William Evan Johnson, PhD

Member, Bioinformatics Graduate Program

William Johnson
617.638.2541
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, Computational Biomedicine, Medicine, Boston University School of Medicine
  • 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
  • Graduate Faculty (Primary Mentor of Grad Students), Boston University School of Medicine, Graduate Medical Sciences
  • Member, Genome Science Institute, Boston University
  • 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 5/13/2020

    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 May 13. PMID: 32401417.

    Read at: PubMed
  • Published on 3/21/2020

    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. PMID: 32209386.

    Read at: PubMed
  • Published on 3/5/2020

    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. PMID: 32138770.

    Read at: PubMed
  • Published on 2/18/2020

    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. PMID: 32071385.

    Read at: PubMed
  • Published on 2/7/2020

    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 Mar; 6(3):192-204. PMID: 32101723.

    Read at: PubMed
  • Published on 1/7/2020

    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 Jan; 120:101898. PMID: 32090859.

    Read at: PubMed
  • Published on 11/25/2019

    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. PMID: 31761933.

    Read at: PubMed
  • Published on 10/10/2019

    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.

    Read at: PubMed
  • Published on 9/5/2019

    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.

    Read at: PubMed
  • Published on 5/2/2019

    Wang Z, Hu J, Johnson WE, Campbell JD. scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data. BMC Bioinformatics. 2019 May 02; 20(1):222. PMID: 31046658.

    Read at: PubMed

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