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

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



Evan 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
Biostatistics


Member
Boston University
BU-BMC Cancer Center


Member
Boston University
Evans Center for Interdisciplinary Biomedical Research


Full Member
Boston University Medical Center
Boston Nutrition Obesity Research Center


Member
Boston University
Bioinformatics Graduate Program


Member
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




Microbial Dysbiosis and Epithelial Dysfunction in Vitamin A-deficient Lungs
04/01/2023 - 03/31/2025 (Key Person / Mentor)
NIH/National Heart, Lung, and Blood Institute
5F31HL162523-02

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
5R21AI154387-02

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
OISE-9531011

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
1R21CA260382-01A1

Removing batch effects in genomic and epigenomic studies
05/01/2018 - 08/31/2022 (PI)
NIH/National Institute of General Medical Sciences
5R01GM127430-04

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
1U19AI162598-01

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
5P30AI042853-21

An interactive analysis toolkit for single cell RNA-seq in cancer research
08/01/2017 - 07/31/2021 (PI)
NIH/National Cancer Institute
5U01CA220413-03

Preprocessing and Analysis Tools for High-Throughput Technologies
09/01/2016 - 06/30/2019 (Subcontract PI)
Dana-Farber Cancer Institute NIH NIGMS
5R01GM083084-13

Showing 10 of 15 results. Show All Results


Title


Yr Title Project-Sub Proj Pubs
2024 Biomarker Signatures of TB Infection in Young Children With and Without HIV 5R01AI175315-02
2024 Systems Biology Core 5U19AI162598-04-6542
2024 Removing batch effects in high-throughput biomedical studies 5R01GM127430-07
2023 Biomarker Signatures of TB Infection in Young Children With and Without HIV 1R01AI175315-01
2023 Microbiome-based biomarkers and models of lung cancer development and treatment 7R21CA260382-02
2023 Systems Biology Core 7U19AI162598-03-6542
2023 Removing batch effects in high-throughput biomedical studies 2R01GM127430-06A1
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
Showing 10 of 32 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. Lapidot R, Faits T, Ismail A, Allam M, Khumalo Z, MacLeod W, Kwenda G, Mupila Z, Nakazwe R, Segrè D, Johnson WE, Thea DM, Mwananyanda L, Gill CJ. Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study. Gates Open Res. 2022; 6:48.View Related Profiles. PMID: 39050991; DOI: 10.12688/gatesopenres.13561.2;
     
  2. Leibler JH, Abdelgadir A, Seidel J, White RF, Johnson WE, Reynolds SJ, Gray GC, Schaeffer JW. Influenza D virus exposure among US cattle workers: A call for surveillance. Zoonoses Public Health. 2023 Mar; 70(2):166-170.View Related Profiles. PMID: 36370131; DOI: 10.1111/zph.13008;
     
  3. VanValkenburg A, Kaipilyawar V, Sarkar S, Lakshminarayanan S, Cintron C, Babu SP, Knudsen S, Joseph NM, Horsburgh CR, Sinha P, Ellner JJ, Narasimhan PB, Johnson WE, Hochberg NS, Salgame P. Corrigendum: Malnutrition leads to increased inflammation and expression of tuberculosis risk signatures in recently exposed household contacts of pulmonary tuberculosis. Front Immunol. 2022; 13:1064883.View Related Profiles. PMID: 36341454; DOI: 10.3389/fimmu.2022.1064883;
     
  4. VanValkenburg A, Kaipilyawar V, Sarkar S, Lakshminarayanan S, Cintron C, Prakash Babu S, Knudsen S, Joseph NM, Horsburgh CR, Sinha P, Ellner JJ, Narasimhan PB, Johnson WE, Hochberg NS, Salgame P. Malnutrition leads to increased inflammation and expression of tuberculosis risk signatures in recently exposed household contacts of pulmonary tuberculosis. Front Immunol. 2022; 13:1011166.View Related Profiles. PMID: 36248906; DOI: 10.3389/fimmu.2022.1011166;
     
  5. 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; DOI: 10.1186/s12879-021-06734-z;
     
  6. 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; DOI: 10.1523/ENEURO.0143-21.2021;
     
  7. 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; DOI: 10.1126/scitranslmed.abe8455;
     
  8. 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; DOI: 10.1093/bioinformatics/btaa986;
     
  9. 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; DOI: 10.1371/journal.ppat.1009589;
     
  10. 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; DOI: 10.1186/s40168-021-01013-0;
     
Showing 10 of 95 results. Show More

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

Bar chart showing 95 publications over 17 distinct years, with a maximum of 13 publications in 2015

YearPublications
20062
20072
20094
20103
20117
20124
20137
20146
201513
20167
20175
20186
20196
202012
20217
20223
20241

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801 Massachusetts Ave
Boston MA 02118
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