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Ben Johnson, Ph.D.
Biography
Dr. Ben Johnson earned his B.S. in biology from Calvin College and his Ph.D. in microbiology and molecular genetics from Michigan State University. His graduate work focused on developing chemical probes to dissect molecular mechanisms of environmental sensing and adaptation in Mycobacterium tuberculosis (TB), with the ultimate goal of identifying new therapies against TB infections. The small molecules identified often would not directly kill TB in vitro and instead acted as anti-virulence compounds, disarming the pathogen during infection. Thus, computational biology approaches were used in conjunction with “wet” experiments to narrow down putative pathways altered in response to treatment with these experimental compounds to generate tractable hypotheses. Following graduate school, he worked as a bioinformatics research scientist in the Bioinformatics and Biostatistics Core at Van Andel Institute doing sequencing data analysis. In 2019, he joined the laboratories of Drs. Tim Triche and Hui Shen as a postdoctoral fellow.
Current research focus
Optimization of whole-genome bisulfite sequencing from low input single-cell and cell-free DNA. This technique will be a powerful method to study DNA methylation changes in cell transformation during tumor progression (single-cell level) and to detect DNA methylation changes in cancer patients’ plasma to serve as biomarkers in early tumorigenesis detection.
Education & Training
Bioinformatics research scientist, Bioinformatics and Biostatistics Core, Van Andel Research Institute
Ph.D. in microbiology and molecular genetics, Michigan State University (Advisor: Dr. Robert Abramovitch)
Thesis: Investigating Mycobacterium tuberculosis pH-dependent adaptations
B.S. in biology, Calvin College
Awards & External Funding
Hsiung-Kimball Award, Michigan State University (2016)
Rudolph Hugh Fellowship, Michigan State University (2015)
National Science Foundation Scientific Computing Scholarship (2010–2011)
Henry Bengelink Scholarship, Department of Biology, Calvin College (2010–2011)
Knollcrest Scholarship, Calvin College (2007–2011)
Teaching assistant selected to train faculty involved in the Science Education Alliance (SEA) HHMI Mycobacteriophage Research Laboratory, HHMI Janelia Farms Research Campus (2010)
Presidential Scholarship, Calvin College (2007)
Society Memberships
International Society for Computational Biology
Publications
To view a list of selected publications click below.
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Grit JL, Johnson BK, Dischinger PS, Essenburg CJ, Adams M, Campbell S, Pollard K, Pratilas CA, Triche TJ Jr., Graveel CR, Steensma MR. 2021. Distinctive epigenomic alterations in NF1-deficient cutaneous and plexiform neurofibromas drive differential MKK/p38 signaling. Epi Chromatin 14(7).
George JW, Fan H, Johnson B, Carpenter TJ, Foy KK, Chatterjee A, Patterson AL, Koeman J, Adams M, Madaj ZB, Chesla D, Marsh EE, Triche TJ, Shen H, Teixeira JM. 2019. Integrated epigenome, exome, and transcriptome analyses reveal molecular subtypes and homeotic transformation in uterine fibroids. Cell Rep.
Capone C, Colombo AR, Johnson BK, Triche TJ Jr., Ramsingh G. 2018. Methylome of human senescent hematopoietic progenitors. Exp Hematol Oncol.
Ziyun W, Senchuk MM, Dues DJ, Johnson BK, Cooper J, Lew L, Machiela E, Schaar CE, DeJonge H, Blackwell K, VanRaamsdonk JM. 2018. Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathways. BMC Biology.
Senchuk MM, Dues DJ, Schaar CE, Johnson BK, Madaj ZM, Bowman MJ, Winn ME, Van Raamsdonk JM. 2018. Activation of DAF-16/FOXO by reactive oxygen species contribute to longevity in long-lived mitochondrial mutants in C. elegans. PLoS Genetics 14(3):e1007268.
Coulson GB*, Johnson BK*, Zheng H, Colvin CJ, Fillinger RJ, Haiderer ER, Hammer ND, Abramovitch RB. 2017. Targeting Mycobacterium tuberculosis sensitivity to thiol stress at acidic pH kills the bacterium and potentiates antibiotics. Cell Chem Biol 24(8):993–1004.e4.
*Equal contributions
Dues DJ, Schaar CE, Johnson BK, Bowman MJ, Winn ME, Senchuk MM, Van Raamsdonk. 2017. Uncoupling of oxidative stress resistance and lifespan in long-lived isp-1 mitochondrial mutants in Caenorhabditis elegans. Free Radic Biol Med 108:362–373.
Johnson BK, Abramovitch RB. 2017. Small molecules that sabotage bacterial virulence. Trends Pharmacol Sci 38(4):339–362.
*Featured review and received the cover for this issue
Zheng H, Colvin CJ, Johnson BK, Kirchhoff PD, Wilson M, Jorgensen-Muga K, Larsen SD, Abramovitch RB. 2017. Inhibitors of Mycobacterium tuberculosis DosRST signaling and persistence. Nat Chem Biol 13(2):218–225.
Williams EA, Mba Medie F, Bosserman RE, Johnson BK, Reyna C, Ferrell MJ, Champion MM, Abramovitch RB, Champion PA. 2017. A nonsense mutation in Mycobacterium marinum that is suppressible by a novel mechanism. Infect Immun 85(2).
Posters/Oral Presentations
Johnson BK, Triche TJ Jr. Semi-supervised manifold learning of chromatin compartmentalization. Biological Data Science, Cold Spring Harbor, New York, 2018
Johnson BK, Zubair A, Triche TJ Jr. ATACseeker: a toolkit for ATAC- and scATAC-seq analysis. Bioconductor, Toronto, Ontario, 2018
Johnson BK, Madaj ZB, Triche TJ Jr. Statistical approaches to improve detection of differential DNA methylation. ISMB/ISCB, Chicago, Illinois, 2018
VanOeveren S, Johnson BK, Bernstein AI. Parkinson’s disease associated alterations in the DNA modifications, 5-methylcytosine and 5-hydroxymethylcytosine. Neuroscience, Washington D.C., District of Colombia, 2017
Johnson BK, Colvin CJ, Needle DB, Mba Medie F, Champion PAD, Abramovitch RB. The carbonic anhydrase inhibitor ethoxzolamide inhibits the Mycobacterium tuberculosis PhoPR-regulon and Esx-1 secretion and attenuates virulence. Microbial Pathogenesis & HostResponse (Cold Spring Harbor Laboratory), Cold Spring Harbor, New York, 2015