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Your search keyword '"John Quackenbush"' showing total 21 results
Start Over Author "John Quackenbush" Publisher american thoracic society
21 results on '"John Quackenbush"'

1. DNA Methylation Is Predictive of Mortality in Current and Former Smokers

Author

Ruth Tal-Singer, MeiLan K. Han, Jarrett D. Morrow, Augustine M.K. Choi, Edwin K. Silverman, Craig P. Hersh, Barry J. Make, Dawn L. DeMeo, Elizabeth A. Regan, and John Quackenbush

Subjects
Pulmonary and Respiratory Medicine, Oncology, COPD, medicine.medical_specialty, business.industry, Critical Care and Intensive Care Medicine, medicine.disease, Former Smoker, respiratory tract diseases, Never smokers, Internal medicine, DNA methylation, behavior and behavior mechanisms, medicine, Life expectancy, Epigenetics, business, Survival analysis, All cause mortality
Abstract

Rationale: Smoking results in at least a decade lower life expectancy. Mortality among current smokers is two to three times as high as never smokers. DNA methylation is an epigenetic modification ...

Published
2020

5. Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci

Author

Craig P. Hersh, George R. Washko, Jarrett D. Morrow, Augustine M.K. Choi, Michael H. Cho, Edwin K. Silverman, Kimberly Glass, Bartolome R. Celli, Victor Pinto-Plata, Dawn L. DeMeo, Raphael Bueno, Nathaniel Marchetti, John Quackenbush, and Gerard J. Criner

Subjects
Adult, Epigenomics, Male, 0301 basic medicine, Pulmonary and Respiratory Medicine, Quantitative Trait Loci, Genome-wide association study, Quantitative trait locus, Critical Care and Intensive Care Medicine, Epigenesis, Genetic, 03 medical and health sciences, Pulmonary Disease, Chronic Obstructive, 0302 clinical medicine, Medicine, Humans, Genetic Predisposition to Disease, Epigenetics, Lung, Aged, Cause of death, Aged, 80 and over, Genetics, COPD, business.industry, Colocalization, Original Articles, Middle Aged, DNA Methylation, medicine.disease, United States, 030104 developmental biology, Gene Expression Regulation, 030228 respiratory system, Fruit, DNA methylation, Female, Identification (biology), business, Genome-Wide Association Study
Abstract

Rationale: As the third leading cause of death in the United States, the impact of chronic obstructive pulmonary disease (COPD) makes identification of its molecular mechanisms of great importance. Genome-wide association studies (GWASs) have identified multiple genomic regions associated with COPD. However, genetic variation only explains a small fraction of the susceptibility to COPD, and sub–genome-wide significant loci may play a role in pathogenesis. Objectives: Regulatory annotation with epigenetic evidence may give priority for further investigation, particularly for GWAS associations in noncoding regions. We performed integrative genomics analyses using DNA methylation profiling and genome-wide SNP genotyping from lung tissue samples from 90 subjects with COPD and 36 control subjects. Methods: We performed methylation quantitative trait loci (mQTL) analyses, testing for SNPs associated with percent DNA methylation and assessed the colocalization of these results with previous COPD GWAS findings using Bayesian methods in the R package coloc to highlight potential regulatory features of the loci. Measurements and Main Results: We identified 942,068 unique SNPs and 33,996 unique CpG sites among the significant (5% false discovery rate) cis-mQTL results. The genome-wide significant and subthreshold (P

Published
2018

6. Multistrain Genetic Comparisons Reveal CCR5 as a Receptor Involved in Airway Hyperresponsiveness

Author

Julia K. L. Walker, David A. Schwartz, John Quackenbush, Adriana Ahumada, Bryan C. Frank, Renee Gaspard, and Katherine G. Berman

