Wei Chen

Work

University of Pittsburgh

US

Education

University of Michigan

United States of America
PhD

Publications

TV-LSTM: Multimodal Deep Learning for Predicting the Progression of Late Age-Related Macular Degeneration Using Longitudinal Fundus Images and Genetic Data

AI Sensors

journal-article

TV-LSTM: Multimodal Deep Learning for Predicting the Progression of Late Age-Related Macular Degeneration Using Longitudinal Fundus Images and Genetic Data

AI Sensors

journal-article

Enhancing privacy in biosecurity with watermarked protein design

Bioinformatics

journal-article

Fast and scalable Wasserstein-1 neural optimal transport solver for single-cell perturbation prediction

Bioinformatics

journal-article

Exposure to Violence and Asthma Endotypes in Puerto Rican Youth

Annals of the American Thoracic Society

journal-article

From Splicing Landscape to Therapeutic Targets: Long-Read Sequencing in Non-Small-Cell Lung Cancer

American Journal of Respiratory Cell and Molecular Biology

journal-article

Long-Term PM2.5 Exposure and Upregulation of CLCA1 Expression in Nasal Epithelium from Youth with Asthma

Annals of the American Thoracic Society

journal-article

Sociocultural Stressors and Asthma among Adults in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

Annals of the American Thoracic Society

journal-article

tdCoxSNN: Time-dependent Cox survival neural network for continuous-time dynamic prediction

Journal of the Royal Statistical Society Series C: Applied Statistics

journal-article

Nasal epithelium transcriptomics predict clinical response to elexacaftor/tezacaftor/ivacaftor

Am. J. Respir. Cell Mol. Biol.

journal-article

Spatial microniches of IL-2 combine with IL-10 to drive lung migratory TH2 cells in response to inhaled allergen

Nat. Immunol.

journal-article

Spatial transcriptomics identifies cellular and molecular characteristics of Scleroderma skin lesions: Pilot study in juvenile Scleroderma

Int. J. Mol. Sci.

journal-article

A unified model-based framework for doublet or multiplet detection in single-cell multiomics data

Nat. Commun.

journal-article

Long-term PM2.5 exposure and upregulation of CLCA1 expression in nasal epithelium from youth with asthma

Ann. Am. Thorac. Soc.

journal-article

A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis

Cell Rep.

journal-article

Identification of a distal enhancer regulating hedgehog interacting protein gene in human lung epithelial cells

EBioMedicine

journal-article

Omics approaches in asthma research: Challenges and opportunities

Chin Med J Pulm Crit Care Med

journal-article

Mapping a new course to understand lung biology mechanisms: LungMAP.Net

Am. J. Respir. Cell Mol. Biol.

journal-article

Innovative super-resolution in spatial transcriptomics: a transformer model exploiting histology images and spatial gene expression

Brief. Bioinform.

journal-article

Nasal epithelial gene expression and total IgE in children and adolescents with asthma

J. Allergy Clin. Immunol.

journal-article

Adverse events during adulthood, child maltreatment, and asthma among British adults in the UK Biobank

Ann. Am. Thorac. Soc.

journal-article

Methyl-TWAS: A powerful method for in silico transcriptome-wide association studies (TWAS) using long-range DNA methylation

bioRxivorg

other

Cis- and trans-eQTM analysis reveals novel epigenetic and transcriptomic immune markers of atopic asthma in airway epithelium

J. Allergy Clin. Immunol.

journal-article

Exposure to violence and asthma in Puerto Rican youth with high Th2 immunity

Pediatr. Pulmonol.

journal-article

Predicting late-stage age-related macular degeneration by integrating marginally weak SNPs in GWA studies

Front. Genet.

journal-article

Heterotypic Influenza Infections Mitigate Susceptibility to Secondary Bacterial Infection

The Journal of Immunology

journal-article

Multimodal genotype and phenotype data integration to improve partial data-based longitudinal prediction

J. Comput. Biol.

journal-article

Nasal DNA methylation at three CpG sites predicts childhood allergic disease

Nat. Commun.

journal-article

Child maltreatment, anxiety and depression, and asthma among British adults in the UK Biobank

