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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<title>The Brubaker Lab</title>
<link rel="icon" type="image/x-icon" href="img/favicon.png">
<meta name="description" content="The Brubaker Lab" />
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<a href="#" class="w3-bar-item w3-button">The Brubaker Lab</a>
<a href="#people" class="w3-bar-item w3-button w3-hide-small">People</a>
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<h1>
Translational Systems Immunology of Host-Microbiome
Interactions
</h1>
<h3>Case Western Reserve University School of Medicine</h3>
<p class="w3-justify">
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.
</p>
<div class="w3-row-padding w3-padding-32">
<div class="w3-quarter w3-padding">
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<p>Microbiome Pharmacology</p>
</div>
<div class="w3-quarter w3-padding">
<i class="fa-solid fa-computer w3-xxlarge"></i>
<p>Computational Preclinical Translation Modeling</p>
</div>
<div class="w3-quarter w3-padding">
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<p>Systems Immunology</p>
</div>
<div class="w3-quarter w3-padding">
<i class="fa-solid fa-person-half-dress w3-xxlarge"></i>
<p>Women's Health And Sex Differences</p>
</div>
</div>
<p>
<a href="#contact">Contact us</a> for our current efforts.
</p>
</div>
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PEOPLE
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<!--Doug's Information-->
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<img class="w3-image w3-hide-medium w3-hide-large w3-card" style="width:66%"
src="img/portraits/Brubaker, Douglas.jpg">
<h3>Douglas Brubaker, Ph.D.</h3>
<p class="w3-opacity">
Assistant Professor, Center for Global Health and
Diseases, Department of Pathology, Case Western
Reserve University School of Medicine
</p>
<!-- Contact icons-->
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<p class="w3-justify">
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.
</p>
<p class="w3-justify">
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.
</p>
<p class="w3-justify">
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.
</p>
<!--
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STAFF
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-->
<h3 class="w3-center">Staff</h3>
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<img class="w3-image" alt="Raymond Krajci" src="img/portraits/Krajci, Raymond.jpg">
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<h4>Raymond Krajci</h4>
<p class="w3-opacity">Data and Operations Engineer</p>
</div>
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</div>
</div>
</div>
<!--
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GRADUATE STUDENTS
***************************************************************
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<div class="w3-card">
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<h4>Alexander Bergendorf</h4>
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<h4>Alexis Heath</h4>
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<h4>Rachel Liu, Pharm.D.</h4>
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<div class="w3-card">
<img class="w3-image" src="img/portraits/Nemecio, Dali.jpg">
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<h4>Dalí Nemecio</h4>
</div>
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</div>
<!--
***************************************************************
AFFILIATES
***************************************************************
-->
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<div class="w3-row-padding w3-stretch">
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***************************************************************
-->
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<h4>Grant Williams</h4>
</div>
</div>
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<h4>Sophia Wang</h4>
</div>
</div>
</div>
</div>
<!--
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<p class="w3-center w3-opacity"><i>Degree/position and destination.</i></p>
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<h4>Brendan Ball, Ph.D.</h4>
<p class="w3-opacity">Ph.D., Purdue University 2025</p>
<p class="w3-opacity">Postdoc at Stanford University in the Gentles Lab</p>
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<h4>Reagan Bushok</h4>
