Ben Johnson, Ph.D.

Ben Johnson, Ph.D.
Postdoctoral fellow, Shen Laboratory


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 and, in 2021, he transitioned fully to the Shen Lab.


Current research focus

My current research focuses on the discovery and characterization of the molecular underpinnings that define the landscape of cellular state and fate in reproductive cancers. To this end, I have developed new experimental and computational methods that provide highly detailed tissue and single-cell level snapshots of this landscape. Through these insights, I am dissecting the origins of reproductive cancers and where clinical intervention can benefit earlier detection and improve patient outcomes.

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


To view a list of selected publications click below.

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Waldhart AN, Muhire B, Johnson B, Pettinga D, Madaj ZB, Wolfrum E, Dysktra H, Wegert V, Pospisilik JA, Han X, Wu N. 2021. Excess dietary carbohydrate affects mitochondrial integrity as observed in brown adipose tissue. Cell Rep 35(5):109488.

Chassé MH, Johnson BK, Boguslawski EA, Sorensen KM, Rosien JE, Kang MH, Reynolds CP, Heo L, Madaj ZB, Beddows I, Foxa GE, Kitchen-Goosen SM, Williams BO, Triche TJ Jr, Grohar PJ. 2021. Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor. EMBO Mol Med 13(2):e12640.

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 persistenceNat 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