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Article
Open AccessHost-response transcriptional biomarkers accurately discriminate bacterial and viral infections of global relevance
Diagnostic limitations challenge management of clinically indistinguishable acute infectious illness globally. Gene expression classification models show great promise distinguishing causes of fever. We genera...
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Article
Open AccessAuthor Correction: Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion
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Article
Open AccessLesion identification and malignancy prediction from clinical dermatological images
We consider machine-learning-based lesion identification and malignancy prediction from clinical dermatological images, which can be indistinctly acquired via smartphone or dermoscopy capture. Additionally, we...
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Article
Open AccessDifferential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion
SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling e...
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Article
Open AccessPredicting in-hospital length of stay: a two-stage modeling approach to account for highly skewed data
In the early stages of the COVID-19 pandemic our institution was interested in forecasting how long surgical patients receiving elective procedures would spend in the hospital. Initial examination of our model...
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Article
Open AccessSystematic comparison of published host gene expression signatures for bacterial/viral discrimination
Measuring host gene expression is a promising diagnostic strategy to discriminate bacterial and viral infections. Multiple signatures of varying size, complexity, and target populations have been described. Ho...
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Article
Open AccessAntibody signatures of asymptomatic Plasmodium falciparum malaria infections measured from dried blood spots
Screening malaria-specific antibody responses on protein microarrays can help identify immune factors that mediate protection against malaria infection, disease, and transmission, as well as markers of past ex...
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Article
Open AccessCPT to RVU conversion improves model performance in the prediction of surgical case length
Methods used to predict surgical case time often rely upon the current procedural terminology (CPT) code as a nominal variable to train machine-learned models, however this limits the ability of the model to i...
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Article
Open AccessThe host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches
Candidemia is one of the most common nosocomial bloodstream infections in the United States, causing significant morbidity and mortality in hospitalized patients, but the breadth of the host response to Candida i...
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Article
Open AccessAn atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility
While genome-wide associations studies (GWAS) have successfully elucidated the genetic architecture of complex human traits and diseases, understanding mechanisms that lead from genetic variation to pathophysi...
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Article
Open AccessDysregulated transcriptional responses to SARS-CoV-2 in the periphery
SARS-CoV-2 infection has been shown to trigger a wide spectrum of immune responses and clinical manifestations in human hosts. Here, we sought to elucidate novel aspects of the host response to SARS-CoV-2 infe...
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Article
Open AccessHealth system utilization before age 1 among children later diagnosed with autism or ADHD
Children with autism spectrum disorder (ASD) or attention deficit hyperactivity disorder (ADHD) have 2–3 times increased healthcare utilization and annual costs once diagnosed, but little is known about their ...
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Article
Open AccessA crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection
The response to respiratory viruses varies substantially between individuals, and there are currently no known molecular predictors from the early stages of infection. Here we conduct a community-based analysi...
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Article
Open AccessA community approach to mortality prediction in sepsis via gene expression analysis
Improved risk stratification and prognosis prediction in sepsis is a critical unmet need. Clinical severity scores and available assays such as blood lactate reflect global illness severity with suboptimal per...
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Chapter and Conference Paper
Laplacian Hamiltonian Monte Carlo
We proposed a Hamiltonian Monte Carlo (HMC) method with Laplace kinetic energy, and demonstrate the connection between slice sampling and proposed HMC method in one-dimensional cases. Based on this connection,...
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Article
Open AccessCancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin
Cancers of unknown primary (CUPs) constitute ~5% of all cancers. The tumors have an aggressive biological and clinical behavior. The aim of the present study has been to uncover whether CUPs exhibit distinct m...
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Article
Open AccessAn integrated transcriptome and expressed variant analysis of sepsis survival and death
Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor o...
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Article
Open AccessA flexible statistical model for alignment of label-free proteomics data - incorporating ion mobility and product ion information
The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, ...
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Chapter and Conference Paper
Probabilistic Kernel Principal Component Analysis Through Time
This paper introduces a temporal version of Probabilistic Kernel Principal Component Analysis by using a hidden Markov model in order to obtain optimized representations of observed data through time. Recently...
