Joshua Campbell | Profiles RNS

Joshua D. Campbell, PhD

Associate Professor

Boston University Chobanian & Avedisian School of Medicine

Medicine

Computational Biomedicine

PhD, Boston University
BS, Anderson University

Pronouns: he/him/his

Websites

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	Campbell Lab

ORCID : 0000-0003-0780-8662

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.

Diversity, Equity, Inclusion and Accessibility

Our research group supports trainees from diverse and underrepresented groups by fostering career development experiences in preparation for an independent career in computational biology and biomedical research. We welcome all trainees including individuals who are first generation college students, LGBTQ+, disabled, or are from underrepresented/minoritized races and ethnicities. Our group values diversity of thought and perspective which can only be obtained by having representation from people with a wide range of experiences and backgrounds. We are specifically looking to train undergraduate and graduate students from minority groups in computational skills and techniques as they are vastly underrepresented in STEM fields.

We are also interested in understanding the mechanisms underlying health disparities in cancer. Some disease such as prostate cancer high higher incidence and mortality rates in African Americans compared to other populations. Many things contribute to this disparity including access to health care and other socioeconomic factors. Our group is determining if underlying biological differences in tumors from African Americans also contributes to cancer disparities. We are characterizing and comparing somatic mutational profiles and transcriptomic states of cancer cells from different ancestral backgrounds. These types of studies will be important for understanding when certain therapies may preferentially benefit African American patients who continue to remain underrepresented in clinical trials.

Member
Boston University
BU-BMC Cancer Center

Member
Boston University
Evans Center for Interdisciplinary Biomedical Research

Member
Boston University
Genome Science Institute

BU Research

Investigating the mechanisms of driver genes associated with ancestry and aggressiveness in prostate cancer
05/10/2021 - 04/30/2027 (PI)
NIH/National Cancer Institute
5R01CA248920-04

Characterizing early-stage lung cancer and lymph nodes at single-cell resolution
01/01/2024 - 12/31/2025 (PI)
Inova Health Care Services

Lung Pre-Cancer Atlas (PCA) Cohort Registry
01/01/2019 - 12/31/2025 (Multi-PI)
PI: Joshua D. Campbell, PhD
Johnson & Johnson

Utilizing Bayesian modeling to improve mutational signature inference in large-scale datasets
09/17/2021 - 08/31/2025 (Multi-PI)
PI: Joshua D. Campbell, PhD
NIH/National Cancer Institute
5U01CA253500-03

Robust, scalable, and accurate discovery of mutational signatures
09/20/2021 - 06/30/2025 (Multi-PI)
PI: Joshua D. Campbell, PhD
NIH/National Institute of General Medical Sciences
5R01GM144963-03

Methods and software for decontamination of single-cell data
07/01/2022 - 01/03/2025 (PI)
Silicon Valley Community Foundation

Novel approaches to characterize the microenvironment of lung cancers and lymph nodes to improve overall staging and survival of cancer patients
01/01/2023 - 12/31/2024 (PI)
Johnson & Johnson Enterprise Innovation, Inc.

An Atlas of Human Prostate Across Ancestries to develop a comprehensive atlas of the human prostate at single-cell resolution with a community engagement plan to maximize impact for the public and cli
12/01/2021 - 11/30/2024 (Subcontract PI)
The Regents of the University of California Silicon Valley C Fdn

Utilizing Bayesian modeling to improve mutational signature inference in large-scale datasets (Restricted Holding Account for 50209293)
09/01/2023 - 08/31/2024 (PI)
NIH/National Cancer Institute
5U01CA253500-03

The Lung PCA: A Multi-Dimensional Atlas of Pulmonary Premalignancy
09/30/2018 - 08/31/2024 (Multi PI of Sub-Project / SP)
PI: Avrum Spira, MD
NIH/National Cancer Institute
3U2CCA233238-01S2

Showing 10 of 20 results. Show All Results

Title

Yr	Title	Project-Sub Proj	Pubs

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Sarfraz I, Wang Y, Shastry A, 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. MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data. Genome Biol. 2024 Aug 01; 25(1):205.View Related Profiles.

Campbell, Joshua
Dries, Ruben

PMID: 39090672; PMCID: PMC11292877; DOI: 10.1186/s13059-024-03349-w;

Sun Y, Benmhammed H, Al Abdullatif S, Habara A, Fu E, Brady J, Williams C, Ilinski A, Sharma A, Mahdaviani K, Alekseyev YO, Campbell JD, Steinberg MH, Cui S. PGC-1a agonism induces fetal hemoglobin and exerts antisickling effects in sickle cell disease. Sci Adv. 2024 Aug 02; 10(31):eadn8750.View Related Profiles.