<p class="w3-opacity">B.S., Purdue University 2024</p>
<p class="w3-opacity">Doctoral Student at Tufts University</p>
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<p class="w3-opacity">B.S., Purdue University 2024</p>
<p class="w3-opacity">Medical Student at Northwestern University</p>
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<h4>Smrutiti Jena, Ph.D.</h4>
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<h4>Damilola Lawore, Ph.D.</h4>
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<h4>Asmi Mukherjee</h4>
<p class="w3-opacity">B.S., Purdue University 2025</p>
<p class="w3-opacity">Clinical Trial Operations Development Program at AbbVie</p>
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<h4>Javier Muñoz Briones, Ph.D.</h4>
<p class="w3-opacity">Ph.D., Purdue University 2024</p>
<p class="w3-opacity">Principal Project Statistician at Eli Lilly and Company</p>
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<h4>Jee Hyun Park, Ph.D.</h4>
<p class="w3-opacity">Ph.D., Purdue University 2025</p>
<p class="w3-opacity">Postdoc at Purdue University in The Baloni Lab</p>
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<h4>Ran Ran</h4>
<p class="w3-opacity">Ph.D., Case Western Reserve University 2025</p>
<p class="w3-opacity">Postdoc at Columbia University in The Farber Lab</p>
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<h4>Nina Render</h4>
<p class="w3-opacity">M.S., Purdue University 2024</p>
<p class="w3-opacity">Medical Student at the University of Kentucky</p>
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<h4>Alison Treichel, M.D.</h4>
<p class="w3-opacity">Dermatology Resident, University Hospitals</p>
<p class="w3-opacity">Faculty at the University of Rochester</p>
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<h4>Alan Trinh, M.D.</h4>
<p class="w3-opacity">M.D., Indiana University School of Medicine 2024</p>
<p class="w3-opacity">Resident at IU School of Medicine</p>
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<h2 class="w3-wide">Publications</h2>
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<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1038/s41526-025-00557-x'>Integrated cross-species translation and
biophysical multi-scale modeling links molecular signatures and locomotory phenotypes in
spaceflight-induced sarcopenia</a>, Ball, Brendan K.; Khan, Hammad F.; Park, Jee Hyun;
Jayant, Krishna; Chan, Deva D.; Brubaker, Douglas K., <i>NPJ microgravity</i>, 2026</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.celrep.2025.116916'>Systems mapping of intra-donor,
cross-tissue T cell clonal expansion and tissue adaptation in the gut-liver-blood axis</a>,
Ran, Ran; Uslu, Merve; Siddiqui, Mohd Farhan; Brubaker, Douglas K.; Trapecar, Martin, <i>Cell
Reports</i>, 2026</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.brainres.2025.149819'>Metabolites associated with type 2
diabetes and Alzheimer's disease trigger differential intracellular signaling responses in
mouse primary neurons</a>, Ball, Brendan K.; Kuhn, Madison K.; Fleeman Bechtel, Rebecca M.;
Proctor, Elizabeth A.; Brubaker, Douglas K., <i>Brain Research</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1038/s41540-025-00539-5'>Translational disease modeling of peripheral
blood identifies type 2 diabetes biomarkers predictive of Alzheimer's disease</a>, Ball,
Brendan K.; Park, Jee Hyun; Bergendorf, Alexander M.; Proctor, Elizabeth A.; Brubaker, Douglas
K., <i>NPJ systems biology and applications</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.25394/PGS.28566110.v1'>Understanding the Risk of Type 2 Diabetes on
Alzheimer's Disease</a>, Ball, Brendan Kazuhiko, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1039/d5bm00033e'>Chondrogenic and chondroprotective response of
composite collagen I/II-hyaluronic acid scaffolds within an inflammatory osteoarthritic
environment</a>, Battistoni, Carly M.; Munoz Briones, Javier; Brubaker, Douglas K.; Panitch,
Alyssa; Liu, Julie C., <i>Biomaterials Science</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1111/aji.70035'>Understanding the Associations of Urogenital
Microbiomes With Fertility and In Vitro Fertilization</a>, Berard, Alicia R.; Brubaker,
Douglas K.; Nemecio, Dalí X.; Farr Zuend, Christina, <i>American Journal of Reproductive
Immunology (New York, N.Y.: 1989)</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.3390/nu17162591'>Oral Contraceptives Induce Time- and Intestinal
