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The seasonal human influenza virus undergoes rapid evolution, leading to significant changes in circulating viral strains from year to year. These changes are typically driven by adaptive mutations, particularly in the antigenic epitopes,…
We analyze 14,651 HIV1 reverse transcriptase (HIV RT) sequences from the Stanford HIV Drug Resistance Database labeled with treatment regimen in order to study the evolution this enzyme under drug selection in the clinic. Our goal is to…
Respondent-driven sampling is a form of link-tracing network sampling, which is widely used to study hard-to-reach populations, often to estimate population proportions. Previous treatments of this process have used a with-replacement…
Motivation: Receptor-binding proteins (RBPs) initiate viral infection and determine host specificity, serving as key targets for phage engineering and therapy. However, the identification of RBPs is complicated by their extreme sequence…
The COVID-19 pandemic forced the rapid development of vaccines and the implementation of mass vaccination programs around the world. However, many hesitated to take the vaccine due to concerns about its effectiveness. By looking at an…
The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive…
The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…
Due to the heterogeneity of the phenotype defined by Diagnostic and Statistical Manual of Mental Disorders (DSM) IV, it is not an optimal option to identify the genetic variation that underlies the risk for alcohol dependence (AD) and…
With the advent of high-throughput sequencing technologies, the fields of immunogenomics and adaptive immune receptor repertoire research are facing both opportunities and challenges. Adaptive immune receptor repertoire sequencing…
We present SSL-HV: Self-Supervised Learning approaches applied to the task of Handwriting Verification. This task involves determining whether a given pair of handwritten images originate from the same or different writer distribution. We…
When evaluating the efficacy of social programs and medical treatments using randomized experiments, the estimated overall average causal effect alone is often of limited value and the researchers must investigate when the treatments do and…
The Covid-19 outbreak of 2020 has required many governments to develop and adopt mathematical-statistical models of the pandemic for policy and planning purposes. To this end, this work provides a tutorial on building a compartmental model…
This study employs a robust analytical framework to uncover patterns in survival outcomes among breast cancer patients from diverse racial and geographical backgrounds. This research uses the SEER 2021 dataset to analyze breast cancer…
Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the…
Predicting an individual's risk of experiencing a future clinical outcome is a statistical task with important consequences for both practicing clinicians and public health experts. Modern observational databases such as electronic health…
We develop a feature allocation model for inference on genetic tumor variation using next-generation sequencing data. Specifically, we record single nucleotide variants (SNVs) based on short reads mapped to human reference genome and…
The pursuit of strategies that minimize the number of individuals needing vaccination to control an outbreak is a well-established area of study in mathematical epidemiology. However, for certain diseases, public policy tends to prioritize…
Cancer is a heterogeneous disease with diverse molecular etiologies and outcomes. The Cancer Genome Atlas (TCGA) has released a large compendium of over 10,000 tumors with RNA-seq gene expression measurements. Gene expression captures the…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
While conducting probabilistic surveys is the gold standard for assessing vaccine coverage, implementing these surveys poses challenges for global health. There is a need for more convenient option that is more affordable and practical.…