Benmhammed, Hajar
Campbell, Joshua
Mahdaviani, Kiana
Steinberg, Martin
Cui, Shuaiying
Alekseyev, Yuriy

PMID: 39083598; PMCID: PMC11290485; DOI: 10.1126/sciadv.adn8750;

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; PMCID: PMC10783508; DOI: 10.1093/nar/gkad1032;

Chevalier 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; PMCID: PMC10635259; DOI: 10.1101/2023.11.03.23297964;

Yanagawa J, Tran LM, Salehi-Rad R, Lim RJ, Dumitras C, Fung E, Wallace WD, Prosper AE, Fishbein G, Shea C, Hong R, Kahangi B, Deng JJ, Gower AC, Liu B, Campbell JD, Mazzilli SA, Beane JE, Kadara H, Lenburg ME, Spira AE, Aberle DR, Krysan K, Dubinett SM. Single-Cell Characterization of Pulmonary Nodules Implicates Suppression of Immunosurveillance across Early Stages of Lung Adenocarcinoma. Cancer Res. 2023 Oct 02; 83(19):3305-3319.View Related Profiles.

Gower, Adam
Spira, Avrum
Campbell, Joshua
Lenburg, Marc
Mazzilli, Sarah

PMID: 37477508; PMCID: PMC10544016; DOI: 10.1158/0008-5472.CAN-23-0128;

O'Neill NK, Stein TD, Hu J, Rehman H, Campbell JD, Yajima M, Zhang X, Farrer LA. Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM. BMC Bioinformatics. 2023 Sep 19; 24(1):349.View Related Profiles.

Campbell, Joshua
Farrer, Lindsay
Stein, Thor

PMID: 37726653; PMCID: PMC10507917; DOI: 10.1186/s12859-023-05476-w;

Pavel 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.View Related Profiles.

Spira, Avrum
Taub, Daniel
Liu, Gang
Tedrow, John
Campbell, Joshua
Luo, Lingqi
Lenburg, Marc
Alekseyev, Yuriy

PMID: 37567908; PMCID: PMC10421936; DOI: 10.1038/s41598-023-39751-w;

Wang 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; PMCID: PMC10436054; DOI: 10.1016/j.patter.2023.100814;

Arceneaux D, Chen Z, Simmons AJ, Heiser CN, Southard-Smith AN, Brenan MJ, Yang Y, Chen B, Xu Y, Choi E, Campbell JD, Liu Q, Lau KS. A contamination focused approach for optimizing the single-cell RNA-seq experiment. iScience. 2023 Jul 21; 26(7):107242. PMID: 37496679; PMCID: PMC10366499; DOI: 10.1016/j.isci.2023.107242;

Yin 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; PMCID: PMC9979990; DOI: 10.1101/2023.01.27.525964;

Showing 10 of 62 results. Show More

Xu 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.View Related Profiles.

Gower, Adam
Spira, Avrum
Billatos, Ehab
Liu, Gang
Duclos, Grant
Liu, Hanqiao
Campbell, Joshua
Lenburg, Marc
Platt, Michael
Mazzilli, Sarah

PMID: 36307504; PMCID: PMC9615627; DOI: 10.1038/s41598-022-17832-6;

Wang Z, Yang S, Koga Y, Corbett SE, Shea CV, Johnson WE, Yajima M, Campbell JD. Celda: a Bayesian model to perform co-clustering of genes into modules and cells into subpopulations using single-cell RNA-seq data. NAR Genom Bioinform. 2022 Sep; 4(3):lqac066. PMID: 36110899; PMCID: PMC9469931; DOI: 10.1093/nargab/lqac066;

Vittoria 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.View Related Profiles.

Tilston-Lunel, Andrew
Lang, Deborah
Xia, Eric
Campbell, Joshua
Kotynkova, Kristyna
Vittoria, Marc
Ganem, Neil
Varelas, Xaralabos

PMID: 35768444; PMCID: PMC9243107; DOI: 10.1038/s41467-022-31399-w;

Chaudhary 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.View Related Profiles.

