Douglas K. Brubaker

Mouse-to-human modeling of microglia single-nuclei transcriptomics identifies immune signaling pathways and potential therapeutic candidates associated with Alzheimer's disease

The paper integrates mouse and human microglia transcriptomics to identify AD-related pathways and drugs using TransComp-R, finding FDA-approved drugs that mimic healthy human microglia in mice.

Rumenomics: Evaluation of rumen metabolites from healthy sheep identifies differentially produced metabolites across sex, age, and weight

Cross-Species Translation Enhances the Use of Mouse Models for Translatability and Drug Discovery in Late-Onset Alzheimer's Disease

The paper develops a cross-species translation framework to identify therapeutic targets for late-onset Alzheimer's disease using mouse models and human data.

Proteomic analysis reveals shared biological pathways linking acrolein to biomolecular changes in the acute phase of rat spinal cord injury

The paper uses proteomic analysis to identify acrolein-induced changes in rat spinal cord injury, revealing shared pathways in complement and coagulation cascades.

A Ligand-Centered Framework for γδ T Cell Activation in Colorectal Cancer Revealed by Single-Cell and Transformer-Based Perturbation

The paper identifies IL-15 and TNFSF9 as ligands promoting γδ T cell effector function in CRC using single-cell RNA-seq and in silico perturbation analysis.

Integrated Cross-Species Translation and Biophysical Multi-Scale Modeling Links Molecular Signatures and Locomotory Phenotypes in Spaceflight-Induced Sarcopenia

The paper identifies conserved molecular pathways in spaceflight-induced sarcopenia using cross-species analysis and develops a model linking transcriptional changes to locomotion deficits.

Computational Translation of Mouse Models of Osteoarthritis Predicts Human Disease

The paper evaluates the translatability of two mouse osteoarthritis models to human transcriptomics data using TransComp-R, finding that ACLR better predicts human OA conditions.

Computational Microbiome Pharmacology Analysis Elucidates the Anti-Cancer Potential of Vaginal Microbes and Metabolites

The paper develops a systems biology framework called the Pharmacobiome to analyze the anti-cancer potential of vaginal microbes and metabolites by comparing their effects on host gene expression to known drugs.

Rethinking the Estrogen Receptor Beta Dominance Hypothesis in Endometriosis: Insights from Single Cell RNA Sequencing Meta-analysis

This study challenges the ER{beta} dominance hypothesis by showing no significant ER{beta} dominance in endometriosis tissues and highlighting cell- and tissue-specific roles of estrogen receptor isoforms.

Identifying a Vaginal Microbiome-Derived Selective Antibiotic Metabolite via Microbiome Pharmacology Analysis

This study identifies a vaginal microbiome-derived antibiotic metabolite, Hydroxyisocaproate, using a systems biology approach to improve BV treatment.

Metabolites associated with type 2 diabetes and Alzheimer's disease trigger differential intracellular signaling responses in mouse primary neurons

The paper investigates how metabolites linked to type 2 diabetes and Alzheimer's disease affect intracellular signaling in mouse neurons, identifying specific pathway activations associated with disease progression or protection.

Cross-disease modeling of peripheral blood identifies biomarkers of type 2 diabetes predictive of Alzheimer's disease

This paper uses cross-disease modeling to identify T2D biomarkers predictive of Alzheimer's disease and suggests a T2D medication that may prevent AD onset.

Personalized Gut-Liver Microphysiological System Maps Donor-Specific Tissue Resident Immunity and Reveals a Conserved Metabolic Crosstalk

The paper builds a personalized gut-liver microphysiological system to study donor-specific immune profiles and reveals a conserved metabolic crosstalk between gut and liver.

Comparative Metabolomic Analysis of Vaginal Microbiota in Planktonic and Biofilm States Unveils Species-Specific Metabolic Signatures

This study compares metabolomic profiles of key vaginal microbes in planktonic and biofilm states, revealing species-specific metabolic shifts and growth mode-dependent differences.

Single-Cell Analysis Reveals Tissue-Specific T Cell Adaptation and Clonal Distribution Across the Human Gut-Liver-Blood Axis

The paper tracks T cell clones across gut, liver, and blood using single-cell RNA and TCR sequencing, revealing tissue-specific adaptations and limited overlap between colonic IELs and lamina propria T cells.

Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation

This paper engineers a synthetic microbial circuit in E. coli to respond to two signals and secrete IL-22 for anti-inflammatory effects in a gut epithelial model.

Systematic Analysis of Human Colorectal Cancer scRNA-seq Revealed Limited Pro-tumoral IL-17 Production Potential in Gamma Delta T Cells

This study analyzes scRNA-seq data from human colorectal cancer to show that gamma delta T cells do not produce pro-tumoral IL-17, functioning mainly as cytotoxic effector cells.

Differential responses of primary neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer's disease-associated metabolites

The paper investigates how primary neurons respond to metabolites linked to type 2 diabetes and Alzheimer's disease, identifying differential secretion of MCP-1 and IL-9.

Enhanced Annotation of CD45RA to Distinguish T cell Subsets in Single Cell RNA-seq via Machine Learning

The paper develops a machine learning classifier to infer CD45RA levels from scRNA-seq data, improving T cell subset annotation with high accuracy.

Latent Interacting Variable-Effects Modeling of Gut Microbiome Multi-Omics in Inflammatory Bowel Disease

This paper introduces LIVE modeling to integrate microbiome multi-omics data in IBD, reducing feature correlations and identifying novel disease mechanisms.

An Inter-Species Translation Model Implicates Integrin Signaling in Infliximab-Resistant Colonic Crohn’s Disease

The paper develops a translation model to identify integrin signaling in anti-TNF-resistant Crohn’s disease and validates it using single-cell RNA sequencing.

C. difficile-associated antibiotics prime the host for infection by a microbiome-independent mechanism.

This study shows that certain antibiotics increase CDAD risk through host-driven changes, not just microbiome disruption, by impairing mucosal barriers and immune function in human gut models.

A framework for translation of genomic responses from mouse models to human inflammatory disease contexts

This paper develops a semi-supervised learning framework to translate genomic responses from mouse models to human inflammatory disease contexts, finding it more accurate than direct generalization.