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

Published by

AI Sensors

Summary

journal-article

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

Published by

AI Sensors

Summary

journal-article

Enhancing privacy in biosecurity with watermarked protein design

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Bioinformatics

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

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Bioinformatics

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Exposure to Violence and Asthma Endotypes in Puerto Rican Youth

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Annals of the American Thoracic Society

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

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American Journal of Respiratory Cell and Molecular Biology

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

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Annals of the American Thoracic Society

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

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Annals of the American Thoracic Society

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

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Journal of the Royal Statistical Society Series C: Applied Statistics

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

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Am. J. Respir. Cell Mol. Biol.

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

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Nat. Immunol.

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

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Int. J. Mol. Sci.

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

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Nat. Commun.

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

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Ann. Am. Thorac. Soc.

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

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Cell Rep.

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

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EBioMedicine

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Omics approaches in asthma research: Challenges and opportunities

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Chin Med J Pulm Crit Care Med

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

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Am. J. Respir. Cell Mol. Biol.

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journal-article

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

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Brief. Bioinform.

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

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J. Allergy Clin. Immunol.

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

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Ann. Am. Thorac. Soc.

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

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bioRxivorg

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other

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

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J. Allergy Clin. Immunol.

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

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Pediatr. Pulmonol.

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

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Front. Genet.

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Heterotypic Influenza Infections Mitigate Susceptibility to Secondary Bacterial Infection

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The Journal of Immunology

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

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J. Comput. Biol.

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Nasal DNA methylation at three CpG sites predicts childhood allergic disease

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Nat. Commun.

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

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Eur. Respir. J.

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

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iScience

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

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PNAS Nexus

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Heterotypic influenza infections mitigate susceptibility to secondary bacterial infection

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J. Immunol.

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Longitudinal analysis of transcriptomic subtypes in trauma patients

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Shock

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journal-article

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

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Genome Biol.

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

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Bioinformatics

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

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Pediatr. Allergy Immunol.

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journal-article

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

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Metabolites

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journal-article

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

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Epigenetics

Summary

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

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PNAS Nexus

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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

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EBioMedicine

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Controlling batch effect in epigenome-wide association study

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Methods Mol. Biol.

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journal-article

DNA methylation and atopic diseases

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Methods Mol. Biol.

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

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Cell Rep.

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

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Bioinformatics

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

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Stat. Med.

Summary

journal-article

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

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Arthritis Rheumatol.

Summary

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

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Pediatr. Pulmonol.

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journal-article

Myofibroblast transcriptome indicates SFRP2hi fibroblast progenitors in systemic sclerosis skin

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Nat. Commun.

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journal-article

Genetic signatures from RNA sequencing of pediatric localized Scleroderma skin

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Front. Pediatr.

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journal-article

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

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Epigenetics

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Deep large-scale multitask learning network for gene expression inference

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J. Comput. Biol.

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

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Eur. Respir. J.

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A genome-wide association study of asthma hospitalizations in adults

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J. Allergy Clin. Immunol.

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Identification of an intraocular microbiota

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Cell Discov.

Summary

journal-article

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

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Ann. Allergy Asthma Immunol.

Summary

journal-article

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

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Transl. Vis. Sci. Technol.

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journal-article

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

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JCI Insight

Summary

journal-article

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

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Adv. Exp. Med. Biol.

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journal-article

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

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J. Am. Stat. Assoc.

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

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Allergy

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journal-article

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

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Stat. Med.

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journal-article

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

Published by

medRxiv

Summary

journal-article

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

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Chest

Summary

journal-article

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

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J. Allergy Clin. Immunol. Pract.

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journal-article

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

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Arthritis Res. Ther.

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journal-article

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

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Front. Physiol.

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journal-article

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

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Thorax

Summary

journal-article

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

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J. Allergy Clin. Immunol.

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journal-article

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

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Bioinformatics

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

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Genome Biol.

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journal-article

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

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JCI Insight

Summary

journal-article

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

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Nucleic Acids Res.

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journal-article

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

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Biometrics

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journal-article

Nasal DNA methylation profiling of asthma and rhinitis

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J. Allergy Clin. Immunol.

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journal-article

PIRs mediate innate myeloid cell memory to nonself MHC molecules

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Science

Summary

journal-article

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

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Eur. Respir. J.

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journal-article

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

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Bioinformatics

Summary

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

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Cytotherapy

Summary

journal-article

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

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Immunity

Summary

journal-article

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

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Nat. Mach. Intell.

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journal-article

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

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Immunity

Summary

journal-article

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

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J. Allergy Clin. Immunol. Pract.

Summary

journal-article

Transcriptomic responses to ivacaftor and prediction of ivacaftor clinical responsiveness

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Am. J. Respir. Cell Mol. Biol.

Summary

journal-article

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

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Postgrad. Med. J.

Summary

journal-article

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

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Am. J. Respir. Crit. Care Med.

Summary

journal-article

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

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Epigenetics

Summary

journal-article

Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis

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Eur. Respir. J.

Summary

journal-article

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

Published by

Lifetime Data Anal.

Summary

journal-article

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

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BMC Cancer

Summary

journal-article

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

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Nat. Immunol.

Summary

journal-article

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

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PLoS Genet.

Summary

journal-article

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

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Eur. Respir. J.

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journal-article

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

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Nat. Commun.

Summary

journal-article

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

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Lancet Respir. Med.

Summary

journal-article

Under-diagnosis of atopic dermatitis in Puerto Rican children

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World Allergy Organ. J.