Jayaraman, Archana
Campbell, Joshua
Bosmann, Markus
Chaudhary, Neha

PMID: 35672453; PMCID: PMC9173662; DOI: 10.1038/s41385-022-00534-7;

Alhousami T, Diny M, Ali F, Shin J, Kumar G, Kumar V, Campbell JD, Noonan V, Hanna GJ, Denis GV, Monti S, Kukuruzinska MA, Varelas X, Bais MV. Inhibition of LSD1 Attenuates Oral Cancer Development and Promotes Therapeutic Efficacy of Immune Checkpoint Blockade and YAP/TAZ Inhibition. Mol Cancer Res. 2022 May 04; 20(5):712-721.View Related Profiles.

Denis, Gerald
Campbell, Joshua
Bais, Manish
Kukuruzinska, Maria
Monti, Stefano
Kumar, Vikas
Noonan, Vikki
Varelas, Xaralabos

PMID: 35105672; PMCID: PMC9081163; DOI: 10.1158/1541-7786.MCR-21-0310;

Kenney DJ, O'Connell AK, Turcinovic J, Montanaro P, Hekman RM, Tamura T, Berneshawi AR, Cafiero TR, Al Abdullatif S, Blum B, Goldstein SI, Heller BL, Gertje HP, Bullitt E, Trachtenberg AJ, Chavez E, Nono ET, Morrison C, Tseng AE, Sheikh A, Kurnick S, Grosz K, Bosmann M, Ericsson M, Huber BR, Saeed M, Balazs AB, Francis KP, Klose A, Paragas N, Campbell JD, Connor JH, Emili A, Crossland NA, Ploss A, Douam F. Humanized mice reveal a macrophage-enriched gene signature defining human lung tissue protection during SARS-CoV-2 infection. Cell Rep. 2022 Apr 19; 39(3):110714.View Related Profiles.

Emili, Andrew
Blum, Benjamin
Huber, Bertrand
Bullitt, Esther
Douam, Florian
Connor, John
Campbell, Joshua
Bosmann, Markus
Saeed, Mohsan
Crossland, Nicholas

PMID: 35421379; PMCID: PMC8977517; DOI: 10.1016/j.celrep.2022.110714;

Hong R, Koga Y, Bandyadka S, Leshchyk A, Wang Y, Akavoor V, Cao X, Sarfraz I, Wang Z, Alabdullatif S, Jansen F, Yajima M, Johnson WE, Campbell JD. Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data. Nat Commun. 2022 Mar 30; 13(1):1688. PMID: 35354805; PMCID: PMC8967915; DOI: 10.1038/s41467-022-29212-9;

Vanuytsel K, Villacorta-Martin C, Lindstrom-Vautrin J, Wang Z, Garcia-Beltran WF, Vrbanac V, Parsons D, Lam EC, Matte TM, Dowrey TW, Kumar SS, Li M, Wang F, Yeung AK, Mostoslavsky G, Dries R, Campbell JD, Belkina AC, Balazs AB, Murphy GJ. Multi-modal profiling of human fetal liver hematopoietic stem cells reveals the molecular signature of engraftment. Nat Commun. 2022 03 01; 13(1):1103.View Related Profiles.

Belkina, Anna
Murphy, George
Mostoslavsky, Gustavo
Campbell, Joshua
Vanuytsel, Kim
Dries, Ruben
Matte, Taylor

PMID: 35232959; PMCID: PMC8888592; DOI: 10.1038/s41467-022-28616-x;

Chevalier A, Yang S, Khurshid Z, Sahelijo N, Tong T, Huggins JH, Yajima M, Campbell JD. The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the Discovery, Prediction, and Exploration of Mutational Signatures. Cancer Res. 2021 12 01; 81(23):5813-5817. PMID: 34625425; PMCID: PMC8639789; DOI: 10.1158/0008-5472.CAN-21-0899;

Sarfraz I, Asif M, Campbell JD. ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects. Bioinformatics. 2021 Sep 29; 37(18):3058-3060. PMID: 33715007; PMCID: PMC9940906; DOI: 10.1093/bioinformatics/btab179;

Maoz A, Merenstein C, Koga Y, Potter A, Gower AC, Liu G, Zhang S, Liu H, Stevenson C, Spira A, Reid ME, Campbell JD, Mazzilli SA, Lenburg ME, Beane J. Elevated T cell repertoire diversity is associated with progression of lung squamous cell premalignant lesions. J Immunother Cancer. 2021 09; 9(9).View Related Profiles.

