William E. Johnson, PhD

Adjunct Associate Professor, Boston University Chobanian & Avedisian School of Medicine

Biography

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.

Publications

  • Published 11/10/2024

    Sanchez GM, Hirsch ES, VanValkenburg A, Mayer DP, Gbedande K, Francis RL, Song W, Antao OQ, Brimmer KE, Lemenze A, Stephens R, Johnson WE, Weinstein JS. Aberrant zonal recycling of germinal center B cells impairs appropriate selection in lupus. Cell Rep. 2024 Nov 26; 43(11):114978. PMID: 39527476.

    Read at: PubMed

  • Published 8/30/2024

    Odom AR, Gill CJ, Pieciak R, Ismail A, Thea D, MacLeod WB, Johnson WE, Lapidot R. Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants. Gates Open Res. 2022; 6:143. PMID: 39345284.

    Read at: PubMed

  • Published 6/22/2024

    Quiles KR, Shao FZ, Johnson WE, Chen F. EPITHELIAL REMODELING AND MICROBIAL DYSBIOSIS IN THE LOWER RESPIRATORY TRACT OF VITAMIN A-DEFICIENT MOUSE LUNGS. bioRxiv. 2024 Jun 22. PMID: 38948802.

    Read at: PubMed

  • Published 6/20/2024

    Wang X, VanValkenberg A, Odom AR, Ellner JJ, Hochberg NS, Salgame P, Patil P, Johnson WE. Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures. BMC Infect Dis. 2024 Jun 20; 24(1):610. PMID: 38902649.

    Read at: PubMed

  • Published 5/31/2024

    Gao X, Johnson WE, Yourick MR, Campasino K, Sprando RL, Yourick JJ. Hepatotoxicity of silver nanoparticles: Benchmark concentration modeling of an in vitro transcriptomics study in human iPSC-derived hepatocytes. Regul Toxicol Pharmacol. 2024 Aug; 151:105653. PMID: 38825064.

    Read at: PubMed

Other Positions

  • Adjunct 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 Chobanian & Avedisian School of Medicine, Graduate Medical Sciences
  • Founding Associate Professor, Computing & Data Sciences Administration
    Boston University

Education

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