Eur. Respir. J.

journal-article

Integrative analysis of spatial transcriptome with single-cell transcriptome and single-cell epigenome in mouse lungs after immunization

iScience

journal-article

SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics

PNAS Nexus

journal-article

Heterotypic influenza infections mitigate susceptibility to secondary bacterial infection

J. Immunol.

journal-article

Longitudinal analysis of transcriptomic subtypes in trauma patients

Shock

journal-article

Comprehensive benchmarking of CITE-seq versus DOGMA-seq single cell multimodal omics

Genome Biol.

journal-article

Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution

Bioinformatics

journal-article

Differential gene expression in nasal airway epithelium from overweight or obese youth with asthma

Pediatr. Allergy Immunol.

journal-article

Metabolomic associations of asthma in the Hispanic community health study/study of Latinos

Metabolites

journal-article

A region-based method for causal mediation analysis of DNA methylation data

Epigenetics

journal-article

LONGL-Net: temporal correlation structure guided deep learning model to predict longitudinal age-related macular degeneration severity

PNAS Nexus

journal-article

The independent prognostic value of global epigenetic alterations: An analysis of single-cell ATAC-seq of circulating leukocytes from trauma patients followed by validation in whole blood leukocyte transcriptomes across three etiologies of critical illness

EBioMedicine

journal-article

Controlling batch effect in epigenome-wide association study

Methods Mol. Biol.

journal-article

DNA methylation and atopic diseases

Methods Mol. Biol.

journal-article

High-dimensional profiling clusters asthma severity by lymphoid and non-lymphoid status

Cell Rep.

journal-article

CHIT: an allele-specific method for testing the association between molecular quantitative traits and phenotype-genotype interaction

Bioinformatics

journal-article

Identification and inference for subgroups with differential treatment efficacy from randomized controlled trials with survival outcomes through multiple testing

Stat. Med.

journal-article

Transcriptomic evaluation of juvenile localized Scleroderma skin with histologic and clinical correlation

Arthritis Rheumatol.

journal-article

Exposure to violence, chronic stress, nasal DNA methylation, and atopic asthma in children

Pediatr. Pulmonol.

journal-article

Myofibroblast transcriptome indicates SFRP2hi fibroblast progenitors in systemic sclerosis skin

Nat. Commun.

journal-article

Genetic signatures from RNA sequencing of pediatric localized Scleroderma skin

Front. Pediatr.

journal-article

A genome-wide study of DNA methylation in white blood cells and asthma in Latino children and youth

Epigenetics

journal-article

Deep large-scale multitask learning network for gene expression inference

J. Comput. Biol.

journal-article

A genome-wide association study of severe asthma exacerbations in Latino children and adolescents

Eur. Respir. J.

journal-article

A genome-wide association study of asthma hospitalizations in adults

J. Allergy Clin. Immunol.

journal-article

Identification of an intraocular microbiota

Cell Discov.

journal-article

Serum insulin-like growth factor-1, asthma, and lung function among British adults

Ann. Allergy Asthma Immunol.

journal-article

Genome-wide association studies-based machine learning for prediction of age-related macular degeneration risk

Transl. Vis. Sci. Technol.

journal-article

A road map from single-cell transcriptome to patient classification for the immune response to trauma

JCI Insight

journal-article

AMD genetics: Methods and analyses for association, progression, and prediction

Adv. Exp. Med. Biol.

journal-article

Gene-based association testing of dichotomous traits with generalized functional linear mixed models using extended pedigrees: Applications to age-related macular degeneration

J. Am. Stat. Assoc.

journal-article

A novel whole blood gene expression signature for asthma, dermatitis, and rhinitis multimorbidity in children and adolescents

Allergy

journal-article

Genome-wide association study-based deep learning for survival prediction

Stat. Med.

journal-article

Exposure to violence, chronic stress, nasal DNA methylation, and atopic asthma in children

medRxiv

journal-article

Expression quantitative trait methylation analysis reveals methylomic associations with gene expression in childhood asthma

Chest

journal-article

Glycated hemoglobin A1c, lung function, and hospitalizations among adults with asthma

