J. Campbell

发表

Elevated T cell repertoire diversity is associated with progression of lung squamous cell premalignant lesions

Joshua D. Campbell, Gang Liu, M. Lenburg, 2021, Journal for ImmunoTherapy of Cancer.

Assessment of a Highly Multiplexed RNA Sequencing Platform and Comparison to Existing High-Throughput Gene Expression Profiling Techniques

Eric R. Reed, Joshua D. Campbell, S. Monti, 2018, bioRxiv.

Abstract 2878: Development of the pre-cancer genome atlas (PCGA) for squamous cell lung carcinoma

S. Monti, Gang Liu, M. Lenburg, 2015 .

Interactive analysis of single-cell data using flexible workflows with SCTK2.0

Joshua D. Campbell, W. Johnson, M. Yajima, 2022, bioRxiv.

Genomic Profiling of Prostate Cancers from Men with African and European Ancestry

Joshua D. Campbell, M. Meyerson, E. Ziv, 2020, Clinical Cancer Research.

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Nancy R. Zhang, Elizabeth H. Williams, Joshua F. McMichael, 2020, Cell.

Genetic regulation of gene expression in the lung identifies CST3 and CD22 as potential causal genes for airflow obstruction

Joshua D. Campbell, Y. Bossé, K. Hao, 2014, Thorax.

A contamination focused approach for optimizing the single-cell RNA-seq experiment

Michael J. Brenan, Joshua D. Campbell, Cody N. Heiser, 2022, bioRxiv.

Pipeliner: A Nextflow-based framework for the definition of sequencing data processing pipelines

S. Monti, Kritika Karri, Anthony Federico, 2018, bioRxiv.

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Nancy R. Zhang, Elizabeth H. Williams, Joshua F. McMichael, 2020, Cell.

Alterations in Bronchial Airway miRNA Expression for Lung Cancer Detection

Joshua D. Campbell, Gang Liu, M. Lenburg, 2017, Cancer Prevention Research.

The cellular and molecular determinants of emphysematous destruction in COPD

J. Cooper, M. Lenburg, A. Spira, 2017, Scientific Reports.

High-throughput Phenotyping of Lung Cancer Somatic Mutations.

Angela N. Brooks, Joshua D. Campbell, Ted E. Natoli, 2016, Cancer cell.

Comprehensive molecular profiling of lung adenocarcinoma

Steven J. M. Jones, Christopher A. Miller, Joshua M. Stuart, 2014, Nature.

Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

Chandra Sekhar Pedamallu, Carrie Cibulskis, Angela N. Brooks, 2016, Nature Genetics.

Inactivation of the Hippo tumor suppressor pathway promotes melanoma

Joshua D. Campbell, Neil J Ganem, C. Ceol, 2021, Nature Communications.

A single-sample microarray normalization method to facilitate personalized-medicine workflows.

Stephen R. Piccolo, Joshua D. Campbell, Ying Sun, 2012, Genomics.

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Kyle J. Gaulton, David S. Fischer, Malte D. Luecken, 2021, Nature Medicine.

Celda: a Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data

Joshua D. Campbell, M. Yajima, Evan Johnson, 2020, bioRxiv.

Detecting Noncoding RNA Expression: From Arrays to Next-Generation Sequencing

Joshua D. Campbell, F. Schembri, C. Perdomo, 2014 .

Decontamination of ambient RNA in single-cell RNA-seq with DecontX

Joshua D. Campbell, W. Johnson, M. Yajima, 2019, Genome Biology.

A single-cell lung atlas of complement genes identifies the mesothelium and epithelium as prominent sources of extrahepatic complement proteins

Joshua D. Campbell, A. Jayaraman, C. Reinhardt, 2022, Mucosal Immunology.

MicroRNA 4423 is a primate-specific regulator of airway epithelial cell differentiation and lung carcinogenesis

Joshua D. Campbell, C. Anderlind, M. Lenburg, 2013, Proceedings of the National Academy of Sciences.

Comparison of Prevalence and Types of Mutations in Lung Cancers Among Black and White Populations

David R Williams, David R. Williams, Paul van Hummelen, 2017, JAMA oncology.

The Case for a Pre-Cancer Genome Atlas (PCGA)

Jennifer Beane, Mary E Reid, Joshua D. Campbell, 2016, Cancer Prevention Research.

Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor.

Aviad Tsherniak, Gavin Ha, William C Hahn, 2017, Cancer discovery.

A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment.

Avrum Spira, Paola Sebastiani, Jeffrey T. Chang, 2013, American journal of respiratory and critical care medicine.

NetSig: network-based discovery from cancer genomes

Joshua D. Campbell, Candace R. Chouinard, W. Hahn, 2017, Nature Methods.

SubmiRine: assessing variants in microRNA targets using clinical genomic data sets

Avrum Spira, Andreas D. Baxevanis, Joshua D. Campbell, 2015, Nucleic acids research.

Resource Genomic , Pathway Networ k , and Immunologic Features Distinguishing Squamous Carcinomas Graphical

Joshua M. Stuart, Joshua D. Campbell, Christopher K. Wong, 2018 .

Comprehensive molecular profiling of lung adenocarcinoma

Steven J. M. Jones, Christopher A. Miller, Joshua M. Stuart, 2014, Nature.

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway

Steven J. M. Jones, Mauro A. A. Castro, Benjamin J. Raphael, 2021, Cell reports.

Cross organelle stress response disruption promotes gentamicin-induced proteotoxicity

Joshua D. Campbell, D. Pimentel, S. Borkan, 2020, Cell Death & Disease.

