Author details

Full Name

Joshua D Campbell

Affiliation

ORCID

Career Start Year

2011

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37973397	Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro.	Nucleic Acids Res	2024
37496679	A contamination focused approach for optimizing the single-cell RNA-seq experiment.	iScience	2023
37567908	Integrative genetic and genomic networks identify microRNA associated with COPD and ILD.	Sci Rep	2023
36945543	Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data.	bioRxiv	2023
36865227	Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro.	bioRxiv	2023
35232959	Multi-modal profiling of human fetal liver hematopoietic stem cells reveals the molecular signature of engraftment.	Nat Commun	2022
36307504	Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways.	Sci Rep	2022
35768444	Inactivation of the Hippo tumor suppressor pathway promotes melanoma.	Nature Communications	2022
35421379	Humanized mice reveal a macrophage-enriched gene signature defining human lung tissue protection during SARS-CoV-2 infection.	Cell Rep	2022
35672453	A single-cell lung atlas of complement genes identifies the mesothelium and epithelium as prominent sources of extrahepatic complement proteins.	Mucosal Immunology	2022
35354805	Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data.	Nat Commun	2022
34625425	The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the Discovery, Prediction, and Exploration of Mutational Signatures.	Cancer Res	2021
33626341	Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.	Cell Rep	2021
33505027	Whole-genome doubling confers unique genetic vulnerabilities on tumour cells.	Nature	2021
33715007	ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects.		2021
33976417	Publisher Correction: Whole-genome doubling confers unique genetic vulnerabilities on tumour cells.	Nature	2021
33037017	Comparative Genomics Reveals Distinct Immune-oncologic Pathways in African American Men with Prostate Cancer.	Clin Cancer Res	2021
34580161	Elevated T cell repertoire diversity is associated with progression of lung squamous cell premalignant lesions.	J Immunother Cancer	2021
32651179	Genomic Profiling of Prostate Cancers from Men with African and European Ancestry.	Clin Cancer Res	2020
32245975	Cross organelle stress response disruption promotes gentamicin-induced proteotoxicity.	Cell Death and Disease	2020
32209571	Generation of Genetically Engineered Mouse Lung Organoid Models for Squamous Cell Lung Cancers Allows for the Study of Combinatorial Immunotherapy.	Clin Cancer Res	2020
31046658	scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data.	BMC Bioinformatics	2019
31844660	Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution.	Sci Adv	2019
31784532	Genomic and immune profiling of pre-invasive lung adenocarcinoma.	Nat Commun	2019
31015447	Molecular subtyping reveals immune alterations associated with progression of bronchial premalignant lesions.	Nat Commun	2019
30891063	Assessment of a Highly Multiplexed RNA Sequencing Platform and Comparison to Existing High-Throughput Gene Expression Profiling Techniques.	Frontiers in Genetics	2019
31316552	Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines.	Frontiers in Genetics	2019
29200198	NetSig: network-based discovery from cancer genomes.	Nat Methods	2018
28963353	Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor.	Cancer Discov	2018
29617660	Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.	Cell Rep	2018
28114446	Comparison of Prevalence and Types of Mutations in Lung Cancers Among Black and White Populations.	JAMA Oncol	2017
28910321	Identification of transforming growth factor-beta-regulated microRNAs and the microRNA-targetomes in primary lung fibroblasts.	PLoS One	2017
28759388	Genomic approaches to accelerate cancer interception.	Lancet Oncol	2017
28842670	The cellular and molecular determinants of emphysematous destruction in COPD.	Sci Rep	2017
28877936	Alterations in Bronchial Airway miRNA Expression for Lung Cancer Detection.	Cancer Prev Res (Phila)	2017
29232558	High-throughput Phenotyping of Lung Cancer Somatic Mutations.	Cancer Cell	2017
27882345	Institutional implementation of clinical tumor profiling on an unselected cancer population.	JCI Insight	2016
26839336	The Case for a Pre-Cancer Genome Atlas (PCGA).	Cancer Prev Res (Phila)	2016
27478040	High-throughput Phenotyping of Lung Cancer Somatic Mutations.	Cancer Cell	2016
27158780	Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas.	Nat Genet	2016
25945594	Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease.	Am J Respir Crit Care Med	2015
25813044	SubmiRine: assessing variants in microRNA targets using clinical genomic data sets.	Nucleic Acids Res	2015
25763778	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.	Respiratory Research	2015
25519487	Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data.	RNA	2015
25122495	MODMatcher: multi-omics data matcher for integrative genomic analysis.	PLoS Comput Biol	2014
25182044	Genetic regulation of gene expression in the lung identifies CST3 and CD22 as potential causal genes for airflow obstruction.	Thorax	2014
23471465	A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment.	Am J Respir Crit Care Med	2013
24158479	MicroRNA 4423 is a primate-specific regulator of airway epithelial cell differentiation and lung carcinogenesis.	Proc Natl Acad Sci U S A	2013
24380442	miR-638 regulates gene expression networks associated with emphysematous lung destruction.	Genome Med	2013
22959562	A single-sample microarray normalization method to facilitate personalized-medicine workflows.	Genomics	2012