J. Allergy Clin. Immunol. Pract.

journal-article

Single-cell transcriptome conservation in a comparative analysis of fresh and cryopreserved human skin tissue: pilot in localized scleroderma

Arthritis Res. Ther.

journal-article

Biliary-atresia-associated Mannosidase-1-alpha-2 gene regulates biliary and ciliary morphogenesis and laterality

Front. Physiol.

journal-article

Serum free testosterone and asthma, asthma hospitalisations and lung function in British adults

Thorax

journal-article

Transcriptome-wide and differential expression network analyses of childhood asthma in nasal epithelium

J. Allergy Clin. Immunol.

journal-article

Artificial-cell-type aware cell-type classification in CITE-seq

Bioinformatics

journal-article

GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing

Genome Biol.

journal-article

Single cell RNA sequencing identifies an early monocyte gene signature in acute respiratory distress syndrome

JCI Insight

journal-article

BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data

Nucleic Acids Res.

journal-article

Gene-based association analysis for bivariate time-to-event data through functional regression with copula models

Biometrics

journal-article

Nasal DNA methylation profiling of asthma and rhinitis

J. Allergy Clin. Immunol.

journal-article

PIRs mediate innate myeloid cell memory to nonself MHC molecules

Science

journal-article

SNPs identified by GWAS affect asthma risk through DNA methylation and expression of cis-genes in airway epithelium

Eur. Respir. J.

journal-article

CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples

Bioinformatics

journal-article

Rapid reconstitution of regulatory T-cell subsets is associated with reduced rates of acute graft-versus-host disease and absence of viremia after cord blood transplantation in children with reduced-intensity conditioning using alemtuzumab

Cytotherapy

journal-article

Immune landscape of viral- and carcinogen-driven head and neck cancer

Immunity

journal-article

Deep-learning-based prediction of late age-related macular degeneration progression

Nat. Mach. Intell.

journal-article

Treg cells promote the SREBP1-dependent metabolic fitness of tumor-promoting macrophages via repression of CD8+ T cell-derived interferon-$γ$

Immunity

journal-article

Serum cadmium and lead, current wheeze, and lung function in a nationwide study of adults in the United States

J. Allergy Clin. Immunol. Pract.

journal-article

Transcriptomic responses to ivacaftor and prediction of ivacaftor clinical responsiveness

Am. J. Respir. Cell Mol. Biol.

journal-article

Clinical utility of ultrahigh fractional exhaled nitric oxide in predicting bronchial hyperresponsiveness in patients with suspected asthma

Postgrad. Med. J.

journal-article

Sleep duration, current asthma, and lung function in a nationwide study of U.s. adults

Am. J. Respir. Crit. Care Med.

journal-article

Epigenome-wide effects of vitamin D on asthma bronchial epithelial cells

Epigenetics

journal-article

Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis

Eur. Respir. J.

journal-article

Copula-based score test for bivariate time-to-event data, with application to a genetic study of AMD progression

Lifetime Data Anal.

journal-article

Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers

BMC Cancer

journal-article

Adaptive plasticity of IL-10+ and IL-35+ Treg cells cooperatively promotes tumor T cell exhaustion

Nat. Immunol.

journal-article

An integrative association method for omics data based on a modified Fisher's method with application to childhood asthma

PLoS Genet.

journal-article

Transcriptomics of atopy and atopic asthma in white blood cells from children and adolescents

Eur. Respir. J.

journal-article

A Bayesian mixture model for clustering droplet-based single-cell transcriptomic data from population studies

Nat. Commun.

journal-article

DNA methylation in nasal epithelium, atopy, and atopic asthma in children: a genome-wide study

Lancet Respir. Med.

journal-article

Under-diagnosis of atopic dermatitis in Puerto Rican children

World Allergy Organ. J.

journal-article

Pancreatic gene expression during recovery after pancreatitis reveals unique transcriptome profiles

Sci. Rep.

journal-article

Bayesian integrative model for multi-omics data with missingness

Bioinformatics

journal-article

A semiparametric imputation approach for regression with censored covariate with application to an AMD progression study

Stat. Med.

journal-article

Statistics for X-chromosome associations

Genet. Epidemiol.

