The Brubaker Lab takes a cross-cutting transdisciplinary approach to multiple disease applications of our core research areas. We believe that insights gleaned from addressing clinical need and elucidating disease mechanisms in one area will catalyze breakthroughs in others. Our lab has projects in the following disease areas which are constantly evolving through collaboration and emphasis varies over time.
Microbiome Pharmacology
Computational Preclinical Translation Modeling
Systems Immunology
Women's Health And Sex Differences
Contact us for our current efforts.
Assistant Professor, Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University School of Medicine
Dr. Brubaker obtained his Ph.D. in Systems Biology and Bioinformatics under the supervision of Dr. Mark R. Chance in the Center for Proteomics and Bioinformatics at Case Western Reserve University. As part of the March of Dimes Prematurity Research Center - Ohio Collaborative, his dissertation focussed on network and dynamical systems modeling of signaling networks in preterm birth.
Dr. Brubaker pursued postdoctoral studies with Dr. Douglas Lauffenburger in the Department of Biological Engineering at MIT where he developed computational methods to translate observations from animal models to humans. Dr. Brubaker started as an Assistant Professor in the Weldon School of Biomedical Engineering at Purdue University in Fall 2020.
The Brubaker Lab aims to understand the core mechanisms by which (i) host physiology is regulated by microbiomes and (ii) microbiome ecology and function are regulated by the host. We are a highly collaborative group with current efforts focused on Inflammatory Bowel Diseases, Musculoskeletal Pathologies, Type 2 Diabetes, and Bacterial Vaginosis.
Post Doctoral Research Assistant
Data and Operations Engineer
Dermatology Resident, University Hospitals
B.S., Purdue University 2024
Doctoral Student at Tufts University
B.S., Purdue University 2024
Medical Student at Northwestern University
Ph.D., Purdue University 2024
Principal Project Statistician at Eli Lilly and Company
M.S., Purdue University 2024
Medical Student at the University of Kentucky
M.D., Indiana University School of Medicine 2024
Resident at IU School of Medicine
Cross-Species Modeling Identifies Gene Signatures in Type 2 Diabetes Mouse Models Predictive of Inflammatory and Estrogen Signaling Pathways Associated with Alzheimer's Disease Outcomes in Humans, Ball, Brendan K.; Proctor, Elizabeth A.; Brubaker, Douglas K., Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2025
SYSTEMS MODELING OF GUT MICROBIOME REGULATION OF ESTROGEN RECEPTOR BETA SIGNALING IN ULCERATIVE COLITIS, Munoz-Briones, Javier; Trinh, Alan; Simpson, Abigail; Stingel, Rachel; Jena, Smrutiti; Doszpoly, Agnes; Urlu, Merve; Trapecar, Martin; Cross, Tzu-Wen; Brubaker, Douglas K, SYSTEMS MODELING OF HOST MICROBIOME INTERACTIONS IN INFLAMMATORY BOWEL DISEASES, 2024
LATENT INTERACTING VARIABLE-EFFECTS (LIVE) MODELING OF GUT MICROBIOME MULTI-OMICS IN INFLAMMATORY BOWEL DISEASE, Munoz-Briones, Javier; Brubaker, Douglas K, SYSTEMS MODELING OF HOST MICROBIOME INTERACTIONS IN INFLAMMATORY BOWEL DISEASES, 2024
Detailed survey of an in vitro intestinal epithelium model by single-cell transcriptomics, Ran, Ran; Muñoz Briones, Javier; Jena, Smrutiti; Anderson, Nicole L.; Olson, Matthew R.; Green, Leopold N.; Brubaker, Douglas K., iScience, 2024
Differential responses of primary neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer's disease-associated metabolites, Ball, Brendan K.; Kuhn, Madison K.; Fleeman Bechtel, Rebecca M.; Proctor, Elizabeth A.; Brubaker, Douglas K., Scientific Reports, 2024
Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation, Merk, Liana N.; Shur, Andrey S.; Jena, Smrutiti; Munoz, Javier; Brubaker, Douglas K.; Murray, Richard M.; Green, Leopold N., ACS synthetic biology, 2024
