William Evan Johnson PhD
Adjunct Associate Professor, Computational Biomedicine
Adjunct Associate Professor, Biostatistics
72 East Concord Street | (617) 638-2541
BU-BMC Cancer Center
Boston Nutrition Obesity Research Center
Evans Center for Interdisciplinary Biomedical Research
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.
Biostatistics, PhD, Harvard University, 2007
Biostatistics, MA, Harvard University, 2006
Statistics, MS, Brigham Young University, 2003
Mathematics, BS, Southern Utah University, 2002
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. PMID: 36370131.Published on 10/20/2022
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. PMID: 36341454.Published on 9/28/2022
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. PMID: 36248906.Published on 10/12/2021
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. PMID: 34641820.Published on 9/20/2021
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). PMID: 34479978.Published on 9/15/2021
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. PMID: 34524859.Published on 7/12/2021
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. PMID: 33245114.Published on 5/18/2021
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. PMID: 34003848.Published on 3/28/2021
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. PMID: 33775256.Published on 1/22/2021
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. PMID: 33482742.