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

PhD, Harvard University
MA, Harvard University
MS, Brigham Young University
BS, Southern Utah 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.

Adjunct 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 Chobanian & Avedisian 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 - 06/30/2023 (PI)
NIH/National Institute of Allergy & Infectious Diseases

Dynamics and immune mechanisms of QFT response in close contacts of TB cases
05/01/2022 - 04/30/2023 (Subcontract PI)
U.S. Civilian Research and Development Foundation National Science Fdn

Microbiome-based biomarkers and models of lung cancer development and treatment
12/08/2021 - 08/31/2022 (Multi-PI)
PI: William Evan Johnson, PhD
NIH/National Cancer Institute

Removing batch effects in genomic and epigenomic studies
05/01/2018 - 08/31/2022 (PI)
NIH/National Institute of General Medical Sciences

Bacterial and Host Heterogeneity in TB latency, persistence and progression
09/23/2021 - 06/30/2022 (Subcontract PI)
Rutgers, The State University of New Jersey NIH NIAID

Epidemiologic and Genomic Evaluation of Influenza D Among Catlte Workers and Their Community
09/01/2018 - 12/31/2021 (Key Person / Mentor)
PI: Jessica Leibler, DrPH, MS
HHS/CDC/National Institute for Occupational Safety and Health

CFAR Developmental Award: Impact of TB and HIV co-infection on host and microbial gene expression in the upper airway
12/01/2019 - 11/30/2021 (Subcontract PI)
The Miriam Hospital NIH NIAID

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

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

Showing 10 of 14 results. Show All Results


Yr Title Project-Sub Proj Pubs
2023 Microbiome-based biomarkers and models of lung cancer development and treatment 7R21CA260382-02
2022 Microbiome-based biomarkers and models of lung cancer development and treatment 1R21CA260382-01A1
2022 Systems Biology Core 5U19AI162598-02-6542
2021 Systems Biology Core 1U19AI162598-01-6542
2021 Signature of profiling and staging the progression of TB from infection to disease. 5R21AI154387-02
2021 Removing batch effects in genomic and epigenomic studies 5R01GM127430-04
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
Showing 10 of 25 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.

iCite Analysis       Copy PMIDs To Clipboard

  1. Cintron C, Narasimhan PB, Locks L, Babu S, Sinha P, Rajkumari N, Kaipilyawar V, Bhargava A, Maloomian K, Chandrasekaran P, Verma S, Joseph N, Johnson WE, Wanke C, Horsburgh CR, Ellner JJ, Sarkar S, Salgame P, Lakshminarayanan S, Hochberg NS. Tuberculosis-Learning the Impact of Nutrition (TB LION): protocol for an interventional study to decrease TB risk in household contacts. BMC Infect Dis. 2021 Oct 12; 21(1):1058.View Related Profiles. PMID: 34641820; PMCID: PMC8506078; DOI: 10.1186/s12879-021-06734-z;
  2. Borrelli KN, Yao EJ, Yen WW, Phadke RA, Ruan QT, Chen MM, Kelliher JC, Langan CR, Scotellaro JL, Babbs RK, Beierle JC, Logan RW, Johnson WE, Wachman EM, Cruz-Martín A, Bryant CD. Sex Differences in Behavioral and Brainstem Transcriptomic Neuroadaptations following Neonatal Opioid Exposure in Outbred Mice. eNeuro. 2021 Sep-Oct; 8(5).View Related Profiles. PMID: 34479978; PMCID: PMC8454922; DOI: 10.1523/ENEURO.0143-21.2021;
  3. Delpech JC, Pathak D, Varghese M, Kalavai SV, Hays EC, Hof PR, Johnson WE, Ikezu S, Medalla M, Luebke JI, Ikezu T. Wolframin-1-expressing neurons in the entorhinal cortex propagate tau to CA1 neurons and impair hippocampal memory in mice. Sci Transl Med. 2021 09 15; 13(611):eabe8455.View Related Profiles. PMID: 34524859; PMCID: PMC8763211; DOI: 10.1126/scitranslmed.abe8455;
  4. Zhang Y, Patil P, Johnson WE, Parmigiani G. Robustifying genomic classifiers to batch effects via ensemble learning. Bioinformatics. 2021 07 12; 37(11):1521-1527.View Related Profiles. PMID: 33245114; PMCID: PMC8485848; DOI: 10.1093/bioinformatics/btaa986;
  5. Braun MR, Noton SL, Blanchard EL, Shareef A, Santangelo PJ, Johnson WE, Fearns R. Respiratory syncytial virus M2-1 protein associates non-specifically with viral messenger RNA and with specific cellular messenger RNA transcripts. PLoS Pathog. 2021 05; 17(5):e1009589.View Related Profiles. PMID: 34003848; PMCID: PMC8162694; DOI: 10.1371/journal.ppat.1009589;
  6. Zhao Y, Federico A, Faits T, Manimaran S, Segrè D, Monti S, Johnson WE. animalcules: interactive microbiome analytics and visualization in R. Microbiome. 2021 03 28; 9(1):76.View Related Profiles. PMID: 33775256; PMCID: PMC8006385; DOI: 10.1186/s40168-021-01013-0;
  7. Johnson WE, Odom A, Cintron C, Muthaiah M, Knudsen S, Joseph N, Babu S, Lakshminarayanan S, Jenkins DF, Zhao Y, Nankya E, Horsburgh CR, Roy G, Ellner J, Sarkar S, Salgame P, Hochberg NS. Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler. BMC Infect Dis. 2021 Jan 22; 21(1):106.View Related Profiles. PMID: 33482742; PMCID: PMC7821401; DOI: 10.1186/s12879-020-05598-z;
  8. Manabe YC, Andrade BB, Gupte N, Leong S, Kintali M, Matoga M, Riviere C, Samaneka 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 Tuberculosis and Mortality in Advanced Human Immunodeficiency Virus. Clin Infect Dis. 2020 12 17; 71(10):2645-2654.View Related Profiles. PMID: 31761933; PMCID: PMC7744990; DOI: 10.1093/cid/ciz1147;
  9. 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; PMCID: PMC7727488; DOI: 10.1093/ajcn/nqaa254;
  10. Sheerin D, Abhimanyu, Wang X, Johnson WE, Coussens A. Systematic evaluation of transcriptomic disease risk and diagnostic biomarker overlap between COVID-19 and tuberculosis: a patient-level meta-analysis. medRxiv. 2020 Nov 26. PMID: 33269371; PMCID: PMC7709192; DOI: 10.1101/2020.11.25.20236646;
Showing 10 of 91 results. Show More

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

Bar chart showing 91 publications over 15 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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