Gower, Adam
Spira, Avrum
Liu, Gang
Liu, Hanqiao
Campbell, Joshua
Lenburg, Marc
Mazzilli, Sarah

PMID: 34580161; PMCID: PMC8477334; DOI: 10.1136/jitc-2021-002647;

Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, Lee JJ, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N, Meyerson M, Govindan R, Imielinski M. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell Rep. 2021 Feb 02; 34(5):108707. PMID: 33535033; PMCID: PMC8009291; DOI: 10.1016/j.celrep.2021.108707;

Quinton RJ, DiDomizio A, Vittoria MA, Kotýnková K, Ticas CJ, Patel S, Koga Y, Vakhshoorzadeh J, Hermance N, Kuroda TS, Parulekar N, Taylor AM, Manning AL, Campbell JD, Ganem NJ. Whole-genome doubling confers unique genetic vulnerabilities on tumour cells. Nature. 2021 02; 590(7846):492-497.View Related Profiles.

Vakhshoorzadeh, Jasmine
Campbell, Joshua
Vittoria, Marc
Ganem, Neil
Quinton, Ryan

PMID: 33505027; PMCID: PMC7889737; DOI: 10.1038/s41586-020-03133-3;

Lashkaripour A, Rodriguez C, Mehdipour N, Mardian R, McIntyre D, Ortiz L, Campbell J, Densmore D. Machine learning enables design automation of microfluidic flow-focusing droplet generation. Nat Commun. 2021 Jan 04; 12(1):25. PMID: 33397940; PMCID: PMC7782806; DOI: 10.1038/s41467-020-20284-z;

Carrot-Zhang J, Soca-Chafre G, Patterson N, Thorner AR, Nag A, Watson J, Genovese G, Rodriguez J, Gelbard MK, Corrales-Rodriguez L, Mitsuishi Y, Ha G, Campbell JD, Oxnard GR, Arrieta O, Cardona AF, Gusev A, Meyerson M. Genetic Ancestry Contributes to Somatic Mutations in Lung Cancers from Admixed Latin American Populations. Cancer Discov. 2021 03; 11(3):591-598.View Related Profiles.

Oxnard, Geoffrey
Campbell, Joshua

PMID: 33268447; PMCID: PMC7933062; DOI: 10.1158/2159-8290.CD-20-1165;

Awasthi S, Berglund A, Abraham-Miranda J, Rounbehler RJ, Kensler K, Serna A, Vidal A, You S, Freeman MR, Davicioni E, Liu Y, Karnes RJ, Klein EA, Den RB, Trock BJ, Campbell JD, Einstein DJ, Gupta R, Balk S, Lal P, Park JY, Cleveland JL, Rebbeck TR, Freedland SJ, Yamoah K. Comparative Genomics Reveals Distinct Immune-oncologic Pathways in African American Men with Prostate Cancer. Clin Cancer Res. 2021 Jan 01; 27(1):320-329. PMID: 33037017; PMCID: PMC8042600; DOI: 10.1158/1078-0432.CCR-20-2925;

Koga Y, Song H, Chalmers ZR, Newberg J, Kim E, Carrot-Zhang J, Piou D, Polak P, Abdulkadir SA, Ziv E, Meyerson M, Frampton GM, Campbell JD, Huang FW. Genomic Profiling of Prostate Cancers from Men with African and European Ancestry. Clin Cancer Res. 2020 09 01; 26(17):4651-4660. PMID: 32651179; PMCID: PMC7597977; DOI: 10.1158/1078-0432.CCR-19-4112;

Igwebuike C, Yaglom J, Huiting L, Feng H, Campbell JD, Wang Z, Havasi A, Pimentel D, Sherman MY, Borkan SC. Cross organelle stress response disruption promotes gentamicin-induced proteotoxicity. Cell Death Dis. 2020 04 03; 11(4):217.View Related Profiles.

Havasi, Andrea
Pimentel, David
Feng, Hui
Campbell, Joshua
Huiting, Leah
Borkan, Steven
Wang, Zhiyong

PMID: 32245975; PMCID: PMC7125232; DOI: 10.1038/s41419-020-2382-7;

Hai J, Zhang H, Zhou J, Wu Z, Chen T, Papadopoulos E, Dowling CM, Pyon V, Pan Y, Liu JB, Bronson RT, Silver H, Lizotte PH, Deng J, Campbell JD, Sholl LM, Ng C, Tsao MS, Thakurdin C, Bass AJ, Wong KK. Generation of Genetically Engineered Mouse Lung Organoid Models for Squamous Cell Lung Cancers Allows for the Study of Combinatorial Immunotherapy. Clin Cancer Res. 2020 Jul 01; 26(13):3431-3442. PMID: 32209571; PMCID: PMC7334092; DOI: 10.1158/1078-0432.CCR-19-1627;

Yang S, Corbett SE, Koga Y, Wang Z, Johnson WE, Yajima M, Campbell JD. Decontamination of ambient RNA in single-cell RNA-seq with DecontX. Genome Biol. 2020 03 05; 21(1):57.View Related Profiles.

