Jonathan Golob

Physician Scientist. Biomedical Engineer and Computer Scientist. Transplant Infectious Disease Specialist. Microbiome Scientist. Software Developer. Improving patient outcomes through innovative treatments.
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As a computational biologist and physician, I specialize in applying AI/ML to enhance human health. With a background in computer science, biomedical engineering, and over two decades in biomedical research, I’m skilled in developing software and computational workflows. My focus is on creating robust, reproducible, and inclusive AI/ML tools for healthcare, with a goal of translating them to benefit patients and providers. Adept at leading teams, I am adaptable and constantly seeking growth through new experiences.

Work Experience

Assistant Professor

University of Michigan Ann Arbor. Internal Medicine / Infectious Diseases | 2018 - Present

I run a research group focused on the practical clinical translation of microbiome science back to patients within the framework of precision medicine. We combine the development of novel computational techniques with cutting edge in vitro and in vivo models. I responded to the COVID-19 pandemic, providing direct patient care to hundreds of critically ill people while developing and implementing human observational and interventional trials.

Senior Fellow / Research Associate / Joel Meyers Endowment Fellow

Fred Hutch / University of Washington | 2016 - 2018

I was a postdoctoral fellow at the Fred Hutch in Seattle. I studied how the gut microbiome relates and mechanistically contributes to outcomes in patients undergoing hematpoietic stem cell transplant. Mentor: David Fredricks.

  • Research fellow, combining the analysis of human observational study data with novel analytic and analysis techniques.
  • Attending physician with a speciality in cancer-related infections.

Doctoral Candidate

University of Washington. Department of Pathology. | 2003 - 2009

My doctoral work focused on using the (then new) pluripotent stem cell model to establish the basic epigenetic mechanisms behind the earliest stages of human development. To do so, I employed some of the earliest ’next generation’ high throughput sequencing data and developed a novel computational pipeline to successfully integrate transcriptional micro-array and tiling array data. Mentor: Charles ‘Chuck’ Murry.

Science Writer

The Stranger. Arstechnica | 2006 - Present

I have written about science and science-related topics for a variety of publications, including the Seattle-Area alt-weekly The Stranger, Arstechnica, and others. This is writing oriented to non-scientists.

  • ‘Dear Science’ column at the Stranger, in which I answered written-in questions by readers.
  • Extensive analysis and coverage of the 2008 financial crisis and 2011 Fukushima disaster.

Projects

The Human Microbiome Atlas

AI/ML and Computational Biology

Building off of the baseline technology in MaLiAmPi we are developing an atlas of the human microbiome in health and disease. This tool allows for harmonization of new raw microbiome data into existing sets of features, and is a key step towards the eventual clinical translation of microbiome-based predictive models like those developed in the DREAM challenge.

Decoding the genetic jigsaw

Clinical translation and science communication

Direct to consumer genetic test enable people to have unprecedented access to their genetics. But decoding the meaning of genetic variation, particularly how to interpret a ‘variant of unknown significance’ is fraught, and a fascinating topic I am thrilled to explore with Ranjani Ramamurthy.

March of Dimes Vaginal Microbiome Preterm Birth Prediction DREAM Challenge

AI/ML

Successful identification of pregnancies at high risk for early preterm birth from vaginal microbiome data on independent datasets harmonized post-hoc. Partners: Marina Sirota and Tomiko Osktosky.

MaLiAmPi: Harmonization and Tokenization of raw microbiome data

Bioinformatics and Software Development

Developed a novel taxonomy-free way of harmonizing technically diverse raw microbiome data and then tokenizing into a stable and biologically meaningful set of features suitable for artificial intelligence, machine learning, and associative modeling.

Geneshot: Enabling gene oriented reference-free metagenomics

Bioinformatics and Software Development

Developed a novel reference-free workflow for tokenizing raw shotgun metagenomics data into biologically meaningful sets of features combined with rigorous and performant dimensionality-reduction tools. Partners: Sam Minot and Amy Willis.

The Microbiome and outcomes for bone marrow transplant patients

Basic Science

Identified the clinical relevance of microbiome butyrate production in inhibiting recovery after injury to the gut during hematopoietic stem cell transplant. This combined human observational data with organoid-based in vitro modeling. Likewise, we dentified latent human herpesvirus 7 infection in epithelium as an important modulator of host-microbiome interactions.

Early phase human clinical trials targeting the microbiome during cancer treatment

Early phase human clinical trials

Developed the biomarker components of a prebiotic human microbiome intervention in patients recieving immune checkpoint inhibitor therapy for skin cancer, with a successfully completed phase 0/1 trial in patients. Completed the analysis of all biomarker data for the same prebiotic intervention (phase 0/1) in patients undergoing hematopoietic stem cell transplant.