Segment-Dependent Shifts in the Gut Microbiota</a>, Clapp Organski, Anna; Reddivari, Anjali;
Reddivari, Lavanya; Brubaker, Douglas K.; Fuller, Kelly N. Z.; Thyfault, John P.; Cross, Tzu-Wen
L., <i>Nutrients</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1101/2025.02.23.639777'>Computational Translation of Mouse Models of
Osteoarthritis Predicts Human Disease</a>, Frost, Maya R.; Ball, Brendan K.; Pendyala,
Meghana; Douglas, Stephen R.; Brubaker, Douglas K.; Chan, Deva D., 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.joca.2025.09.010'>Computational Translation of Mouse Models of
Osteoarthritis Predicts Human Disease</a>, Frost, Maya R.; Ball, Brendan K.; Pendyala,
Meghana; Douglas, Stephen R.; Brubaker, Douglas K.; Chan, Deva D., <i>Osteoarthritis and
Cartilage</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://www.sri-online.org/events/2025/'>O-134: Characterizing Heterogeneity of Estrogen
Receptor Isoform Expression in Endometriosis: Rethinking the ERβ Dominance Hypothesis</a>,
Heath, Alexis, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1101/2025.09.15.676330'>Rethinking the Estrogen Receptor Beta
Dominance Hypothesis in Endometriosis: Insights from Single Cell RNA Sequencing
Meta-analysis</a>, Heath, Alexis; Zuend, Christina Farr; Goodman, Wendy A.; Koyuturk,
Mehmet; Brubaker, Douglas, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.bioflm.2025.100330'>Characterizing Species-Specific Metabolic
Signatures in Vaginal Microbiota Across Planktonic and Biofilm States</a>, Jena, Smrutiti;
Lawore, Damilola; Green, Leopold N.; Brubaker, Douglas K., <i>Biofilm</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.bioflm.2025.100330'>Characterizing species-specific metabolic
signatures in vaginal microbiota across planktonic and biofilm states</a>, Jena, Smrutiti;
Lawore, Damilola; Green, Leopold N.; Brubaker, Douglas K., <i>Biofilm</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.3389/fmicb.2025.1602217'>Computational microbiome pharmacology
analysis elucidates the anti-cancer potential of vaginal microbes and metabolites</a>,
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., <i>Frontiers in Microbiology</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1186/s12859-025-06134-z'>A framework for predictive modeling of
microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling</a>, Munoz
Briones, Javier; Brubaker, Douglas K., <i>BMC bioinformatics</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1101/2025.02.05.636747'>Rumenomics: Evaluation of rumen metabolites
from healthy sheep identifies differentially produced metabolites across sex, age, and
weight</a>, Munoz-Briones, Javier; Ball, Brendan K.; Jena, Smrutiti; Lescun, Timothy B.;
Chan, Deva D.; Brubaker, Douglas K., 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://www.sri-online.org/events/2025/'>O-091: Leveraging Host Omic-Response Signatures
to Identify Microbiome Metabolizers of Drugs: A Case Study of Tenofovir Metabolism by the
Vaginal Microbiome</a>, Nemecio, Dalí X., 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1093/jimmun/vkaf283.2785'>Integrative single-cell and computational
analysis reveals ligands modulating human gamma delta T cell phenotypes in colorectal cancer
9375</a>, Ran, Ran; Brubaker, Douglas, <i>The Journal of Immunology</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.3389/fimmu.2025.1715827'>A ligand-centered framework for γδ T cell
activation in colorectal cancer revealed by single-cell and transformer-based
perturbation</a>, Ran, Ran; Brubaker, Douglas K., <i>Frontiers in Immunology</i>, 2025</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1101/2024.12.11.627991'>Cross-disease modeling of peripheral blood
identifies biomarkers of type 2 diabetes predictive of Alzheimer's disease</a>, Ball,
Brendan K.; Hyun Park, Jee; Proctor, Elizabeth A.; Brubaker, Douglas K., 2024</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1038/s41598-024-62155-3'>Differential responses of primary
neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer's disease-associated
metabolites</a>, Ball, Brendan K.; Kuhn, Madison K.; Fleeman Bechtel, Rebecca M.; Proctor,
Elizabeth A.; Brubaker, Douglas K., <i>Scientific Reports</i>, 2024</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1142/9789819807024_0031'>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</a>, Ball, Brendan K.;
