Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations

[1]  R. Louis,et al.  Cytokine-targeted therapies for asthma and COPD , 2023, European Respiratory Review.

[2]  S. Pavlidis,et al.  CEACAM5 is an IL‐13‐regulated epithelial gene that mediates transcription in type‐2 (T2) high severe asthma , 2022, Allergy.

[3]  H. Hakonarson,et al.  Genome-wide association study in minority children with asthma implicates DNAH5 in bronchodilator responsiveness , 2022, Scientific Reports.

[4]  Matthew C. Altman,et al.  DNA methylation signatures in airway cells from adult children of asthmatic mothers reflect subtypes of severe asthma , 2022, Proceedings of the National Academy of Sciences of the United States of America.

[5]  C. Auffray,et al.  Clinical and transcriptomic features of persistent exacerbation‐prone severe asthma in U‐BIOPRED cohort , 2022, Clinical and translational medicine.

[6]  Yubiao Guo,et al.  Elevated CEACAM5 Levels in Patients with Asthma , 2022, International Archives of Allergy and Immunology.

[7]  Alicia R. Martin,et al.  Multi-ancestry meta-analysis of asthma identifies novel associations and highlights the value of increased power and diversity , 2021, medRxiv.

[8]  Ya-Na Cao,et al.  Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis , 2021, BMC Medical Genomics.

[9]  A. Dahlin,et al.  Novel genetic variants associated with inhaled corticosteroid treatment response in older adults with asthma , 2021, Thorax.

[10]  J. Celedón,et al.  Pharmacogenetic Polygenic Risk Score for Bronchodilator Response in Children and Adolescents with Asthma: Proof-of-Concept , 2021, Journal of personalized medicine.

[11]  Scott R. Presnell,et al.  Endotype of Allergic Asthma with Airway Obstruction in Urban Children. , 2021, The Journal of allergy and clinical immunology.

[12]  T. Guilbert,et al.  Use of the Composite Asthma Severity Index in a Pediatric Subspecialty Clinic. , 2021, Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology.

[13]  D. Nicolae,et al.  Altered transcriptional and chromatin responses to rhinovirus in bronchial epithelial cells from adults with asthma , 2020, Communications Biology.

[14]  T. Homma,et al.  Airway Epithelial Dysfunction in Asthma: Relevant to Epidermal Growth Factor Receptors and Airway Epithelial Cells , 2020, Journal of clinical medicine.

[15]  S. Sørensen,et al.  Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age. , 2020, The Journal of allergy and clinical immunology.

[16]  E. Eskin,et al.  Genome-wide analysis highlights contribution of immune system pathways to the genetic architecture of asthma , 2020, Nature Communications.

[17]  Ke Shi,et al.  Coordinated DNA Methylation and Gene Expression Data for Identification of the Critical Genes Associated with Childhood Atopic Asthma , 2020, J. Comput. Biol..

[18]  G. Pejler.  The emerging role of mast cell proteases in asthma , 2019, European Respiratory Journal.

[19]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[20]  Tamar Sofer,et al.  Genetic association testing using the GENESIS R/Bioconductor package , 2019, Bioinform..

[21]  Scott R. Presnell,et al.  Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children , 2019, Nature Immunology.

[22]  Zachary A. Szpiech,et al.  Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations , 2019, Nature Communications.

[23]  A. Iqbal,et al.  Racial Disparities in Asthma-Related Health Outcomes in Children with Severe/Difficult-to-Treat Asthma. , 2019, The journal of allergy and clinical immunology. In practice.

[24]  B. Modena,et al.  Dysfunctional ErbB2, an EGF receptor family member, hinders repair of airway epithelial cells from asthmatic patients. , 2019, The Journal of allergy and clinical immunology.

[25]  Gabrielle Deschamps-Francoeur,et al.  CoCo: RNA-seq read assignment correction for nested genes and multimapped reads , 2018, bioRxiv.

[26]  C. Ober,et al.  Lessons Learned From GWAS of Asthma , 2018, Allergy, asthma & immunology research.

[27]  Jan Gorodkin,et al.  Cytoscape stringApp: Network analysis and visualization of proteomics data , 2018, bioRxiv.

[28]  Chris McKennan,et al.  Estimating and Accounting for Unobserved Covariates in High-Dimensional Correlated Data , 2018, Journal of the American Statistical Association.

[29]  Ivana V. Yang,et al.  Meta-analysis of airway epithelium gene expression in asthma , 2018, European Respiratory Journal.

[30]  Manuel A. R. Ferreira,et al.  Multiancestry association study identifies new asthma risk loci that colocalize with immune cell enhancer marks , 2017, Nature Genetics.

[31]  Brent S. Pedersen,et al.  The nasal methylome and childhood atopic asthma , 2017, The Journal of allergy and clinical immunology.

[32]  Ivana V. Yang,et al.  The Nasal Methylome: A Key to Understanding Allergic Asthma. , 2017, American journal of respiratory and critical care medicine.

[33]  P. Gergen,et al.  Minimally important differences and risk levels for the Composite Asthma Severity Index. , 2017, The Journal of allergy and clinical immunology.

[34]  Zachary A. Szpiech,et al.  A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome , 2016, Nature Communications.

[35]  Jean-Philippe Fortin,et al.  Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi , 2016, bioRxiv.

[36]  E. Burchard,et al.  Assessing differences in inhaled corticosteroid response by self-reported race-ethnicity and genetic ancestry among asthmatic subjects. , 2016, The Journal of allergy and clinical immunology.