Generation of Genetically Engineered Mouse Lung Organoid Models for Squamous Cell Lung Cancers Allows for the Study of Combinatorial Immunotherapy

Joshua D. Campbell, A. Bass, Kwok-Kin Wong, 2020, Clinical Cancer Research.

Genetics of Lung Cancer

Joshua D. Campbell, K. Steiling, J. Campbell, 2020, Precision in Pulmonary, Critical Care, and Sleep Medicine.

Genomic and immune profiling of pre-invasive lung adenocarcinoma

Joshua D. Campbell, Lindsay C. Westlake, Ashton C. Berger, 2019, Nature Communications.

Expanding discovery from cancer genomes by integrating protein network analyses with in vivo tumorigenesis assays

Joshua D. Campbell, Candace R. Chouinard, W. Hahn, 2017, bioRxiv.

MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis

Tao Huang, Avrum Spira, Jun Zhu, 2014, PLoS Comput. Biol..

Comparative Genomics Reveals Distinct Immune-oncologic Pathways in African American Men with Prostate Cancer

Joshua D. Campbell, B. Trock, T. Rebbeck, 2020, Clinical Cancer Research.

Multi-modal profiling of human fetal liver hematopoietic stem cells reveals the molecular signature of engraftment

Joshua D. Campbell, Taylor M. Matte, Todd W. Dowrey, 2021, Nature Communications.

Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data

Zhe Wang, Yichen Wang, Xinyun Cao, 2020, Nature Communications.

Multi-Modal Profiling of Human Fetal Liver-Derived Hematopoietic Stem Cells Reveals the Molecular Signature of Engraftment Potential

Joshua D. Campbell, Taylor M. Matte, Todd W. Dowrey, 2020, bioRxiv.

Institutional implementation of clinical tumor profiling on an unselected cancer population.

Marian Harris, Ethan Cerami, Frank C Kuo, 2016, JCI insight.

High-throughput Phenotyping of Lung Cancer Somatic Mutations.

Angela N. Brooks, Joshua D. Campbell, Ted E. Natoli, 2016, Cancer cell.

Applying gene expression microarrays to pulmonary disease

Joshua D. Campbell, M. Lenburg, A. Spira, 2011, Respirology.

Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution

Joshua D. Campbell, Gang Liu, M. Lenburg, 2018, Science Advances.

Genomic approaches to accelerate cancer interception.

Joshua D. Campbell, A. Spira, J. Beane, 2017, The Lancet. Oncology.

Whole genome doubling confers unique genetic vulnerabilities on tumor cells

Joshua D. Campbell, Neil J Ganem, Alison M. Taylor, 2020, Nature.

Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data

Avrum Spira, Ivana V. Yang, Stefano Monti, 2015, RNA.

miR-638 regulates gene expression networks associated with emphysematous lung destruction

Avrum Spira, Dirkje S Postma, Joshua D. Campbell, 2013, Genome Medicine.

Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data

Timothy L. Tickle, Joshua D. Campbell, N. Gehlenborg, 2023, bioRxiv.

Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro

Joshua D. Campbell, M. Yajima, J. Campbell, 2023, bioRxiv.

Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD

Joshua D. Campbell, E. Schadt, Jun Zhu, 2015, PLoS genetics.

Correction: Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD

Joshua D. Campbell, E. Schadt, Jun Zhu, 2015, PLoS genetics.

Humanized mice reveal a macrophage-enriched gene signature defining human lung tissue protection during SARS-CoV-2 infection

Joshua D. Campbell, A. Emili, A. Balazs, 2022, Cell Reports.

Macrophages govern antiviral responses in human lung tissues protected from SARS-CoV-2 infection

Joshua D. Campbell, A. Emili, M. Ericsson, 2021, bioRxiv.

Transcription factor and microRNA interactions in lung cells: an inhibitory link between NK2 homeobox 1, miR-200c and the developmental and oncogenic factors Nfib and Myb

Joshua D. Campbell, J. Tagne, M. I. Ramirez, 2015, Respiratory Research.

A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK

Avrum Spira, Julie E. Zeskind, Dirkje S Postma, 2012, Genome Medicine.

Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq

Avrum Spira, Yuriy O Alekseyev, Pierre P Massion, 2011, Cancer Prevention Research.

Single-Cell RNA Sequencing of the Bronchial Epithelium in Smokers With Lung Cancer

Joshua D. Campbell, J. Campbell, Grant E. Duclos, 2015 .

Smoking Modulates Different Secretory Subpopulations Expressing SARS-CoV-2 Entry Genes in the Nasal and Bronchial Airways

Joshua D. Campbell, Gang Liu, M. Lenburg, 2021, Scientific Reports.

The cellular and molecular determinants of emphysematous destruction in COPD

Joshua D. Campbell, J. Cooper, M. Lenburg, 2017, Scientific Reports.

Publisher Correction: Whole-genome doubling confers unique genetic vulnerabilities on tumour cells

Alison M. Taylor, Ryan J. Quinton, A. Manning, 2021, Nature.

Molecular subtyping reveals immune alterations associated with progression of bronchial premalignant lesions

C. Stevenson, Gang Liu, M. Lenburg, 2018, bioRxiv.

Identification of transforming growth factor-beta-regulated microRNAs and the microRNA-targetomes in primary lung fibroblasts

D. Postma, M. Lenburg, A. Spira, 2017, PloS one.

The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the Discovery, Prediction, and Exploration of Mutational Signatures

Aaron Chevalier, Shiyi Yang, Masanao Yajima, 2020, Cancer Research.

scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data

Evan Johnson, Zhe Wang, J. Campbell, 2019, bioRxiv.