Computational Microbiome Pharmacology Analysis Elucidates the Anti-Cancer Potential of Vaginal Microbes and Metabolites, Lawore, Damilola C.; Jena, Smrutiti; Berard, Alicia R.; Birse, Kenzie; Lamont, Alana; Mackelprang, Romel D.; Noel-Romas, Laura; Perner, Michelle; Hou, Xuanlin; Irungu, Elizabeth; Mugo, Nelly; Knodel, Samantha; Muwonge, Timothy R.; Katabira, Elly; Hughes, Sean M.; Levy, Claire; Calienes, Fernanda L.; Hladik, Florian; Lingappa, Jairam R.; Burgener, Adam D.; Green, Leopold N.; Brubaker, Douglas K., bioRxiv: The Preprint Server for Biology, 2024
Cross-disease modeling of peripheral blood identifies biomarkers of type 2 diabetes predictive of Alzheimer's disease, Ball, Brendan K.; Hyun Park, Jee; Proctor, Elizabeth A.; Brubaker, Douglas K., bioRxiv: The Preprint Server for Biology, 2024
Systematic analysis of human colorectal cancer scRNA-seq revealed limited pro-tumoral IL-17 production potential in gamma delta T cells, Ran, Ran; Trapecar, Martin; Brubaker, Douglas K., Neoplasia (New York, N.Y.), 2024
Association Between Intestinal Changes and Systemic Cytokines in Mouse Dysbiosis Models, Jeffries, Alison; Villarreal, Cameron; Brubaker, Douglas; Chan, Deva, Proceedings of IMPRS, 2023
Vaginal epithelial dysfunction is mediated by the microbiome, metabolome, and mTOR signaling, Berard, Alicia R.; Brubaker, Douglas K.; Birse, Kenzie; Lamont, Alana; Mackelprang, Romel D.; Noël-Romas, Laura; Perner, Michelle; Hou, Xuanlin; Irungu, Elizabeth; Mugo, Nelly; Knodel, Samantha; Muwonge, Timothy R.; Katabira, Elly; Hughes, Sean M.; Levy, Claire; Calienes, Fernanda L.; Lauffenburger, Douglas A.; Baeten, Jared M.; Celum, Connie; Hladik, Florian; Lingappa, Jairam; Burgener, Adam D., Cell Reports, 2023
TRANS-OMIC KNOWLEDGE TRANSFER MODELING INFERS GUT MICROBIOME BIOMARKERS OF ANTI-TNF RESISTANCE IN ULCERATIVE COLITIS, Trinh, Alan; Ran, Ran; Brubaker, Douglas K., Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2023
Differential responses of primary neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer's disease-associated metabolites, Ball, Brendan K.; Kuhn, Madison K.; Fleeman, Rebecca M.; Proctor, Elizabeth A.; Brubaker, Douglas K., bioRxiv: The Preprint Server for Biology, 2023
Enhanced annotation of CD45RA to distinguish T cell subsets in single-cell RNA-seq via machine learning, Ran, Ran; Brubaker, Douglas K., Bioinformatics Advances, 2023
Latent Interacting Variable-Effects Modeling of Gut Microbiome Multi-Omics in Inflammatory Bowel Disease, Munoz, Javier. E.; Brubaker, Douglas. K., , 2022
Method Development Involving Modeling Bacterial Metabolite Regulation of Vaginal Epithelial Cell Signaling in Bacterial Vaginosis, Trinh, Alan; Brubaker, Douglas, , 2022
Endogenous production of hyaluronan, PRG4, and cytokines is sensitive to cyclic loading in synoviocytes, Pendyala, Meghana; Woods, Paige S.; Brubaker, Douglas K.; Blaber, Elizabeth A.; Schmidt, Tannin A.; Chan, Deva D., PloS One, 2022
Cross-species transcriptomic signatures predict response to MK2 inhibition in mouse models of chronic inflammation, Suarez-Lopez, Lucia; Shui, Bing; Brubaker, Douglas K.; Hill, Marza; Bergendorf, Alexander; Changelian, Paul S.; Laguna, Aisha; Starchenko, Alina; Lauffenburger, Douglas A.; Haigis, Kevin M., iScience, 2021
Computational Interspecies Translation Between Alzheimer's Disease Mouse Models and Human Subjects Identifies Innate Immune Complement, TYROBP, and TAM Receptor Agonist Signatures, Distinct From Influences of Aging, Lee, Meelim J.; Wang, Chuangqi; Carroll, Molly J.; Brubaker, Douglas K.; Hyman, Bradley T.; Lauffenburger, Douglas A., Frontiers in Neuroscience, 2021
Cell surface integrin α5ß1 clustering negatively regulates receptor tyrosine kinase signaling in colorectal cancer cells via glycogen synthase kinase 3, Starchenko, Alina; Graves-Deal, Ramona; Brubaker, Douglas; Li, Cunxi; Yang, Yuping; Singh, Bhuminder; Coffey, Robert J.; Lauffenburger, Douglas A., Integrative Biology: Quantitative Biosciences from Nano to Macro, 2021
Translating preclinical models to humans, Brubaker, Douglas K.; Lauffenburger, Douglas A., Science (New York, N.Y.), 2020
Clostridioides difficile-Associated Antibiotics Alter Human Mucosal Barrier Functions by Microbiome-Independent Mechanisms, Kester, Jemila C.; Brubaker, Douglas K.; Velazquez, Jason; Wright, Charles; Lauffenburger, Douglas A.; Griffith, Linda G., Antimicrobial Agents and Chemotherapy, 2020