Summary

journal-article

Pancreatic gene expression during recovery after pancreatitis reveals unique transcriptome profiles

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Sci. Rep.

Summary

journal-article

Bayesian integrative model for multi-omics data with missingness

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Bioinformatics

Summary

journal-article

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

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Stat. Med.

Summary

journal-article

Statistics for X-chromosome associations

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Genet. Epidemiol.

Summary

journal-article

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

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PLoS Comput. Biol.

Summary

journal-article

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

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Am. J. Respir. Crit. Care Med.

Summary

journal-article

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

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Bioinformatics

Summary

journal-article

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

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J. Invest. Dermatol.

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journal-article

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

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Hum. Mol. Genet.

Summary

journal-article

Association of IGFN1 variant with polypoidal choroidal vasculopathy

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J. Gene Med.

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journal-article

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

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Bioinformatics

Summary

journal-article

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

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Genetics

Summary

journal-article

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

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Invest. Ophthalmol. Vis. Sci.

Summary

journal-article

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

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Am. J. Respir. Cell Mol. Biol.

Summary

journal-article

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

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J. Allergy Clin. Immunol.

Summary

journal-article

LAIT: a local ancestry inference toolkit

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BMC Genet.

Summary

journal-article

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

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J. Allergy Clin. Immunol.

Summary

journal-article

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

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J. Immunol.

Summary

journal-article

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

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Eur. Respir. J.

Summary

journal-article

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

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Eur. J. Hum. Genet.

Summary

journal-article

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

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Genetics

Summary

journal-article

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

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Cell Host Microbe

Summary

journal-article

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

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JCI Insight

Summary

journal-article

The impact of genotype calling errors on family-based studies

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Sci. Rep.

Summary

journal-article

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

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Nat. Commun.

Summary

journal-article

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

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Am. J. Hum. Genet.

Summary

journal-article

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

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Genet. Epidemiol.

Summary

journal-article

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

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PLoS Comput. Biol.

Summary

journal-article

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

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Genet. Epidemiol.

Summary

journal-article

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

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Epigenetics

Summary

journal-article

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

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BMC Bioinformatics

Summary

journal-article

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

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Bioinformatics

Summary

journal-article

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

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Genetics

Summary

journal-article

A global reference for human genetic variation

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Nature

Summary

journal-article

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

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Am. J. Respir. Crit. Care Med.

Summary

journal-article

DISSCO: direct imputation of summary statistics allowing covariates

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Bioinformatics

Summary

journal-article

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

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Genetics

Summary

journal-article

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

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Am. J. Respir. Crit. Care Med.

Summary

journal-article

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

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PLoS Genet.

Summary

journal-article

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

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Bioinformatics

Summary

journal-article

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

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Ann. Am. Thorac. Soc.

Summary

journal-article

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

Published by

PLoS One

Summary

journal-article

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

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Epigenetics

Summary

journal-article

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

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Hum. Hered.

Summary

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?

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J. Alzheimers. Dis.

Summary

journal-article

Stress and bronchodilator response in children with asthma

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Am. J. Respir. Crit. Care Med.

Summary

journal-article

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

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Curr. Genomics

Summary

journal-article

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

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Hum. Genet.

Summary

journal-article

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

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Chest

Summary

journal-article

Genotype calling and haplotyping in parent-offspring trios

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Genome Res.

Summary

journal-article

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

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Stat. Biosci.

Summary

journal-article

Seven new loci associated with age-related macular degeneration

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Nat. Genet.

Summary

journal-article

ADCYAP1R1 and asthma in Puerto Rican children

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Am. J. Respir. Crit. Care Med.

Summary

journal-article

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

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PLoS One

Summary

journal-article

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

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PLoS Genet.

Summary

journal-article

The 1000 Genomes Project: data management and community access

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Nat. Methods

Summary

journal-article

Mapping copy number variation by population-scale genome sequencing

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Nature

Summary

journal-article

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

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Colorectal Dis.

Summary

journal-article

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

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Colorectal Dis.

Summary

journal-article

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

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Nat. Genet.

Summary

journal-article

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

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Hum. Mutat.

Summary

journal-article

Complement factor D in age-related macular degeneration

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Invest. Ophthalmol. Vis. Sci.

Summary

journal-article

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

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PLoS One

Summary

journal-article

The functional spectrum of low-frequency coding variation

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Genome Biol.

Summary

journal-article

The variant call format and VCFtools

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Bioinformatics

Summary

journal-article

Demographic history and rare allele sharing among human populations

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

Summary

journal-article

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

Published by

Mod. Pathol.

Summary

journal-article

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

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Am. J. Epidemiol.

Summary

journal-article

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

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Clin. Colorectal Cancer

Summary

journal-article

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

Published by

Mol. Vis.

Summary

journal-article

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

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

Summary

journal-article

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

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Am. J. Hum. Genet.

Summary

journal-article

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

Published by

Int. J. Colorectal Dis.

Summary

journal-article

Diversity of human copy number variation and multicopy genes

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Science

Summary

journal-article

A map of human genome variation from population-scale sequencing

Published by

Nature

Summary

journal-article

E2-2 protein and Fuchs's corneal dystrophy

Published by

N. Engl. J. Med.

Summary

journal-article

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

Published by

Bioinformatics

Summary

journal-article

A genome-wide association study of global gene expression

Published by

Nat. Genet.

Summary

journal-article

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

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

Summary

journal-article

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

Published by

Hum. Mol. Genet.

Summary

journal-article