Proctor, Elizabeth A.; Brubaker, Douglas K., <i>Biocomputing 2025</i>, 2024</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1101/2024.10.10.616351'>Computational Microbiome Pharmacology
Analysis Elucidates the Anti-Cancer Potential of Vaginal Microbes and Metabolites</a>,
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., 2024</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1021/acssynbio.3c00668'>Diagnostic and Therapeutic Microbial Circuit
with Application to Intestinal Inflammation</a>, Merk, Liana N.; Shur, Andrey S.; Jena,
Smrutiti; Munoz, Javier; Brubaker, Douglas K.; Murray, Richard M.; Green, Leopold N., <i>ACS
synthetic biology</i>, 2024</p>
</li>
<li class='publication w3-hide'>
<p><a href=''>LATENT INTERACTING VARIABLE-EFFECTS (LIVE) MODELING OF GUT MICROBIOME MULTI-OMICS IN
INFLAMMATORY BOWEL DISEASE</a>, Munoz-Briones, Javier; Brubaker, Douglas K, <i>SYSTEMS
MODELING OF HOST MICROBIOME INTERACTIONS IN INFLAMMATORY BOWEL DISEASES</i>, 2024</p>
</li>
<li class='publication w3-hide'>
<p><a href=''>SYSTEMS MODELING OF GUT MICROBIOME REGULATION OF ESTROGEN RECEPTOR BETA SIGNALING IN
ULCERATIVE COLITIS</a>, Munoz-Briones, Javier; Trinh, Alan; Simpson, Abigail; Stingel,
Rachel; Jena, Smrutiti; Doszpoly, Agnes; Urlu, Merve; Trapecar, Martin; Cross, Tzu-Wen;
Brubaker, Douglas K, <i>SYSTEMS MODELING OF HOST MICROBIOME INTERACTIONS IN INFLAMMATORY BOWEL
DISEASES</i>, 2024</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.isci.2024.109383'>Detailed survey of an in vitro intestinal
epithelium model by single-cell transcriptomics</a>, Ran, Ran; Muñoz Briones, Javier; Jena,
Smrutiti; Anderson, Nicole L.; Olson, Matthew R.; Green, Leopold N.; Brubaker, Douglas K.,
<i>iScience</i>, 2024</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.neo.2024.101072'>Systematic analysis of human colorectal
cancer scRNA-seq revealed limited pro-tumoral IL-17 production potential in gamma delta T
cells</a>, Ran, Ran; Trapecar, Martin; Brubaker, Douglas K., <i>Neoplasia (New York,
N.Y.)</i>, 2024</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1101/2023.11.17.567595'>Differential responses of primary
neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer's disease-associated
metabolites</a>, Ball, Brendan K.; Kuhn, Madison K.; Fleeman, Rebecca M.; Proctor, Elizabeth
A.; Brubaker, Douglas K., 2023</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.celrep.2023.112474'>Vaginal epithelial dysfunction is mediated
by the microbiome, metabolome, and mTOR signaling</a>, 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., <i>Cell
Reports</i>, 2023</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.18060/26896'>Association Between Intestinal Changes and Systemic
Cytokines in Mouse Dysbiosis Models</a>, Jeffries, Alison; Villarreal, Cameron; Brubaker,
Douglas; Chan, Deva, <i>Proceedings of IMPRS</i>, 2023</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1093/bioadv/vbad159'>Enhanced annotation of CD45RA to distinguish T
cell subsets in single-cell RNA-seq via machine learning</a>, Ran, Ran; Brubaker, Douglas
K., <i>Bioinformatics Advances</i>, 2023</p>
</li>
<li class='publication w3-hide'>
<p><a href=''>TRANS-OMIC KNOWLEDGE TRANSFER MODELING INFERS GUT MICROBIOME BIOMARKERS OF ANTI-TNF
RESISTANCE IN ULCERATIVE COLITIS</a>, Trinh, Alan; Ran, Ran; Brubaker, Douglas K.,
<i>Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</i>, 2023</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1101/2022.07.08.499280'>Latent Interacting Variable-Effects Modeling
of Gut Microbiome Multi-Omics in Inflammatory Bowel Disease</a>, Munoz-Briones, Javier;
Brubaker, Douglas. K., 2022</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1371/journal.pone.0267921'>Endogenous production of hyaluronan, PRG4,
and cytokines is sensitive to cyclic loading in synoviocytes</a>, Pendyala, Meghana; Woods,
Paige S.; Brubaker, Douglas K.; Blaber, Elizabeth A.; Schmidt, Tannin A.; Chan, Deva D., <i>PloS
One</i>, 2022</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://hdl.handle.net/1805/31369'>Method Development Involving Modeling Bacterial
Metabolite Regulation of Vaginal Epithelial Cell Signaling in Bacterial Vaginosis</a>,
Trinh, Alan; Brubaker, Douglas, 2022</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.3389/fnins.2021.727784'>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</a>, Lee, Meelim J.; Wang, Chuangqi; Carroll, Molly J.; Brubaker, Douglas K.; Hyman,