An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease, Brubaker, Douglas K.; Kumar, Manu P.; Chiswick, Evan L.; Gregg, Cecil; Starchenko, Alina; Vega, Paige N.; Southard-Smith, Austin N.; Simmons, Alan J.; Scoville, Elizabeth A.; Coburn, Lori A.; Wilson, Keith T.; Lau, Ken S.; Lauffenburger, Douglas A., Science Signaling, 2020
Coagulopathy signature precedes and predicts severity of end-organ heat stroke pathology in a mouse model, Proctor, Elizabeth A.; Dineen, Shauna M.; Van Nostrand, Stephen C.; Kuhn, Madison K.; Barrett, Christopher D.; Brubaker, Douglas K.; Yaffe, Michael B.; Lauffenburger, Douglas A.; Leon, Lisa R., Journal of thrombosis and haemostasis: JTH, 2020
Tissue-Specific Oncogenic Activity of KRASA146T, Poulin, Emily J.; Bera, Asim K.; Lu, Jia; Lin, Yi-Jang; Strasser, Samantha Dale; Paulo, Joao A.; Huang, Tannie Q.; Morales, Carolina; Yan, Wei; Cook, Joshua; Nowak, Jonathan A.; Brubaker, Douglas K.; Joughin, Brian A.; Johnson, Christian W.; DeStefanis, Rebecca A.; Ghazi, Phaedra C.; Gondi, Sudershan; Wales, Thomas E.; Iacob, Roxana E.; Bogdanova, Lana; Gierut, Jessica J.; Li, Yina; Engen, John R.; Perez-Mancera, Pedro A.; Braun, Benjamin S.; Gygi, Steven P.; Lauffenburger, Douglas A.; Westover, Kenneth D.; Haigis, Kevin M., Cancer Discovery, 2019
Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation, Brubaker, Douglas K.; Paulo, Joao A.; Sheth, Shikha; Poulin, Emily J.; Popow, Olesja; Joughin, Brian A.; Strasser, Samantha Dale; Starchenko, Alina; Gygi, Steven P.; Lauffenburger, Douglas A.; Haigis, Kevin M., Cell Systems, 2019
Substrate-based kinase activity inference identifies MK2 as driver of colitis, Strasser, Samantha Dale; Ghazi, Phaedra C.; Starchenko, Alina; Boukhali, Myriam; Edwards, Amanda; Suarez-Lopez, Lucia; Lyons, Jesse; Changelian, Paul S.; Monahan, Joseph B.; Jacobsen, Jon; Brubaker, Douglas K.; Joughin, Brian A.; Yaffe, Michael B.; Haas, Wilhelm; Lauffenburger, Douglas A.; Haigis, Kevin M., Integrative Biology: Quantitative Biosciences from Nano to Macro, 2019
Computational translation of genomic responses from experimental model systems to humans, Brubaker, Douglas K.; Proctor, Elizabeth A.; Haigis, Kevin M.; Lauffenburger, Douglas A., PLoS computational biology, 2019
Integrated microRNA and mRNA network analysis of the human myometrial transcriptome in the transition from quiescence to labor, Ackerman, William E.; Buhimschi, Irina A.; Brubaker, Douglas; Maxwell, Sean; Rood, Kara M.; Chance, Mark R.; Jing, Hongwu; Mesiano, Sam; Buhimschi, Catalin S., Biology of Reproduction, 2018
Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis, Lyons, Jesse; Brubaker, Douglas K.; Ghazi, Phaedra C.; Baldwin, Katherine R.; Edwards, Amanda; Boukhali, Myriam; Strasser, Samantha Dale; Suarez-Lopez, Lucia; Lin, Yi-Jang; Yajnik, Vijay; Kissil, Joseph L.; Haas, Wilhelm; Lauffenburger, Douglas A.; Haigis, Kevin M., Science Signaling, 2018
FREQUENT SUBGRAPH MINING OF PERSONALIZED SIGNALING PATHWAY NETWORKS GROUPS PATIENTS WITH FREQUENTLY DYSREGULATED DISEASE PATHWAYS AND PREDICTS PROGNOSIS, Durmaz, Arda; Henderson, Tim A. D.; Brubaker, Douglas; Bebek, Gurkan, Pacific Symposium on Biocomputing, 2017
Computational Investigation of Biological Networks and Progesterone Signaling Dynamics in Preterm Birth, Brubaker, Douglas K.; Barnholtz-Sloan, Jill; Mesiano, Sam; Barbaro, Alethea, , 2016
A dynamical systems model of progesterone receptor interactions with inflammation in human parturition, Brubaker, Douglas; Barbaro, Alethea; R Chance, Mark; Mesiano, Sam, BMC systems biology, 2016
Finding lost genes in GWAS via integrative-omics analysis reveals novel sub-networks associated with preterm birth, Brubaker, Douglas; Liu, Yu; Wang, Junye; Tan, Huiqing; Zhang, Ge; Jacobsson, Bo; Muglia, Louis; Mesiano, Sam; Chance, Mark R., Human Molecular Genetics, 2016
Drug Intervention Response Predictions with PARADIGM (DIRPP) identifies drug resistant cancer cell lines and pathway mechanisms of resistance, Brubaker, Douglas; Difeo, Analisa; Chen, Yanwen; Pearl, Taylor; Zhai, Kaide; Bebek, Gurkan; Chance, Mark; Barnholtz-Sloan, Jill, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2014