Campbell, Joshua
Johnson, William

PMID: 32138770; PMCID: PMC7059395; DOI: 10.1186/s13059-020-1950-6;

Duclos GE, Teixeira VH, Autissier P, Gesthalter YB, Reinders-Luinge MA, Terrano R, Dumas YM, Liu G, Mazzilli SA, Brandsma CA, van den Berge M, Janes SM, Timens W, Lenburg ME, Spira A, Campbell JD, Beane J. Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution. Sci Adv. 2019 12; 5(12):eaaw3413.View Related Profiles.

Spira, Avrum
Liu, Gang
Duclos, Grant
Campbell, Joshua
Lenburg, Marc
Mazzilli, Sarah
Dumas, Yves-Martine

PMID: 31844660; PMCID: PMC6905872; DOI: 10.1126/sciadv.aaw3413;

Chen H, Carrot-Zhang J, Zhao Y, Hu H, Freeman SS, Yu S, Ha G, Taylor AM, Berger AC, Westlake L, Zheng Y, Zhang J, Ramachandran A, Zheng Q, Pan Y, Zheng D, Zheng S, Cheng C, Kuang M, Zhou X, Zhang Y, Li H, Ye T, Ma Y, Gao Z, Tao X, Han H, Shang J, Yu Y, Bao D, Huang Y, Li X, Zhang Y, Xiang J, Sun Y, Li Y, Cherniack AD, Campbell JD, Shi L, Meyerson M. Genomic and immune profiling of pre-invasive lung adenocarcinoma. Nat Commun. 2019 Nov 29; 10(1):5472. PMID: 31784532; PMCID: PMC6884501; DOI: 10.1038/s41467-019-13460-3;

Federico A, Karagiannis T, Karri K, Kishore D, Koga Y, Campbell JD, Monti S. Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines. Front Genet. 2019; 10:614.View Related Profiles.

Campbell, Joshua
Monti, Stefano

PMID: 31316552; PMCID: PMC6609566; DOI: 10.3389/fgene.2019.00614;

Wang Z, Hu J, Johnson WE, Campbell JD. scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data. BMC Bioinformatics. 2019 May 02; 20(1):222.View Related Profiles.

Campbell, Joshua
Johnson, William

PMID: 31046658; PMCID: PMC6498700; DOI: 10.1186/s12859-019-2797-2;

Beane JE, Mazzilli SA, Campbell JD, Duclos G, Krysan K, Moy C, Perdomo C, Schaffer M, Liu G, Zhang S, Liu H, Vick J, Dhillon SS, Platero SJ, Dubinett SM, Stevenson C, Reid ME, Lenburg ME, Spira AE. Molecular subtyping reveals immune alterations associated with progression of bronchial premalignant lesions. Nat Commun. 2019 04 23; 10(1):1856.View Related Profiles.

Spira, Avrum
Liu, Gang
Duclos, Grant
Liu, Hanqiao
Beane-Ebel, Jennifer
Campbell, Joshua
Lenburg, Marc
Mazzilli, Sarah

PMID: 31015447; PMCID: PMC6478943; DOI: 10.1038/s41467-019-09834-2;

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 04 03; 23(1):194-212.e6. PMID: 29617660; PMCID: PMC6002769; DOI: 10.1016/j.celrep.2018.03.063;

Horn H, Lawrence MS, Chouinard CR, Shrestha Y, Hu JX, Worstell E, Shea E, Ilic N, Kim E, Kamburov A, Kashani A, Hahn WC, Campbell JD, Boehm JS, Getz G, Lage K. NetSig: network-based discovery from cancer genomes. Nat Methods. 2018 Jan; 15(1):61-66. PMID: 29200198; PMCID: PMC5985961; DOI: 10.1038/nmeth.4514;

Zhang X, Choi PS, Francis JM, Gao GF, Campbell JD, Ramachandran A, Mitsuishi Y, Ha G, Shih J, Vazquez F, Tsherniak A, Taylor AM, Zhou J, Wu Z, Berger AC, Giannakis M, Hahn WC, Cherniack AD, Meyerson M. Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor. Cancer Discov. 2018 Jan; 8(1):108-125. PMID: 28963353; PMCID: PMC5760289; DOI: 10.1158/2159-8290.CD-17-0532;

Ong J, Timens W, Rajendran V, Algra A, Spira A, Lenburg ME, Campbell JD, van den Berge M, Postma DS, van den Berg A, Kluiver J, Brandsma CA. Identification of transforming growth factor-beta-regulated microRNAs and the microRNA-targetomes in primary lung fibroblasts. PLoS One. 2017; 12(9):e0183815.View Related Profiles.

