William Evan Johnson, PhD
Associate Professor
Boston University School of Medicine
Dept of Medicine
Computational Biomedicine

PhD, Harvard University
MA, Harvard University
MS, Brigham Young University

William Johnson specializes in computational biology and biostatistics, developing new tools to investigate disease prognoses and causes and to help determine effective regimens based on individual patients’ risk factors. He has published in the journals Cell, Proceedings of the National Academy of Sciences, Biometrics, Nature Reviews Genetics, Annals of Applied Statistics, and Biostatistics. His work has been funded by the NIH.

The focus of his group's research is to develop computational and statistical tools to investigate core components that contribute to disease prognosis and etiology, and for the accurate determination of optimal diagnostic, prognostic, and therapeutic regimens for individual patients. They are actively developing methods and software tools for data preprocessing, integration, and downstream analysis, and applying these tools in a variety of clinical and biomedical applications. Their work includes a balance between statistical methods development, algorithm optimization, and clinical application. Statistical innovation focuses on the development of clinically motivated tools that integrate linear modeling, Bayesian methods, factor analysis and structural equations models, Hidden Markov models, mixture models, dynamic programming, and high-performance parallel computing. This work has resulted in widely used tools and algorithms for profiling transcription factors (MAT, MA2C), preprocessing and integrating of genomic data (ComBat, BatchQC, SCAN-UPC), aligning sequencing reads (GNUMAP), developing multi-gene biomarker signatures (ASSIGN), and metagenomic profiling (PathoScope). They have successfully applied their tools in several biomedical and clinical scenarios, ranging from mechanistic studies and to precision genomics.

Associate Professor
Boston University School of Public Health

Boston University
BU-BMC Cancer Center

Boston University
Evans Center for Interdisciplinary Biomedical Research

Full Member
Boston University Medical Center
Boston Nutrition Obesity Research Center

Boston University
Bioinformatics Graduate Program

Boston University
Genome Science Institute

Graduate Faculty (Primary Mentor of Grad Students)
Boston University School of Medicine, Graduate Medical Sciences

Founding Associate Professor
Boston University
Computing & Data Sciences Administration

Signature profiling and staging the progression of TB from infection to disease.
07/10/2020 - 06/30/2022 (PI)
NIH/National Institute of Allergy & Infectious Diseases

Removing batch effects in genomic and epigenomic studies
05/01/2018 - 04/30/2022 (PI)
NIH/National Institute of General Medical Sciences

An interactive analysis toolkit for single cell RNA-seq in cancer research
08/01/2017 - 07/31/2021 (PI)
NIH/National Cancer Institute

CFAR Developmental Award: Impact of TB and HIV co-infection on host and microbial gene expression in the upper airway
12/01/2019 - 11/30/2020 (Subcontract PI)
The Miriam Hospital NIH NIAID

Preprocessing and Analysis Tools for High-Throughput Technologies
09/01/2016 - 06/30/2019 (Subcontract PI)
Dana-Farber Cancer Institute NIH NIGMS

DFCI Billing Agreement for Yuqing Zhang
09/01/2016 - 02/28/2018 (PI)
Dana-Farber Cancer Institute

Integrative analyses of reference epigenomic maps and applications
09/18/2014 - 08/31/2017 (PI)
NIH/National Institute of Environmental Health Sciences

Integrative signaling models to decipher complex cancer phenotypes
08/08/2012 - 07/31/2017 (Subcontract PI)
University of Utah NIH NCI

Billing Agreement for Heather Selby
07/01/2014 - 06/30/2017 (PI)
Dana-Farber Cancer Institute

Statistical Tools and Methods for Next-Generation Sequencing in Epigenetics
03/01/2012 - 02/29/2016 (PI)
NIH/National Human Genome Research Institute


Yr Title Project-Sub Proj Pubs
2020 Signature of profiling and staging the progression of TB from infection to disease. 1R21AI154387-01
2020 Removing batch effects in genomic and epigenomic studies 5R01GM127430-03
2019 Removing batch effects in genomic and epigenomic studies 5R01GM127430-02
2019 An interactive analysis toolkit for single cell RNA-seq in cancer research 5U01CA220413-03 2
2018 Removing batch effects in genomic and epigenomic studies 1R01GM127430-01
2018 An interactive analysis toolkit for single cell RNA-seq in cancer research 5U01CA220413-02 2
2017 An interactive analysis toolkit for single cell RNA-seq in cancer research 1U01CA220413-01 2
2016 Integrative signaling models to decipher complex cancer phenotypes 4U01CA164720-05 13
2015 Integrative analyses of reference epigenomic maps and applications 5R01ES025002-02 4
2015 Integrative signaling models to decipher complex cancer phenotypes 5U01CA164720-04 13
Showing 10 of 19 results. Show All Results

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.

