an auditor to determine…
Molecular subtypes of colorectal cancer (CRC) significantly influence treatment decisions. While convolutional neural networks (CNNs) have recently been introduced for automated CRC subtype identification using H&E stained histopathological…