Yi‐Hui Zhou
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View article: Detecting Algorithmic Bias in ICU Clinical Decision: A Doubly-Robust Framework for Auditing Treatment Recommendation Disparities
Detecting Algorithmic Bias in ICU Clinical Decision: A Doubly-Robust Framework for Auditing Treatment Recommendation Disparities Open
Clinical decision support systems increasingly guide ICU care, but may perpetu-ate or amplify existing healthcare disparities. We develop a doubly-robust statistical framework for detecting and quantifying algorithmic bias in ICU treatment…
View article: Visualization of robust L1PCA
Visualization of robust L1PCA Open
Robust principal components are particularly challenging to find for high‐dimensional data sets, including genomic data. Conventional principal component analysis is often unduly influenced by a few closely related family members. This phe…
View article: Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients.
Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients. Open
Rationale: Lung disease is the major cause of morbidity and mortality in persons with cystic fibrosis (pwCF). Variability in CF lung disease has substantial non-CFTR (CF transmembrane conductance regulator) genetic influen…
View article: Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis
Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis Open
View article: Leveraging TOPMed imputation server and constructing a cohort-specific imputation reference panel to enhance genotype imputation among cystic fibrosis patients
Leveraging TOPMed imputation server and constructing a cohort-specific imputation reference panel to enhance genotype imputation among cystic fibrosis patients Open
View article: Organophosphate Flame Retardants Disrupt Autism-Relevant Gene Networks Across Development: A Cross-Species Multi-Omics Study
Organophosphate Flame Retardants Disrupt Autism-Relevant Gene Networks Across Development: A Cross-Species Multi-Omics Study Open
Organophosphate flame retardants (OPFRs) are widely used environmental contaminants with suspected developmental neurotoxicity, yet their stage-specific molecular impacts and potential relevance to autism spectrum disorder (ASD) remain poo…
View article: Inducible genome-wide mutagenesis for improvement of pDNA production by E. coli
Inducible genome-wide mutagenesis for improvement of pDNA production by E. coli Open
View article: Inducible genome-wide mutagenesis for improvement of pDNA production by <i>E. coli</i>
Inducible genome-wide mutagenesis for improvement of pDNA production by <i>E. coli</i> Open
Plasmid DNA (pDNA) is a cost-driving reagent for the production of gene therapies and DNA vaccines. Improving pDNA production in the most common production host ( E. coli ) has faced obstacles arising from the complex network of genes resp…
View article: HAP-SAMPLE2: data-based resampling for association studies with admixture
HAP-SAMPLE2: data-based resampling for association studies with admixture Open
Motivation HAP-SAMPLE2 extends the functionality of the original HAP-SAMPLE tool for simulating genotype-phenotype data, now with features to handle population admixture and rare variant analysis. It allows users to define parameters such …
View article: An approach to uncover significant direct and mediated relationships in multi-dimensional new approach methods (NAMs) data: A case study of hazard evaluation of petroleum UVCBs
An approach to uncover significant direct and mediated relationships in multi-dimensional new approach methods (NAMs) data: A case study of hazard evaluation of petroleum UVCBs Open
New Approach Methods (NAMs) encompass a wide range of data types; it is increasingly common to have highly multi-dimensional data (e.g., cellular, molecular and gene expression effects) on the same chemicals. In addition, chemical structur…
View article: Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits
Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits Open
Understanding the molecular mechanisms of complex traits is essential for developing targeted interventions. We analyzed liver expression quantitative-trait locus (eQTL) meta-analysis data on 1,183 participants to identify conditionally di…
View article: <i>CHP2</i> Modifies Chronic <i>Pseudomonas aeruginosa</i> Airway Infection Risk in Cystic Fibrosis
<i>CHP2</i> Modifies Chronic <i>Pseudomonas aeruginosa</i> Airway Infection Risk in Cystic Fibrosis Open
Rationale: Chronic Pseudomonas aeruginosa (Pa) airway infection is common and a key contributor to diminished lung function and early mortality in persons with cystic fibrosis (PwCF). Risk factors for chronic Pa…
View article: Control of false discoveries in grouped hypothesis testing for eQTL data
Control of false discoveries in grouped hypothesis testing for eQTL data Open
View article: Characterizing PFAS hazards and risks: a human population-based in vitro cardiotoxicity assessment strategy
Characterizing PFAS hazards and risks: a human population-based in vitro cardiotoxicity assessment strategy Open
Per- and poly-fluoroalkyl substances (PFAS) are emerging contaminants of concern because of their wide use, persistence, and potential to be hazardous to both humans and the environment. Several PFAS have been designated as substances of c…