journal-article

SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks

PLoS Comput. Biol.

journal-article

A genome-wide association Study in Hispanics/Latinos identifies novel signals for lung function. The Hispanic Community Health Study/Study of Latinos

Am. J. Respir. Crit. Care Med.

journal-article

KMgene: a unified R package for gene-based association analysis for complex traits

Bioinformatics

journal-article

SFRP2/DPP4 and FMO1/LSP1 define major fibroblast populations in human skin

J. Invest. Dermatol.

journal-article

Genome-wide analysis of disease progression in age-related macular degeneration

Hum. Mol. Genet.

journal-article

Association of IGFN1 variant with polypoidal choroidal vasculopathy

J. Gene Med.

journal-article

DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data

Bioinformatics

journal-article

Bivariate analysis of age-related macular degeneration progression using genetic risk scores

Genetics

journal-article

The influence of age and sex on ocular surface Microbiota in healthy adults

Invest. Ophthalmol. Vis. Sci.

journal-article

A multiomics approach to identify genes associated with childhood asthma risk and morbidity

Am. J. Respir. Cell Mol. Biol.

journal-article

Genome-wide interaction study of dust mite allergen on lung function in children with asthma

J. Allergy Clin. Immunol.

journal-article

LAIT: a local ancestry inference toolkit

BMC Genet.

journal-article

An epigenome-wide association study of total serum IgE in Hispanic children

J. Allergy Clin. Immunol.

journal-article

AIM2 inflammasome is critical for influenza-induced lung injury and mortality

J. Immunol.

journal-article

A meta-analysis of genome-wide association studies of asthma in Puerto Ricans

Eur. Respir. J.

journal-article

Meta-analysis of quantitative pleiotropic traits for next-generation sequencing with multivariate functional linear models

Eur. J. Hum. Genet.

journal-article

Meta-analysis of complex diseases at gene level with generalized functional linear models

Genetics

journal-article

IL-17 receptor signaling in the lung epithelium is required for mucosal chemokine gradients and pulmonary host defense against K. pneumoniae

Cell Host Microbe

journal-article

Antiinflammatory effects of bromodomain and extraterminal domain inhibition in cystic fibrosis lung inflammation

JCI Insight

journal-article

The impact of genotype calling errors on family-based studies

Sci. Rep.

journal-article

CXXC finger protein 1 is critical for T-cell intrathymic development through regulating H3K4 trimethylation

Nat. Commun.

journal-article

Control for population structure and relatedness for binary traits in genetic association studies via logistic mixed models

Am. J. Hum. Genet.

journal-article

A pipeline for classifying relationships using dense SNP/SNV data and putative pedigree information

Genet. Epidemiol.

journal-article

FastGGM: An efficient algorithm for the inference of Gaussian graphical model in biological networks

PLoS Comput. Biol.

journal-article

Gene-based association analysis for censored traits via fixed effect functional regressions

Genet. Epidemiol.

journal-article

Imputation of missing covariate values in epigenome-wide analysis of DNA methylation data

Epigenetics

journal-article

A computational method for genotype calling in family-based sequencing data

BMC Bioinformatics

journal-article

A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis

Bioinformatics

journal-article

Associating multivariate quantitative phenotypes with genetic variants in family samples with a novel kernel machine regression method

Genetics

journal-article

A global reference for human genetic variation

Nature

journal-article

A genome-wide association study of post-bronchodilator lung function in children with asthma

Am. J. Respir. Crit. Care Med.

journal-article

DISSCO: direct imputation of summary statistics allowing covariates

Bioinformatics

journal-article

Gene level meta-analysis of quantitative traits by functional linear models

Genetics

journal-article

RNA-seq in pulmonary medicine: How much is enough?

Am. J. Respir. Crit. Care Med.

journal-article

Leveraging identity-by-descent for accurate genotype inference in family sequencing data

PLoS Genet.

journal-article

A Bayesian framework for de novo mutation calling in parents-offspring trios

Bioinformatics

journal-article

A genome-wide association study of chronic obstructive pulmonary disease in Hispanics

Ann. Am. Thorac. Soc.

journal-article

Expression quantitative trait loci (eQTL) mapping in Puerto Rican children

PLoS One

journal-article

A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data

Epigenetics

journal-article

Rare-variant kernel machine test for longitudinal data from population and family samples

Hum. Hered.

journal-article

Translation of pre-clinical studies into successful clinical trials for Alzheimer's disease: What are the roadblocks and how can they be overcome?