Subjects
Pulmonary and Respiratory Medicine, Receptors, CCR5, Microarray, Ovalbumin, Clinical Biochemistry, Disease, Biology, medicine.disease_cause, Bronchoalveolar Lavage, Mice, Allergen, Respiratory Hypersensitivity, medicine, Animals, Genetic Predisposition to Disease, Receptor, Molecular Biology, Oligonucleotide Array Sequence Analysis, Asthma, Mice, Knockout, Genetics, Mice, Inbred BALB C, Gene Expression Profiling, Articles, Cell Biology, medicine.disease, Phenotype, respiratory tract diseases, Mice, Inbred C57BL, Gene expression profiling, Disease Models, Animal, DNA microarray
Abstract

Asthma is a ubiquitous disease with a broad range of clinical phenotypes. To better understand the complex genetic and environmental interactions underlying asthma, we compared the gene-gene interactions of four genetically distinct mouse strains that demonstrate biologically distinct responses to allergen. Using DNA microarrays and knock-out mouse studies, we showed that CCR5 plays a definitive role in the development of ovalbumin-induced allergic airway inflammatory disease. In addition, gene expression profiling data have revealed other potential novel targets for therapeutics-based research and has enhanced the understanding of the molecular mechanisms underlying the etiology of "asthma."

Published
2006

7. The Expression Of Long Intergenic Noncoding RNAs In Idiopathic Pulmonary Fibrosis And Their Possible Role As Suppressors Of Proliferation

Author

Lara Chensny, Mick Correll, Kevin F. Gibson, John Quackenbush, Brenda Juan Guardela, Frank C. Sciurba, David A. Schwartz, Jose D. Herazo, Kusum Pandit, John Tedrow, Thomas J. Richards, Naftali Kaminski, Mark W. Geraci, and Avrum Spira

Subjects
Pathology, medicine.medical_specialty, Idiopathic pulmonary fibrosis, Intergenic region, law, Cancer research, medicine, Suppressor, Biology, medicine.disease, law.invention
Published
2012

9. Characterizing The Small RNA Transcriptome Associated With COPD And ILD Using Next Generation Sequencing

Author

Jennifer Beane, David A. Schwartz, Marc E. Lenburg, Joshua D. Campbell, John Quackenbush, Brenda Juan-Guardela, Frank C. Sciurba, Lingqi Luo, Yuriy Aleksyev, Joseph Gerrein, Ivana V. Yang, Ji Xiao, Gang Liu, John Tedrow, Mark W. Geraci, Naftali Kaminski, Mick Correll, and Avrum Spira

Subjects
Transcriptome, COPD, Small RNA, medicine, Computational biology, Biology, medicine.disease, Bioinformatics, DNA sequencing
Published
2012

10. Comprehensive Genomic Profiling Of The Lung Transcriptome In Emphysema And IPF Using RNA-Seq

Author

Rebecca L. Kusko, John Brothers II, Gang Liu, Lingqi Luo, Brenda J. Guardela, John R. Tedrow, Yuriy Aleksyev, Ivana V. Yang, Mick Correll, Mark Geraci, John Quackenbush, Frank C. Sciurba, Marc Lenburg, David A. Schwartz, Jennifer Beane, Naftali Kaminski, and Avrum Spira

Subjects
Transcriptome, Genomic profiling, Lung, medicine.anatomical_structure, medicine, RNA-Seq, Computational biology, Biology
Published
2012

12. Identification Of Lung Disease-Associated Novel Transcripts And Alternative Splicing By RNA-Sequencing

Author

John F. Brothers, Rebecca L. Kusko, Gang Liu, Lingqi Luo, Brenda Juan Guardela, John Tedrow, Yuriy Alekseyev, Ivana V. Yang, Mick Correll, Mark Geraci, John Quackenbush, Frank C. Sciurba, Paola Sebastiani, Marc Lenburg, Naftali Kaminski, David A. Schwartz, Avrum Spira, and Jennifer Beane

Subjects
Lung disease, Alternative splicing, RNA, Identification (biology), Computational biology, Biology
Published
2012