Spira, Avrum
Campbell, Joshua
Lenburg, Marc

PMID: 28910321; PMCID: PMC5599028; DOI: 10.1371/journal.pone.0183815;

Pavel AB, Campbell JD, Liu G, Elashoff D, Dubinett S, Smith K, Whitney D, Lenburg ME, Spira A. Alterations in Bronchial Airway miRNA Expression for Lung Cancer Detection. Cancer Prev Res (Phila). 2017 Nov; 10(11):651-659.View Related Profiles.

Spira, Avrum
Liu, Gang
Campbell, Joshua
Lenburg, Marc

PMID: 28877936; PMCID: PMC6758560; DOI: 10.1158/1940-6207.CAPR-17-0098;

Suzuki M, Sze MA, Campbell JD, Brothers JF, Lenburg ME, McDonough JE, Elliott WM, Cooper JD, Spira A, Hogg JC. The cellular and molecular determinants of emphysematous destruction in COPD. Sci Rep. 2017 08 25; 7(1):9562.View Related Profiles.

Spira, Avrum
Campbell, Joshua
Lenburg, Marc

PMID: 28842670; PMCID: PMC5573394; DOI: 10.1038/s41598-017-10126-2;

Beane J, Campbell JD, Lel J, Vick J, Spira A. Genomic approaches to accelerate cancer interception. Lancet Oncol. 2017 Aug; 18(8):e494-e502.View Related Profiles.

Spira, Avrum
Beane-Ebel, Jennifer
Campbell, Joshua

PMID: 28759388; PMCID: PMC6020676; DOI: 10.1016/S1470-2045(17)30373-X;

Campbell JD, Lathan C, Sholl L, Ducar M, Vega M, Sunkavalli A, Lin L, Hanna M, Schubert L, Thorner A, Faris N, Williams DR, Osarogiagbon RU, van Hummelen P, Meyerson M, MacConaill L. Comparison of Prevalence and Types of Mutations in Lung Cancers Among Black and White Populations. JAMA Oncol. 2017 Jun 01; 3(6):801-809. PMID: 28114446; PMCID: PMC5464986; DOI: 10.1001/jamaoncol.2016.6108;

Sholl LM, Do K, Shivdasani P, Cerami E, Dubuc AM, Kuo FC, Garcia EP, Jia Y, Davineni P, Abo RP, Pugh TJ, van Hummelen P, Thorner AR, Ducar M, Berger AH, Nishino M, Janeway KA, Church A, Harris M, Ritterhouse LL, Campbell JD, Rojas-Rudilla V, Ligon AH, Ramkissoon S, Cleary JM, Matulonis U, Oxnard GR, Chao R, Tassell V, Christensen J, Hahn WC, Kantoff PW, Kwiatkowski DJ, Johnson BE, Meyerson M, Garraway LA, Shapiro GI, Rollins BJ, Lindeman NI, MacConaill LE. Institutional implementation of clinical tumor profiling on an unselected cancer population. JCI Insight. 2016 11 17; 1(19):e87062.View Related Profiles.

Oxnard, Geoffrey
Campbell, Joshua
Jia, Yonghui

PMID: 27882345; PMCID: PMC5111542; DOI: 10.1172/jci.insight.87062;

Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, Kaplan N, Campbell JD, Singh S, Root DE, Narayan R, Natoli T, Lahr DL, Tirosh I, Tamayo P, Getz G, Wong B, Doench J, Subramanian A, Golub TR, Meyerson M, Boehm JS. High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell. 2016 Aug 08; 30(2):214-228. PMID: 27478040; PMCID: PMC5003022; DOI: 10.1016/j.ccell.2016.06.022;

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, 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. PMID: 27158780; PMCID: PMC4884143; DOI: 10.1038/ng.3564;

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.View Related Profiles.

Spira, Avrum
Beane-Ebel, Jennifer
Campbell, Joshua
Mazzilli, Sarah

PMID: 26839336; DOI: 10.1158/1940-6207.CAPR-16-0024;

Sze MA, Dimitriu PA, Suzuki M, McDonough JE, Campbell JD, Brothers JF, Erb-Downward JR, Huffnagle GB, Hayashi S, Elliott WM, Cooper J, Sin DD, Lenburg ME, Spira A, Mohn WW, Hogg JC. Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med. 2015 Aug 15; 192(4):438-45.View Related Profiles.

