Joshua D. Campbell, Ph.D.
Assistant Professor, Division of Computational Biomedicine, Department of Medicine
Member of the BU-BMC Cancer Center
Affiliate member, Broad Institute of MIT and Harvard
Scholarships and career development awards:
Boston University Ralph Edwards Career Development Professorship
LUNGevity Career Development Award
Boston University Clinical and Translational Science Institute (CTSI) KL2 Scholar
Postdoctoral fellowship in cancer genomics:
Lab of Matthew Meyerson
Dana-Farber Cancer Institute and the Broad Institute of MIT and Harvard
Ph.D. in Bioinformatics
Boston University, Boston, MA
B.A. in Biology, Computer Science, & Mathematics
Anderson University, Anderson, IN
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 quickly 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 have developed the Celda framework (CEllular Latent Dirichlet Allocation), which can be used to identify hidden transcriptional states and cellular populations in count-based single-cell RNA-seq data. A beta version of this software can be accessed at github:
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.
Full list of publications: https://scholar.google.com/citations?user=Xsn1VsgAAAAJ&hl=en
Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G; Cancer Genome Atlas Research Network, Artyomov MN, Schreiber R, Govindan R, Meyerson M. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet. 2016 Jun;48(6):607-16. doi: 10.1038/ng.3564. Epub 2016 May 9.
Campbell JD, Mazzilli SA, Reid ME, Dhillon SS, Platero S, Beane J, Spira AE. The Case for a Pre-Cancer Genome Atlas (PCGA). Cancer Prev Res (Phila). 2016 Feb;9(2):119-24. doi: 10.1158/1940-6207.CAPR-16-0024. Epub 2016 Feb 1.
Campbell JD, Liu G, Luo L, Xiao J, Gerrein J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Correll M6, Geraci M, Quackenbush J, Sciurba F, Schwartz DA, Kaminski N, Johnson WE, Monti S, Spira A, Beane J, Lenburg ME. Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. RNA. 2015 Feb;21(2):164-71.
Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31;511(7511):543-50.
-Roles: DNA-sequencing team and manuscript coordinator
Perdomo C, Campbell JD, Gerrein J, Tellez CS, Garrison CB, Walser TC, Drizik E, Si H, Gower AC, Vick J, Anderlind C, Jackson GR, Mankus C, Schembri F, O’Hara C, Gomperts BN, Dubinett SM, Hayden P, Belinsky SA, Lenburg ME, Spira A. miR-4423 is a Primate-Specific Regulator of Airway Epithelial Cell Differentiation and Lung Carcinogenesis. Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18946-51.
Campbell JD, McDonough JE, Zeskind JE, Hackett TL, Pechkovsky DV, Brandsma CA, Suzuki M, Gosselink JV, Liu G, AAlekseyev YO, Xiao J, Zhang X, Shizu Hayashi, Joel D. Cooper, Timens W, Postma DS, Knight DA, Lenburg ME, Hogg JC, Spira A. A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK. Genome Med. 2012 Aug 31;4(8):67.