13. Characterizing The Lung Disease Transcriptome With Next Generation Rna-Sequencing

Author

Rebecca L. Kusko, Jennifer Beane, John F. Brothers, Gang Liu, Lingqi Luo, Brenda Juan Guardela, John Tedrow, Yuriy Aleksyev, Ivana V. Yang, Mick Correll, Mark W. Geraci, John Quackenbush, Frank C. Sciurba, Marc Lenburg, David A. Schwartz, Naftali Kaminski, and Avrum Spira

Subjects
Transcriptome, Lung disease, RNA, Computational biology, Biology
Published
2011

14. Genome-Wide DNA Methylation Patterns In Interstitial Lung Disease (ild) And Chronic Obstructive Lung Disease (COPD)

Author

Brenda Juan Guardela, Mick Correll, John Tedrow, Megan Bonney, Sonia M. Leach, Corinne E. Hennessy, Elizabeth J. Davidson, John Quackenbush, David A. Schwartz, Julia Turner, Avrum Spira, Frank C. Sciurba, Joseph Brown, Brent S. Pedersen, Mark W. Geraci, Ivana V. Yang, and Naftali Kaminski

Subjects
COPD, Pathology, medicine.medical_specialty, business.industry, DNA methylation, Interstitial lung disease, Medicine, business, medicine.disease, Genome, Obstructive lung disease
Published
2011

15. Emphysema Gene Expression Signatures

Author

David Gur, John Quackenbush, Avrum Spira, Frank C. Sciurba, David A. Schwartz, Mick Correll, Brenda Juan-Guardela, Lara Chensny, Mark W. Geraci, Naftali Kaminski, John Tedrow, Joseph K. Leader, Steven D. Shapiro, and Thomas J. Richards

Subjects
Gene expression, Biology, Molecular biology
Published
2011

17. Genome-Wide Analysis Of Somatic Genetic Alterations In Severe Lung Disease

Author

John Quackenbush, Naftali Kaminski, Sonia M. Leach, David A. Schwartz, Ivana V. Yang, Avrum Spira, Frank C. Sciurba, Mark W. Geraci, Bifing Gao, Elissa Murphy, Jessica L. Rice, and Christopher D. Coldren

Subjects
Genetics, Somatic cell, Lung disease, Genome wide analysis, Biology
Published
2011

18. Identifying Novel Transcripts And Alternative Splicing Associated With The ILD And COPD Lung Transcriptome Using MRNA-Seq

Author

John F. Brothers, Rebecca L. Kusko, Lingqi Luo, Gang Liu, Brenda J. Guardela, John Tedrow, Yuriy Alekseyev, Ivana V. Yang, Mick Correll, Mark W. Geraci, John Quackenbush, Frank C. Sciurba, Paola Sebastiani, Marc Lenburg, Naftali Kaminski, David A. Schwartz, Avrum Spira, and Jennifer Beane

Subjects
Transcriptome, COPD, Messenger RNA, Lung, medicine.anatomical_structure, Alternative splicing, medicine, Computational biology, Biology, medicine.disease
Published
2011

20. Somatic Mutations In The Lungs Of Patients With Idiopathic Pulmonary Fibrosis

Author

Julia Turner, Sonia M. Leach, Mark W. Geraci, Elissa Murphy, John Quackenbush, Ivana V. Yang, Avrum Spira, Naftali Kaminski, Christopher D. Coldren, Zhiyong Wang, Joseph Brown, Nicholas Sisneros, Frank C. Sciurba, Mick Correll, David A. Schwartz, Nathan Kummer, and Eveline Farias-Hesson

Subjects
Idiopathic pulmonary fibrosis, Pathology, medicine.medical_specialty, business.industry, Somatic cell, Medicine, business, medicine.disease
Published
2011

21. Microrna Expression Profiles In Emphysema

Author

David Gur, Kusum Pandit, Avrum Spira, Frank C. Sciurba, David A. Schwartz, John Tedrow, Rodney J. Landreneau, Joseph K. Leader, Brenda Juan-Guardela, Mark W. Geraci, Naftali Kaminski, Thomas J. Richards, John Quackenbush, Lara Chensny, and Mick Correll

Subjects
Expression (architecture), microRNA, Cancer research, Biology
Published
2011

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