View article: Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits
Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits Open
View article: Estimation of cis-eQTL Effect Sizes Using a Log of Linear Model
Estimation of cis-eQTL Effect Sizes Using a Log of Linear Model Open
The study of expression Quantitative Trait Loci (eQTL) is an important problem in genomics and biomedicine. While detection (testing) of eQTL associations has been widely studied, less work has been devoted to the estimation of eQTL effect…
View article: Predicting Microbiome Growth Dynamics under Environmental Perturbations
Predicting Microbiome Growth Dynamics under Environmental Perturbations Open
MicroGrowthPredictor is a model that leverages Long Short-Term Memory (LSTM) networks to predict dynamic changes in microbiome growth in response to varying environmental perturbations. In this article, we present the innovative capabiliti…
View article: Control of false discoveries in grouped hypothesis testing for eQTL data
Control of false discoveries in grouped hypothesis testing for eQTL data Open
View article: Hazard and risk characterization of 56 structurally diverse PFAS using a targeted battery of broad coverage assays using six human cell types
Hazard and risk characterization of 56 structurally diverse PFAS using a targeted battery of broad coverage assays using six human cell types Open
View article: AI in healthcare: navigating opportunities and challenges in digital communication
AI in healthcare: navigating opportunities and challenges in digital communication Open
The landscape of healthcare communication is undergoing a profound transformation in the digital age, and at the heart of this evolution are AI-powered chatbots. This mini-review delves into the role of AI chatbots in digital health, provi…
View article: Integrative Chemical–Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams
Integrative Chemical–Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams Open
Human cell-based test methods can be used to evaluate potential hazards of mixtures and products of petroleum refining (“unknown or variable composition, complex reaction products, or biological materials” substances, UVCBs). Analyses of b…
View article: Integrative Chemical–Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams
Integrative Chemical–Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams Open
Human cell-based test methods can be used to evaluate potential hazards of mixtures and products of petroleum refining (“unknown or variable composition, complex reaction products, or biological materials” substances, UVCBs). Analyses of b…
View article: Simultaneous modeling of multivariate heterogeneous responses and heteroskedasticity via a two‐stage composite likelihood
Simultaneous modeling of multivariate heterogeneous responses and heteroskedasticity via a two‐stage composite likelihood Open
Multivariate heterogeneous responses and heteroskedasticity have attracted increasing attention in recent years. In genome‐wide association studies, effective simultaneous modeling of multiple phenotypes would improve statistical power and…
View article: Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients
Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients Open
Rationale: Lung disease is the major cause of morbidity and mortality in persons with cystic fibrosis (pwCF). Variability in CF lung disease has substantial non-CFTR (CF transmembrane conductance regulator) genetic influence. Identi…
View article: Leveraging Scheme for Cross-Study Microbiome Machine Learning Prediction and Feature Evaluations
Leveraging Scheme for Cross-Study Microbiome Machine Learning Prediction and Feature Evaluations Open
The microbiota has proved to be one of the critical factors for many diseases, and researchers have been using microbiome data for disease prediction. However, models trained on one independent microbiome study may not be easily applicable…
View article: A Double Penalty Model for Ensemble Learning
A Double Penalty Model for Ensemble Learning Open
Modern statistical learning techniques often include learning ensembles, for which the combination of multiple separate prediction procedures (ensemble components) can improve prediction accuracy. Although ensemble approaches are widely us…
View article: C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data
C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data Open
View article: MagicalRsq: Machine-learning-based genotype imputation quality calibration
MagicalRsq: Machine-learning-based genotype imputation quality calibration Open
Whole-genome sequencing (WGS) is the gold standard for fully characterizing genetic variation but is still prohibitively expensive for large samples. To reduce costs, many studies sequence only a subset of individuals or genomic regions, a…
View article: Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis
Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis Open
View article: A resource for integrated genomic analysis of the human liver
A resource for integrated genomic analysis of the human liver Open