J. Alzheimers. Dis.

journal-article

Stress and bronchodilator response in children with asthma

Am. J. Respir. Crit. Care Med.

journal-article

Using current data to define new approach in age related macular degeneration: need to accelerate translational research

Curr. Genomics

journal-article

Genome-wide association study and meta-analysis of intraocular pressure

Hum. Genet.

journal-article

Native American ancestry, lung function, and COPD in Costa Ricans

Chest

journal-article

Genotype calling and haplotyping in parent-offspring trios

Genome Res.

journal-article

Single nucleotide polymorphism (SNP) detection and genotype calling from massively parallel sequencing (MPS) data

Stat. Biosci.

journal-article

Seven new loci associated with age-related macular degeneration

Nat. Genet.

journal-article

ADCYAP1R1 and asthma in Puerto Rican children

Am. J. Respir. Crit. Care Med.

journal-article

Association between CFH Y402H polymorphism and age related macular degeneration in North Indian cohort

PLoS One

journal-article

A likelihood-based framework for variant calling and de novo mutation detection in families

PLoS Genet.

journal-article

The 1000 Genomes Project: data management and community access

Nat. Methods

journal-article

Mapping copy number variation by population-scale genome sequencing

Nature

journal-article

Oncological outcome of T1 rectal cancer undergoing standard resection and local excision

Colorectal Dis.

journal-article

Prognostic analysis for carcinoid tumours of the rectum: a single institutional analysis of 106 patients

Colorectal Dis.

journal-article

Variation in genome-wide mutation rates within and between human families

Nat. Genet.

journal-article

Evidence of association of APOE with age-related macular degeneration: a pooled analysis of 15 studies

Hum. Mutat.

journal-article

Complement factor D in age-related macular degeneration

Invest. Ophthalmol. Vis. Sci.

journal-article

A 32 kb critical region excluding Y402H in CFH mediates risk for age-related macular degeneration

PLoS One

journal-article

The functional spectrum of low-frequency coding variation

Genome Biol.

journal-article

The variant call format and VCFtools

Bioinformatics

journal-article

Demographic history and rare allele sharing among human populations

Proc. Natl. Acad. Sci. U. S. A.

journal-article

EZH2 and ALDH-1 mark breast epithelium at risk for breast cancer development

Mod. Pathol.

journal-article

Variations in apolipoprotein E frequency with age in a pooled analysis of a large group of older people

Am. J. Epidemiol.

journal-article

Long-term outcome of early-stage rectal cancer undergoing standard resection and local excision

Clin. Colorectal Cancer

journal-article

Age-related macular degeneration-associated variants at chromosome 10q26 do not significantly alter ARMS2 and HTRA1 transcript levels in the human retina

Mol. Vis.

journal-article

Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration

Proc. Natl. Acad. Sci. U. S. A.

journal-article

Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals

Am. J. Hum. Genet.

journal-article

Integration of genetic signature and TNM staging system for predicting the relapse of locally advanced colorectal cancer

Int. J. Colorectal Dis.

journal-article

Diversity of human copy number variation and multicopy genes

Science

journal-article

A map of human genome variation from population-scale sequencing

Nature

journal-article

E2-2 protein and Fuchs's corneal dystrophy

N. Engl. J. Med.

journal-article

GWAS GUI: graphical browser for the results of whole-genome association studies with high-dimensional phenotypes

Bioinformatics

journal-article

A genome-wide association study of global gene expression

Nat. Genet.

journal-article

A variant of mitochondrial protein LOC387715/ARMS2, not HTRA1, is strongly associated with age-related macular degeneration

Proc. Natl. Acad. Sci. U. S. A.

journal-article

Genetic susceptibility to age-related macular degeneration: a paradigm for dissecting complex disease traits

Hum. Mol. Genet.

journal-article