Joseph A. Wayman

Gene regulatory networks define human airway epithelial cell types and their distinct responses to type I interferon

The paper characterizes gene regulatory networks in human airway epithelial cells and identifies cell type-specific responses to type I interferon.

Gene regulatory network determinants of rapid recall in human memory CD4+ T cells

This study identifies gene regulatory networks in human memory CD4+ T cells that drive rapid recall, linking specific transcription factors to immune-mediated disease risk.

Epithelial-intrinsic nitric oxide synthase 2 sustains host-microbiota dynamics that promote colitis

This study shows that epithelial nitric oxide synthase 2 (Nos2) influences host-microbiota interactions in IBD by regulating intestinal nitrates and nitrate-metabolizing bacteria, with implications for disease management.

Nutrient starvation activates ECM remodeling gene enhancers associated with inflammatory bowel disease risk in fibroblasts

The paper shows nutrient starvation activates ECM remodeling gene enhancers linked to IBD risk in fibroblasts, suggesting a mechanism for pathological fibroblast activation in IBD.

Cholestasis alters polarization and suppressor function of hepatic regulatory T cells.

This study shows cholestasis shifts hepatic Tregs to a Th17 phenotype and impairs their suppressor function, with bile acid levels influencing Treg activity and liver injury.

Multiome-seq links inflammatory bowel disease polygenic risk to TNF inhibitor response

The paper links IBD polygenic risk to TNFi response using multiome-seq and genetic data from pediatric IBD patients.

maxATAC: genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks

maxATAC provides deep learning models for predicting transcription factor binding sites from ATAC-seq data, improving prediction in primary and single-cell contexts.

High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk

The paper maps promoter interactions in human ILC3s using PCHi-C and links GWAS risk variants to target genes, identifying new autoimmune disease risk genes.

Alveolar epithelial progenitor cells drive lung regeneration via dynamic changes in chromatin topology modulated by lineage-specific Nkx2-1 activity

This study identifies Nkx2-1-driven chromatin topology changes in alveolar epithelial progenitor cells that regulate lung regeneration and differentiation.

Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates

This study shows that blocking inflammation in preterm primates prevents lung injury, preserving alveolar structure and function similar to chronic lung disease in newborns.

Toward a Genome Scale Sequence Specific Dynamic Model of Cell-Free Protein Synthesis in Escherichia coli

This study develops a dynamic model of E. coli cell-free protein synthesis, showing that oxidative phosphorylation, glycolysis, and amino acid biosynthesis are key for productivity.

Improving Designer Glycan Production in Escherichia coli through Model-Guided Metabolic Engineering

This study uses metabolic modeling to design E. coli strains that overproduce glycan precursors for glycoprotein production.

Sequence Specific Modeling of E. coli Cell-Free Protein Synthesis

This paper uses sequence-specific constraint-based modeling to estimate the performance of E. coli cell-free protein synthesis systems using limited parameters.

Modeling and Analysis of Hormone and Mitogenic Signal Integration in Prostate Cancer

This study uses mathematical models to analyze hormone and mitogenic signaling in prostate cancer, finding that combining inhibitors targeting multiple pathways improves efficacy against castration-resistant prostate cancer.