Human interventional and observational trials for the COVID-19 Pandemic

Late phase human clinical trials

I am the unblinded study physician for an international COVID-19 vaccine trial. I was on he organizing committee for a cell-therapy trial during the COVID-19 pandemic, and a site PI. I developed the strategy to validate the COVID-19 serology testing for the University of Michigan clinical laboratory. I developed one of the earliest case series of COVID-19 patients, leading to early identification of IL6 blockade as a viable candidate for severely ill patients.

Information

Personal Interests

Board games, Photography, Travelling, Writing, Cycling, Cross-country Skiing

Selected Peer-Reviewed Publications

  • J. Hédou et al., “Discovery of sparse, reliable omic biomarkers with Stabl,” Nat Biotechnol, Jan. 2024, doi: 10.1038/s41587-023-02033-x
  • J. L. Golob et al., “Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research,” Cell Rep Med, p. 101350, Dec. 2023, doi: 10.1016/j.xcrm.2023.101350
  • S. S. Minot et al., “MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies,” Cell Reports Methods, p. 100639, Nov. 2023, doi: 10.1016/j.crmeth.2023.100639
  • J. Golob et al., “The Microbiome in Quiescent Crohn’s Disease with Persistent Symptoms Show Disruptions in Microbial Sulfur and Tryptophan Pathways,” Gastro Hep Advances, p. S2772572323001802, Nov. 2023, doi: 10.1016/j.gastha.2023.11.005
  • J. L. Golob, “Human Microbiomes and Disease for the Biomedical Data Scientist,” Annu Rev Biomed Data Sci, vol. 6, pp. 259–273, Aug. 2023, doi: 10.1146/annurev-biodatasci-020722-043017
  • M. E. Bowdish et al., “A Randomized Trial of Mesenchymal Stromal Cells for Moderate to Severe ARDS From COVID-19,” Am J Respir Crit Care Med, Sep. 2022, doi: 10.1164/rccm.202201-0157OC
  • C. Ogimi et al., “Exposure to antibiotics with anaerobic activity before respiratory viral infection is associated with respiratory disease progression after hematopoietic cell transplant,” Bone Marrow Transplant, Sep. 2022, doi: 10.1038/s41409-022-01790-8
  • K. Sugihara et al., “Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction,” Cell Rep, vol. 40, no. 3, p. 111093, Jul. 2022, doi: 10.1016/j.celrep.2022.111093
  • M. J. Pianko and J. L. Golob, “Host-microbe interactions and outcomes in multiple myeloma and hematopoietic stem cell transplantation,” Cancer Metastasis Rev, vol. 41, no. 2, pp. 367–382, Jun. 2022, doi: 10.1007/s10555-022-10033-7
  • J. Imai et al., “A potential pathogenic association between periodontal disease and Crohn’s disease,” JCI Insight, vol. 6, no. 23, p. e148543, Dec. 2021, doi: 10.1172/jci.insight.148543
  • R. J. Cieza, J. L. Golob, J. A. Colacino, and C. E. Wobus, “Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses,” Viruses, vol. 13, no. 6, p. 1059, Jun. 2021, doi: 10.3390/v13061059
  • J. L. Golob, N. Lugogo, A. S. Lauring, and A. S. Lok, “SARS-CoV-2 vaccines: a triumph of science and collaboration,” JCI Insight, vol. 6, no. 9, p. 149187, May 2021, doi: 10.1172/jci.insight.149187
  • S. S. Minot, K. C. Barry, C. Kasman, J. L. Golob, and A. D. Willis, “geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response,” Genome Biol, vol. 22, no. 1, p. 135, May 2021, doi: 10.1186/s13059-021-02355-6
  • J. L. Golob and K. Rao, “Signal vs. noise: how to analyze the microbiome and make progress on antimicrobial resistance,” J Infect Dis, Apr. 2021, doi: 10.1093/infdis/jiab184
  • A. E. Chang, J. L. Golob, T. M. Schmidt, D. C. Peltier, C. D. Lao, and M. Tewari, “Targeting the Gut Microbiome to Mitigate Immunotherapy-Induced Colitis in Cancer,” Trends Cancer, Mar. 2021, doi: 10.1016/j.trecan.2021.02.005
  • E. J. Dela Cruz et al., “Genetic Variation in Toll-Like Receptor 5 and Colonization with Flagellated Bacterial Vaginosis-Associated Bacteria,” Infect Immun, vol. 89, no. 3, Feb. 2021, doi: 10.1128/IAI.00060-20
  • C. A. Goldstein et al., “The prevalence and impact of pre-existing sleep disorder diagnoses and objective sleep parameters in patients hospitalized for COVID-19,” J Clin Sleep Med, Feb. 2021, doi: 10.5664/jcsm.9132
  • E. R. Duke et al., “CMV viral load kinetics as surrogate endpoints after allogeneic transplantation,” J Clin Invest, vol. 131, no. 1, Jan. 2021, doi: 10.1172/JCI133960
