Joshua D. Campbell PhD
Associate Professor, Computational Biomedicine
Member, Genome Science Institute
72 East Concord Street | (617) 358-7260camp@bu.edu
Sections
Computational Biomedicine
Centers
BU-BMC Cancer Center
Evans Center for Interdisciplinary Biomedical Research
Biography
Computational biology and bioinformatics.
High-throughput genomic technologies are rapidly evolving including the areas of DNA and RNA sequencing. Novel types of complex data are being rapidly generated and require novel methods for quality control and analysis. We are currently focused on developing and/or applying methods for identifying genomic alterations in cancer, quantifying the mutagenic effect of carcinogens, and characterizing cellular heterogeneity using single cell RNA sequencing. We are applying these methods in the areas of lung cancer development and premalignancy as well as COPD pathogenesis as described below.
Identifying early drivers of lung cancer.
Lung adenocarcinomas and lung squamous cell carcinomas are the most common types of lung cancer and remain major causes of death worldwide despite advances in smoking cessation, early detection, and targeted and immunological therapies. Many patients have lung cancers that do not harbor a known activating mutation and therefore cannot be given targeted therapies. In collaboration with labs from Dana-Farber Cancer Institute, the Broad Institute, and The Cancer Genome Atlas (TCGA) consortium, we analyze next-generation sequencing data to identify novel drivers of lung tumorigenesis. Targeting these genes with novel therapies will hopefully lead to a reduction in overall lung cancer mortality. In collaboration with the Spira/Lenburg lab at BUSM, we are identifying the genomic alterations in premalignant lesions for squamous cell carcinoma with the ultimate goal of defining strategies for early detection.
Therapeutic development and pathogenesis of COPD.
Chronic Obstructive Pulmonary Disease (COPD) is the 4th leading cause of death in the world. Our understanding of the molecular mechanisms responsible for the initiation and progression of this disease are limited. By examining expression differences between individuals with and without COPD or differences within a person along a gradient of disease, we hope to elucidate the molecular mechanisms that responsible for disease initiation. Utilizing publicly available resources such as the Connectivity Map, we are also using gene expression data to predict novel therapeutics for the treatment of COPD.
Education
Bioinformatics, PhD, Boston University
Computer Science/Biology, BS, Anderson University
Publications
Yin Y, Yajima M, Campbell JD. Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro. Nucleic Acids Res. 2024 Jan 11; 52(1):e4. PMID: 37973397.
Published on 11/4/2023Chevalier A, Guo T, Gurevich NQ, Xu J, Yajima M, Campbell JD. Characterization of highly active mutational signatures in tumors from a large Chinese population. medRxiv. 2023 Nov 04. PMID: 37961450.
Published on 8/11/2023Pavel AB, Garrison C, Luo L, Liu G, Taub D, Xiao J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Geraci MW, Sciurba F, Schwartz DA, Kaminski N, Beane J, Spira A, Lenburg ME, Campbell JD. Integrative genetic and genomic networks identify microRNA associated with COPD and ILD. Sci Rep. 2023 Aug 11; 13(1):13076. PMID: 37567908.
Published on 8/3/2023Wang Y, Sarfraz I, Pervaiz N, Hong R, Koga Y, Akavoor V, Cao X, Alabdullatif S, Zaib SA, Wang Z, Jansen F, Yajima M, Johnson WE, Campbell JD. Interactive analysis of single-cell data using flexible workflows with SCTK2. Patterns (N Y). 2023 Aug 11; 4(8):100814. PMID: 37602214.
Published on 3/7/2023Wang Y, Sarfraz I, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD. Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data. bioRxiv. 2023 Mar 07. PMID: 36945543.
Published on 3/7/2023Wang Y, Sarfraz I, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD. Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data. bioRxiv. 2023 Mar 07. PMID: 36945543.
Published on 2/24/2023Yin Y, Yajima M, Campbell JD. Characterization and decontamination of background noise in droplet-based single-cell protein expression data with DecontPro. bioRxiv. 2023 Feb 24. PMID: 36865227.
Published on 10/28/2022Xu K, Shi X, Husted C, Hong R, Wang Y, Ning B, Sullivan TB, Rieger-Christ KM, Duan F, Marques H, Gower AC, Xiao X, Liu H, Liu G, Duclos G, Platt M, Spira AE, Mazzilli SA, Billatos E, Lenburg ME, Campbell JD, Beane JE. Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways. Sci Rep. 2022 Oct 28; 12(1):18168. PMID: 36307504.
Published on 6/29/2022Vittoria MA, Kingston N, Kotynkova K, Xia E, Hong R, Huang L, McDonald S, Tilston-Lunel A, Darp R, Campbell JD, Lang D, Xu X, Ceol CJ, Varelas X, Ganem NJ. Inactivation of the Hippo tumor suppressor pathway promotes melanoma. Nat Commun. 2022 Jun 29; 13(1):3732. PMID: 35768444.
Published on 6/7/2022Chaudhary N, Jayaraman A, Reinhardt C, Campbell JD, Bosmann M. A single-cell lung atlas of complement genes identifies the mesothelium and epithelium as prominent sources of extrahepatic complement proteins. Mucosal Immunol. 2022 May; 15(5):927-939. PMID: 35672453.
Media Mentions
Published on 11/20/2023
New Method Removes Background Noise from CITE-Seq Data
Published on 11/17/2023
BU researchers develop new method to help with analysis of single cell data
Published on 8/22/2020
Biological Differences in Prostate Cancers of African American and European American Men
Published on 8/11/2020
Genomic Profiles of Prostate Cancers Differ Between Men of African and European Ancestry
Published on 7/13/2020
African American, European Ancestry Men Benefit from Same Targeted Prostate Cancer Therapies
Published on 7/13/2020
Analysis identifies genomic treatment targets in African American men with prostate cancer
View full list of 6 media mentions.