Bradley T.; Lauffenburger, Douglas A., <i>Frontiers in Neuroscience</i>, 2021</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1093/intbio/zyab009'>Cell surface integrin α5ß1 clustering negatively
regulates receptor tyrosine kinase signaling in colorectal cancer cells via glycogen
synthase kinase 3</a>, Starchenko, Alina; Graves-Deal, Ramona; Brubaker, Douglas; Li, Cunxi;
Yang, Yuping; Singh, Bhuminder; Coffey, Robert J.; Lauffenburger, Douglas A., <i>Integrative
Biology: Quantitative Biosciences from Nano to Macro</i>, 2021</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.isci.2021.103406'>Cross-species transcriptomic signatures
predict response to MK2 inhibition in mouse models of chronic inflammation</a>,
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., <i>iScience</i>, 2021</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1126/scisignal.aay3258'>An interspecies translation model implicates
integrin signaling in infliximab-resistant inflammatory bowel disease</a>, 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., <i>Science Signaling</i>, 2020</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1126/science.aay8086'>Translating preclinical models to humans</a>,
Brubaker, Douglas K.; Lauffenburger, Douglas A., <i>Science (New York, N.Y.)</i>, 2020</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1128/AAC.01404-19'>Clostridioides difficile-Associated Antibiotics
Alter Human Mucosal Barrier Functions by Microbiome-Independent Mechanisms</a>, Kester,
Jemila C.; Brubaker, Douglas K.; Velazquez, Jason; Wright, Charles; Lauffenburger, Douglas A.;
Griffith, Linda G., <i>Antimicrobial Agents and Chemotherapy</i>, 2020</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1111/jth.14875'>Coagulopathy signature precedes and predicts severity
of end-organ heat stroke pathology in a mouse model</a>, 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., <i>Journal of
thrombosis and haemostasis: JTH</i>, 2020</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1016/j.cels.2019.07.006'>Proteogenomic Network Analysis of
Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation</a>, 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., <i>Cell Systems</i>, 2019</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1371/journal.pcbi.1006286'>Computational translation of genomic
responses from experimental model systems to humans</a>, Brubaker, Douglas K.; Proctor,
Elizabeth A.; Haigis, Kevin M.; Lauffenburger, Douglas A., <i>PLoS computational biology</i>,
2019</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1158/2159-8290.CD-18-1220'>Tissue-Specific Oncogenic Activity of
KRASA146T</a>, 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., <i>Cancer
Discovery</i>, 2019</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1093/intbio/zyz025'>Substrate-based kinase activity inference
identifies MK2 as driver of colitis</a>, 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., <i>Integrative
Biology: Quantitative Biosciences from Nano to Macro</i>, 2019</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1093/biolre/ioy040'>Integrated microRNA and mRNA network analysis of
the human myometrial transcriptome in the transition from quiescence to labor</a>, Ackerman,
William E.; Buhimschi, Irina A.; Brubaker, Douglas; Maxwell, Sean; Rood, Kara M.; Chance, Mark
R.; Jing, Hongwu; Mesiano, Sam; Buhimschi, Catalin S., <i>Biology of Reproduction</i>, 2018</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1126/scisignal.aan3580'>Integrated in vivo multiomics analysis
identifies p21-activated kinase signaling as a driver of colitis</a>, 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., <i>Science Signaling</i>,
2018</p>
</li>
<li class='publication w3-hide'>
<p><a href='https://doi.org/10.1142/9789813207813_0038'>FREQUENT SUBGRAPH MINING OF PERSONALIZED
SIGNALING PATHWAY NETWORKS GROUPS PATIENTS WITH FREQUENTLY DYSREGULATED DISEASE PATHWAYS AND
PREDICTS PROGNOSIS</a>, Durmaz, Arda; Henderson, Tim A. D.; Brubaker, Douglas; Bebek,
Gurkan, <i>Pacific Symposium on Biocomputing</i>, 2017</p>
</li>
<li class='publication w3-hide'>
<p><a href=''>Computational Investigation of Biological Networks and Progesterone Signaling Dynamics
in Preterm Birth</a>, Brubaker, Douglas K.; Barnholtz-Sloan, Jill; Mesiano, Sam; Barbaro,
Alethea, 2016</p>
</li>