  • P. Sharma et al., “COVID-19 Outcomes Among Solid Organ Transplant Recipients: A Case-control Study,” Transplantation, vol. 105, no. 1, pp. 128–137, Jan. 2021, doi: 10.1097/TP.0000000000003447
  • J. L. Golob and S. S. Minot, “In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision,” BMC Bioinformatics, vol. 21, no. 1, p. 459, Oct. 2020, doi: 10.1186/s12859-020-03802-0
  • E. R. Duke et al., “Cytomegalovirus viral load kinetics as surrogate endpoints after allogeneic transplantation,” J Clin Invest, Sep. 2020, doi: 10.1172/JCI133960
  • P. Sharma et al., “COVID-19 Outcomes Among Solid Organ Transplant Recipients: A Case-Control Study,” Transplantation, Sep. 2020, doi: 10.1097/TP.0000000000003447
  • E. C. Somers et al., “Tocilizumab for treatment of mechanically ventilated patients with COVID-19,” Clinical Infectious Diseases, p. ciaa954, Jul. 2020, doi: 10.1093/cid/ciaa954
  • J. L. Golob et al., “Butyrogenic bacteria after acute graft-versus-host disease (GVHD) are associated with the development of steroid-refractory GVHD,” Blood Adv, vol. 3, no. 19, pp. 2866–2869, Oct. 2019, doi: 10.1182/bloodadvances.2019000362
  • J. L. Golob et al., “HIV DNA levels and decay in a cohort of 111 long-term virally suppressed patients,” AIDS, vol. 32, no. 15, pp. 2113–2118, Sep. 2018, doi: 10.1097/QAD.0000000000001948
  • T. J. MacAllister, Z. Stednick, J. L. Golob, M.-L. Huang, and S. A. Pergam, “Underutilization of norovirus testing in hematopoietic cell transplant recipients at a large cancer center,” Am J Infect Control, vol. 46, no. 1, pp. 100–102, Jan. 2018, doi: 10.1016/j.ajic.2017.06.010
  • C. Ogimi et al., “Antibiotic Exposure Prior to Respiratory Viral Infection Is Associated with Progression to Lower Respiratory Tract Disease in Allogeneic Hematopoietic Cell Transplant Recipients,” Biol. Blood Marrow Transplant., vol. 24, no. 11, pp. 2293–2301, 2018, doi: 10.1016/j.bbmt.2018.05.016
  • J. L. Golob et al., “Stool Microbiota at Neutrophil Recovery Is Predictive for Severe Acute Graft vs Host Disease After Hematopoietic Cell Transplantation,” Clin. Infect. Dis., vol. 65, no. 12, pp. 1984–1991, Nov. 2017, doi: 10.1093/cid/cix699
  • A. Bhattacharyya et al., “Graft-Derived Reconstitution of Mucosal-Associated Invariant T Cells after Allogeneic Hematopoietic Cell Transplantation,” Biol. Blood Marrow Transplant., Oct. 2017, doi: 10.1016/j.bbmt.2017.10.003
  • J. L. Golob, E. Margolis, N. G. Hoffman, and D. N. Fredricks, “Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities,” BMC Bioinformatics, vol. 18, no. 1, p. 283, May 2017, doi: 10.1186/s12859-017-1690-0
  • J. L. Golob et al., “Evidence that gene activation and silencing during stem cell differentiation requires a transcriptionally paused intermediate state,” PLoS ONE, vol. 6, no. 8, p. e22416, 2011, doi: 10.1371/journal.pone.0022416
  • J. L. Golob, S. L. Paige, V. Muskheli, L. Pabon, and C. E. Murry, “Chromatin remodeling during mouse and human embryonic stem cell differentiation,” Dev. Dyn., vol. 237, no. 5, pp. 1389–1398, May 2008, doi: 10.1002/dvdy.21545
  • S. Ueno et al., “Biphasic role for Wnt/beta-catenin signaling in cardiac specification in zebrafish and embryonic stem cells,” Proc. Natl. Acad. Sci. U.S.A., vol. 104, no. 23, pp. 9685–9690, Jun. 2007, doi: 10.1073/pnas.0702859104
  • T. E. Boursalian, J. Golob, D. M. Soper, C. J. Cooper, and P. J. Fink, “Continued maturation of thymic emigrants in the periphery,” Nat. Immunol., vol. 5, no. 4, pp. 418–425, Apr. 2004, doi: 10.1038/ni1049
  • Y. Cui, J. Golob, E. Kelleher, Z. Ye, D. Pardoll, and L. Cheng, “Targeting transgene expression to antigen-presenting cells derived from lentivirus-transduced engrafting human hematopoietic stem/progenitor cells,” Blood, vol. 99, no. 2, pp. 399–408, Jan. 2002, doi: 10.1182/blood.v99.2.399
  • Z. Gao, J. Golob, V. M. Tanavde, C. I. Civin, R. G. Hawley, and L. Cheng, “High levels of transgene expression following transduction of long-term NOD/SCID-repopulating human cells with a modified lentiviral vector,” Stem Cells, vol. 19, no. 3, pp. 247–259, 2001, doi: 10.1634/stemcells.19-3-247