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  1. Faits T, Walker ME, Rodriguez-Morato J, Meng H, Gervis JE, Galluccio JM, Lichtenstein AH, Johnson WE, Matthan NR. Exploring changes in the human gut microbiota and microbial-derived metabolites in response to diets enriched in simple, refined, or unrefined carbohydrate-containing foods: a post hoc analysis of a randomized clinical trial. Am J Clin Nutr. 2020 12 10; 112(6):1631-1641.View Related Profiles. PMID: 32936872
  2. Ruan QT, Yazdani N, Reed ER, Beierle JA, Peterson LP, Luttik KP, Szumlinski KK, Johnson WE, Ash PEA, Wolozin B, Bryant CD. 5' UTR variants in the quantitative trait gene Hnrnph1 support reduced 5' UTR usage and hnRNP H protein as a molecular mechanism underlying reduced methamphetamine sensitivity. FASEB J. 2020 Jul; 34(7):9223-9244.View Related Profiles. PMID: 32401417
  3. Babbs RK, Beierle JA, Yao EJ, Kelliher JC, Medeiros AR, Anandakumar J, Shah AA, Chen MM, Johnson WE, Bryant CD. The effect of the demyelinating agent cuprizone on binge-like eating of sweetened palatable food in female and male C57BL/6 substrains. Appetite. 2020 07 01; 150:104678.View Related Profiles. PMID: 32209386
  4. 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. PMID: 32138770
  5. Ikezu S, Yeh H, Delpech JC, Woodbury ME, Van Enoo AA, Ruan Z, Sivakumaran S, You Y, Holland C, Guillamon-Vivancos T, Yoshii-Kitahara A, Botros MB, Madore C, Chao PH, Desani A, Manimaran S, Kalavai SV, Johnson WE, Butovsky O, Medalla M, Luebke JI, Ikezu T. Inhibition of colony stimulating factor 1 receptor corrects maternal inflammation-induced microglial and synaptic dysfunction and behavioral abnormalities. Mol Psychiatry. 2020 Feb 18.View Related Profiles. PMID: 32071385
  6. Xavier JB, Young VB, Skufca J, Ginty F, Testerman T, Pearson AT, Macklin P, Mitchell A, Shmulevich I, Xie L, Caporaso JG, Crandall KA, Simone NL, Godoy-Vitorino F, Griffin TJ, Whiteson KL, Gustafson HH, Slade DJ, Schmidt TM, Walther-Antonio MRS, Korem T, Webb-Robertson BM, Styczynski MP, Johnson WE, Jobin C, Ridlon JM, Koh AY, Yu M, Kelly L, Wargo JA. The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends Cancer. 2020 03; 6(3):192-204. PMID: 32101723
  7. Leong S, Zhao Y, Ribeiro-Rodrigues R, Jones-López EC, Acuña-Villaorduña C, Rodrigues PM, Palaci M, Alland D, Dietze R, Ellner JJ, Johnson WE, Salgame P. Cross-validation of existing signatures and derivation of a novel 29-gene transcriptomic signature predictive of progression to TB in a Brazilian cohort of household contacts of pulmonary TB. Tuberculosis (Edinb). 2020 01; 120:101898.View Related Profiles. PMID: 32090859
  8. Manabe YC, Andrade BB, Gupte N, Leong S, Kintali M, Matoga M, Riviere C, Sameneka W, Lama JR, Naidoo K, Zhao Y, Johnson WE, Ellner JJ, Hosseinipour MC, Bisson GP, Salgame P, Gupta A. A Parsimonious Host Inflammatory Biomarker Signature Predicts Incident TB and Mortality in Advanced HIV. Clin Infect Dis. 2019 Nov 25.View Related Profiles. PMID: 31761933
  9. Buwembo W, Munabi IG, Kaddumukasa M, Kiryowa H, Nankya E, Johnson WE, Okello E, Sewankambo N. Periodontitis and Rheumatoid Arthritis in sub-Saharan Africa, gaps and way forward: a systematic review and meta-analysis. Open J Stomatol. 2019 Oct; 9(10):215-226. PMID: 31695961; DOI: 10.4236/ojst.2019.910023;
  10. McQuerry JA, Jenkins DF, Yost SE, Zhang Y, Schmolze D, Johnson WE, Yuan Y, Bild AH. Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes. BMC Cancer. 2019 Sep 05; 19(1):881. PMID: 31488082; DOI: 10.1186/s12885-019-6052-z;
Showing 10 of 79 results. Show More

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

Bar chart showing 79 publications over 14 distinct years, with a maximum of 13 publications in 2015

Contact for Mentoring:

72 E. Concord St Evans Building
Boston MA 02118
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