Emily R. Miraldi

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

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.

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.

This study identifies macrophage-driven fibrotic gene programs in periductal fibroblasts of PSC using multi-omics data, highlighting potential therapeutic targets.

This study uses structural antibody information to improve disease prediction from bulk IgH data, showing better performance for food allergen sensitization and comparable results for HIV.

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.

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.

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

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

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.

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

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

The paper introduces Inferelator 3.0, a tool for inferring gene regulatory networks from single-cell data, showing improved performance on yeast and mouse brain datasets.

The paper identifies 482 SLE risk variants with enhancer activity and characterizes allelic regulatory mechanisms at 27 risk loci using MPRA.

The paper develops methods to infer transcriptional regulatory networks in Th17 cells using ATAC-seq and RNA-seq data, revealing new roles for transcription factors and their modules.

This study improves gene regulatory network inference by integrating multiple datasets using multitask learning, showing better network reconstruction and robustness to dataset heterogeneity.

The paper introduces 4Tran, a method to study transposon interactions in the genome, revealing their role in chromatin organization and gene regulation.

This paper introduces 4C-ker, a method that improves the reproducibility of identifying genome-wide interactions from 4C-Seq data by accounting for signal biases and varying resolution.