PUBLICATIONS

VAGINAL EPITHELIAL DYSFUNCTION IS MEDIATED BY THE MICROBIOME, METABOLOME, AND MTOR SIGNALING

Berard, et al. Cell Reports, 2023

DETAILED SURVEY OF AN IN-VITRO INTESTINAL EPITHELIUM MODEL BY SINGLE-CELL TRANSCRIPTOMICS

Ran, et al. bioRxiv, 2023 (Preprint)

ENHANCED ANNOTATION OF CD45RA TO DISTINGUISH T CELL SUBSETS IN SINGLE CELL RNA-SEQ VIA MACHINE LEARNING

Ran, Brubaker, bioRxiv, 2023 (Preprint)

ENDOGENOUS PRODUCTION OF HYALURONAN, PRG4, AND CYTOKINES IS SENSITIVE TO CYCLIC LOADING IN SYNOVIOCYTES

Pendyala, et al. PLOS ONE, 2022

LATENT INTERACTING VARIABLE-EFFECTS MODELING OF GUT MICROBIOME MULTI-OMICS IN INFLAMMATORY BOWEL DISEASE

Munoz, Brubaker, bioRxiv, 2022 (Preprint)

METHOD DEVELOPMENT INVOLVING MODELING BACTERIAL METABOLITE REGULATION OF VAGINAL EPITHELIAL CELL SIGNALING IN BACTERIAL VAGINOSIS

Trinh, Brubaker, IUSM Education Day, 2022 (Poster)

ASSOCIATION BETWEEN INTESTINAL CHANGES AND SYSTEMIC CYTOKINES IN MOUSE DYSBIOSIS MODELS

Jeffries, et al. Proceedings of IMPRS, 2022

TRANS-OMIC KNOWLEDGE TRANSFER MODELING INFERS GUT MICROBIOME BIOMARKERS OF ANTI-TNF RESISTANCE IN ULCERATIVE COLITIS

Trinh, Ran, Brubaker, Biocomputing, 2023

CROSS-SPECIES TRANSCRIPTOMIC SIGNATURES PREDICT RESPONSE TO MK2 INHIBITION IN MOUSE MODELS OF CHRONIC INFLAMMATION

Suarez-Lopez, et al. 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, et al. 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, et al. Integrative Biology, 2021

AN INTERSPECIES TRANSLATION MODEL IMPLICATES INTEGRIN SIGNALING IN INFLIXIMAB-RESISTANT INFLAMMATORY BOWEL DISEASE

Brubaker, et al. Science Signaling, 2020

COAGULOPATHY SIGNATURE PRECEDES AND PREDICTS SEVERITY OF END‐ORGAN HEAT STROKE PATHOLOGY IN A MOUSE MODEL

Proctor, et al. Journal of Thrombosis and Haemostasis, 2020

CLOSTRIDIOIDES DIFFICILE-ASSOCIATED ANTIBIOTICS ALTER HUMAN MUCOSAL BARRIER FUNCTIONS BY MICROBIOME-INDEPENDENT MECHANISMS

Kester, et al. Antimicrobial Agents and Chemotherapy, 2020

TRANSLATING PRECLINICAL MODELS TO HUMANS

Brubaker, Lauffenburger, Science, 2020

PROTEOGENOMIC NETWORK ANALYSIS OF CONTEXT-SPECIFIC KRAS SIGNALING IN MOUSE-TO-HUMAN CROSS-SPECIES TRANSLATION

Brubaker, et al. Cell Systems, 2019

SUBSTRATE-BASED KINASE ACTIVITY INFERENCE IDENTIFIES MK2 AS DRIVER OF COLITIS

Strasser, et al. Integrative Biology, 2019

TISSUE-SPECIFIC ONCOGENIC ACTIVITY OF KRASA146T

Poulin, et al. Cancer Discovery, 2019

COMPUTATIONAL TRANSLATION OF GENOMIC RESPONSES FROM EXPERIMENTAL MODEL SYSTEMS TO HUMANS

Brubaker, et al. PLOS Computational Biology, 2019

INTEGRATED MICRORNA AND MRNA NETWORK ANALYSIS OF THE HUMAN MYOMETRIAL TRANSCRIPTOME IN THE TRANSITION FROM QUIESCENCE TO LABOR

Ackerman, et al. Biology of Reproduction, 2018

INTEGRATED IN VIVO MULTIOMICS ANALYSIS IDENTIFIES P21-ACTIVATED KINASE SIGNALING AS A DRIVER OF COLITIS

Lyons, et al. Science Signaling, 2018

FREQUENT SUBGRAPH MINING OF PERSONALIZED SIGNALING PATHWAY NETWORKS GROUPS PATIENTS WITH FREQUENTLY DYSREGULATED DISEASE PATHWAYS AND PREDICTS PROGNOSIS

Durmaz, et al. Biocomputing, 2017

FINDING LOST GENES IN GWAS VIA INTEGRATIVE—OMICS ANALYSIS REVEALS NOVEL SUB-NETWORKS ASSOCIATED WITH PRETERM BIRTH

Brubaker, et al. Human Molecular Genetics, 2016

A DYNAMICAL SYSTEMS MODEL OF PROGESTERONE RECEPTOR INTERACTIONS WITH INFLAMMATION IN HUMAN PARTURITION

Brubaker, et al. BMC Systems Biology, 2016

COMPUTATIONAL INVESTIGATION OF BIOLOGICAL NETWORKS AND PROGESTERONE SIGNALING DYNAMICS IN PRETERM BIRTH

Brubaker, 2016 (Dissertation)

PREDICTIONS WITH PARADIGM (DIRPP) IDENTIFIES DRUG RESISTANT CANCER CELL LINES AND PATHWAY MECHANISMS OF RESISTANCE

Brubaker, et al. Biocomputing, 2014

Publications : List