William Evan Johnson, PhD

Associate Professor, Medicine

William Johnson
617.358.7048
72 E. Concord St Evans Building

Biography

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.

Other Positions

  • Associate Professor, Biostatistics, Boston University School of Public Health
  • Member, BU-BMC Cancer Center, Boston University
  • Member, Evans Center for Interdisciplinary Biomedical Research, Boston University
  • Full Member, Boston Nutrition Obesity Research Center, Boston University Medical Center
  • Member, Bioinformatics Graduate Program, Boston University
  • Member, Genome Science Institute, Boston University
  • Graduate Faculty (Primary Mentor of Grad Students), Boston University School of Medicine, Graduate Medical Sciences
  • Founding Associate Professor, Computing & Data Sciences Administration, Boston University

Education

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

Publications

  • 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.

    Read at: PubMed
  • 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.

    Read at: PubMed
  • 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.

    Read at: PubMed
  • 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.

    Read at: PubMed
  • 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.

    Read at: PubMed
  • 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.

    Read at: PubMed
  • 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.

    Read at: PubMed
  • Published on 12/17/2020

    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. PMID: 31761933.

    Read at: PubMed
  • Published on 12/10/2020

    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. PMID: 32936872.

    Read at: PubMed
  • Published on 11/26/2020

    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.

    Read at: PubMed

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