[37]  Sohini Ramachandran,et al.  pong: fast analysis and visualization of latent clusters in population genetic data , 2015, bioRxiv.

[38]  M. Kubo,et al.  Genome-wide association study of leukotriene modifier response in asthma , 2015, The Pharmacogenomics Journal.

[39]  D. Postma,et al.  ST13 polymorphisms and their effect on exacerbations in steroid‐treated asthmatic children and young adults , 2015, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[40]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[41]  Christopher R. Gignoux,et al.  Dissecting childhood asthma with nasal transcriptomics distinguishes subphenotypes of disease. , 2014, The Journal of allergy and clinical immunology.

[42]  Mario Castro,et al.  Effect of rare variants in ADRB2 on risk of severe exacerbations and symptom control during longacting β agonist treatment in a multiethnic asthma population: a genetic study. , 2014, The Lancet. Respiratory medicine.

[43]  Andreas Krämer,et al.  Causal analysis approaches in Ingenuity Pathway Analysis , 2013, Bioinform..

[44]  I. Rudan,et al.  An estimate of asthma prevalence in Africa: a systematic analysis , 2013, Croatian medical journal.

[45]  Ingo Ruczinski,et al.  African Ancestry is a Risk Factor for Asthma and High Total IgE Levels in African Admixed Populations , 2013, Genetic epidemiology.

[46]  F. Holsboer,et al.  Dexamethasone Stimulated Gene Expression in Peripheral Blood is a Sensitive Marker for Glucocorticoid Receptor Resistance in Depressed Patients , 2012, Neuropsychopharmacology.

[47]  John D. Storey,et al.  Bioinformatics Applications Note Gene Expression the Sva Package for Removing Batch Effects and Other Unwanted Variation in High-throughput Experiments , 2022 .

[48]  P. Gergen,et al.  Development and validation of the Composite Asthma Severity Index--an outcome measure for use in children and adolescents. , 2012, The Journal of allergy and clinical immunology.

[49]  Andrey A. Shabalin,et al.  Matrix eQTL: ultra fast eQTL analysis via large matrix operations , 2011, Bioinform..

[50]  Josyf Mychaleckyj,et al.  Robust relationship inference in genome-wide association studies , 2010, Bioinform..

[51]  K. Barnes.  Genomewide association studies in allergy and the influence of ethnicity , 2010, Current opinion in allergy and clinical immunology.

[52]  Leopold Parts,et al.  A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies , 2010, PLoS Comput. Biol..

[53]  R. Beyer,et al.  Decreased fibronectin production significantly contributes to dysregulated repair of asthmatic epithelium. , 2010, American journal of respiratory and critical care medicine.

[54]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[55]  Barmak Modrek,et al.  T-helper type 2-driven inflammation defines major subphenotypes of asthma. , 2009, American journal of respiratory and critical care medicine.

[56]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[57]  P. Harris,et al.  Research electronic data capture (REDCap) - A metadata-driven methodology and workflow process for providing translational research informatics support , 2009, J. Biomed. Informatics.

[58]  B. Aronow,et al.  Unique and overlapping gene expression patterns driven by IL-4 and IL-13 in the mouse lung. , 2009, The Journal of allergy and clinical immunology.

[59]  D. Boakye,et al.  Out of Africa: what can be learned from the studies of allergic disorders in Africa and Africans? , 2008, Current opinion in allergy and clinical immunology.

[60]  P. J. Barnes,et al.  Global strategy for asthma management and prevention: GINA executive summary , 2008, European Respiratory Journal.

[61]  R. Mei,et al.  A genomewide admixture mapping panel for Hispanic/Latino populations. , 2007, American journal of human genetics.

[62]  N. Pearce,et al.  Worldwide trends in the prevalence of asthma symptoms: phase III of the International Study of Asthma and Allergies in Childhood (ISAAC) , 2007, Thorax.

[63]  M. Kurrer,et al.  VSIG4, a B7 family-related protein, is a negative regulator of T cell activation. , 2006, The Journal of clinical investigation.

[64]  D. Leung,et al.  Racial differences in T-lymphocyte response to glucocorticoids. , 2005, Chest.

[65]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[66]  J. Smolen,et al.  Competing interests , 2003, Nature Biotechnology.

[67]  D. Hocking.  Fibronectin matrix deposition and cell contractility: implications for airway remodeling in asthma. , 2002, Chest.

[68]  THE WORLD HEALTH ORGANIZATION , 1954 .

[69]  E. Binder,et al.  Gene–Stress–Epigenetic Regulation of FKBP5: Clinical and Translational Implications , 2016, Neuropsychopharmacology.

[70]  J. Black,et al.  Differential deposition of fibronectin by asthmatic bronchial , 2015 .

[71]  D. Meyers,et al.  Pharmacogenetics: implications of race and ethnicity on defining genetic profiles for personalized medicine. , 2014, The Journal of allergy and clinical immunology.

[72]  Expert Panel Report 3 (EPR-3): Guidelines for the Diagnosis and Management of Asthma-Summary Report 2007. , 2007, The Journal of allergy and clinical immunology.

[73]  K. Barnes,et al.  African Americans with asthma: genetic insights. , 2007, Proceedings of the American Thoracic Society.

[74]  G. Menz,et al.  Activin A is an acute allergen-responsive cytokine and provides a link to TGF-beta-mediated airway remodeling in asthma. , 2006, The Journal of allergy and clinical immunology.