Spira, Avrum
Campbell, Joshua
Lenburg, Marc

PMID: 25945594; PMCID: PMC4595667; DOI: 10.1164/rccm.201502-0223OC;

Maxwell EK, Campbell JD, Spira A, Baxevanis AD. SubmiRine: assessing variants in microRNA targets using clinical genomic data sets. Nucleic Acids Res. 2015 Apr 30; 43(8):3886-98.View Related Profiles.

Spira, Avrum
Campbell, Joshua

PMID: 25813044; PMCID: PMC4417167; DOI: 10.1093/nar/gkv256;

Tagne JB, Mohtar OR, Campbell JD, Lakshminarayanan M, Huang J, Hinds AC, Lu J, Ramirez MI. 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. Respir Res. 2015; 16:22.View Related Profiles.

Tagne, Jean-Bosco
Lu, Jining
Campbell, Joshua
Ramirez, Maria
Mohtar, Omar

PMID: 25763778; PMCID: PMC4335692; DOI: 10.1186/s12931-015-0186-6;

Yoo S, Takikawa S, Geraghty P, Argmann C, Campbell J, Lin L, Huang T, Tu Z, Foronjy RF, Feronjy R, Spira A, Schadt EE, Powell CA, Zhu J. Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD. PLoS Genet. 2015 Jan; 11(1):e1004898.View Related Profiles.

Spira, Avrum
Campbell, Joshua

PMID: 25569234; PMCID: PMC4287352; DOI: 10.1371/journal.pgen.1004898;

Campbell JD, Liu G, Luo L, Xiao J, Gerrein J, Juan-Guardela B, Tedrow J, Alekseyev YO, Yang IV, Correll M, 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.View Related Profiles.

Spira, Avrum
Liu, Gang
Beane-Ebel, Jennifer
Tedrow, John
Campbell, Joshua
Luo, Lingqi
Lenburg, Marc
Monti, Stefano
Johnson, William
Alekseyev, Yuriy

PMID: 25519487; PMCID: PMC4338344; DOI: 10.1261/rna.046060.114;

Lamontagne M, Timens W, Hao K, Bossé Y, Laviolette M, Steiling K, Campbell JD, Couture C, Conti M, Sherwood K, Hogg JC, Brandsma CA, van den Berge M, Sandford A, Lam S, Lenburg ME, Spira A, Paré PD, Nickle D, Sin DD, Postma DS. Genetic regulation of gene expression in the lung identifies CST3 and CD22 as potential causal genes for airflow obstruction. Thorax. 2014 Nov; 69(11):997-1004.View Related Profiles.

Spira, Avrum
Campbell, Joshua
Steiling, Katrina
Lenburg, Marc

PMID: 25182044; DOI: 10.1136/thoraxjnl-2014-205630;

Yoo S, Huang T, Campbell JD, Lee E, Tu Z, Geraci MW, Powell CA, Schadt EE, Spira A, Zhu J. MODMatcher: multi-omics data matcher for integrative genomic analysis. PLoS Comput Biol. 2014 Aug; 10(8):e1003790.View Related Profiles.

Spira, Avrum
Campbell, Joshua

PMID: 25122495; PMCID: PMC4133046; DOI: 10.1371/journal.pcbi.1003790;

Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31; 511(7511):543-50.View Related Profiles.

Burks, Eric
Campbell, Joshua

PMID: 25079552; PMCID: PMC4231481; DOI: 10.1038/nature13385;

Christenson SA, Brandsma CA, Campbell JD, Knight DA, Pechkovsky DV, Hogg JC, Timens W, Postma DS, Lenburg M, Spira A. miR-638 regulates gene expression networks associated with emphysematous lung destruction. Genome Med. 2013; 5(12):114.View Related Profiles.

Spira, Avrum
Campbell, Joshua
Lenburg, Marc

PMID: 24380442; PMCID: PMC3971345; DOI: 10.1186/gm519;

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. MicroRNA 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.View Related Profiles.

Gower, Adam
Spira, Avrum
O'Hara, Carl
Garrison, Carly
Schembri, Frank
Campbell, Joshua
Lenburg, Marc

PMID: 24158479; PMCID: PMC3839685; DOI: 10.1073/pnas.1220319110;

Steiling K, van den Berge M, Hijazi K, Florido R, Campbell J, Liu G, Xiao J, Zhang X, Duclos G, Drizik E, Si H, Perdomo C, Dumont C, Coxson HO, Alekseyev YO, Sin D, Pare P, Hogg JC, McWilliams A, Hiemstra PS, Sterk PJ, Timens W, Chang JT, Sebastiani P, O'Connor GT, Bild AH, Postma DS, Lam S, Spira A, Lenburg ME. A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment. Am J Respir Crit Care Med. 2013 May 1; 187(9):933-42.View Related Profiles.

Spira, Avrum
Dumont, Charles
Liu, Gang
O'Connor, George
Duclos, Grant
Campbell, Joshua
Steiling, Katrina
Lenburg, Marc
Sebastiani, Paola
Alekseyev, Yuriy

PMID: 23471465; PMCID: PMC3707363; DOI: 10.1164/rccm.201208-1449OC;

Campbell JD, McDonough JE, Zeskind JE, Hackett TL, Pechkovsky DV, Brandsma CA, Suzuki M, Gosselink JV, Liu G, Alekseyev YO, Xiao J, Zhang X, Hayashi S, Cooper JD, 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; 4(8):67.View Related Profiles.

Spira, Avrum
Liu, Gang
Campbell, Joshua
Lenburg, Marc
Alekseyev, Yuriy

PMID: 22937864; PMCID: PMC4064320; DOI: 10.1186/gm368;

Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH, Johnson WE. A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics. 2012 Dec; 100(6):337-44.View Related Profiles.

Campbell, Joshua
Lenburg, Marc
Piccolo, Stephen
Johnson, William

PMID: 22959562; PMCID: PMC3508193; DOI: 10.1016/j.ygeno.2012.08.003;

Beane J, Vick J, Schembri F, Anderlind C, Gower A, Campbell J, Luo L, Zhang XH, Xiao J, Alekseyev YO, Wang S, Levy S, Massion PP, Lenburg M, Spira A. Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq. Cancer Prev Res (Phila). 2011 Jun; 4(6):803-17.View Related Profiles.

Gower, Adam
Spira, Avrum
Schembri, Frank
Beane-Ebel, Jennifer
Campbell, Joshua
Luo, Lingqi
Lenburg, Marc
Alekseyev, Yuriy

PMID: 21636547; PMCID: PMC3694393; DOI: 10.1158/1940-6207.CAPR-11-0212;

Campbell JD, Spira A, Lenburg ME. Applying gene expression microarrays to pulmonary disease. Respirology. 2011 Apr; 16(3):407-18.View Related Profiles.

Spira, Avrum
Campbell, Joshua
Lenburg, Marc

PMID: 21299687; DOI: 10.1111/j.1440-1843.2011.01942.x;

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 62 publications over 14 distinct years, with a maximum of 8 publications in 2022

Bar chart showing 62 publications over 14 distinct years, with a maximum of 8 publications in 2022

Year	Publications
2011	2
2012	2
2013	3
2014	4
2015	4
2016	4
2017	7
2018	1
2019	5
2020	6
2021	6
2022	8
2023	7
2024	3

Media Mentions
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New Method Removes Background Noise from CITE-Seq Data

AZO Life Sciences 11/20/2023

BU researchers develop new method to help with analysis of single cell data

ScienMag 11/17/2023

Biological Differences in Prostate Cancers of African American and European American Men

Cancer Network 8/22/2020

Genomic Profiles of Prostate Cancers Differ Between Men of African and European Ancestry

Medscape 8/11/2020

African American, European Ancestry Men Benefit from Same Targeted Prostate Cancer Therapies

Clinical OMICs 7/13/2020

Analysis identifies genomic treatment targets in African American men with prostate cancer

Urology Times 7/13/2020

2021 Boston University: Shipley Pilot Award

2019 Boston University : Hariri Institute Junior Faculty Fellowship

2019 Boston University : Dahod Pilot Award for Breast Cancer

2018 National Cancer Institute: Cancer Disparities Research Network Travel Award

2018 Boston University : American Cancer Society Pilot Award

2018 Boston University : Genome Science Institute Seed Award

2018 Karin Grunebaum Cancer Research Foundation Faculty Research Fellowship

2016 Clinical & Translational Science Institute KL2 Scholar

2016 Boston University: Ralph Edwards Career Development Professorship

2015 Dana Farber/Harvard Cancer Center : Lung Cancer Symposium Abstract Award

2013 American Thoracic Society: Abstract Scholarship Award

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