Emily R. Miraldi

Clonal hematopoiesis-associated DNMT3A mutations derepress bivalent Polycomb target genes and enhance macrophage migration

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.

Macrophages drive a fibrogenic gene program of periductal fibroblasts in pediatric primary sclerosing cholangitis

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

Use of Antibody Structural Information in Disease Prediction Models Reveals Antigen Specific B Cell Receptor Sequences in Bulk Repertoire Data

This study uses structural information of antibodies to identify convergent antibodies in bulk IgH data, improving disease prediction for food sensitization and matching HIV prediction performance.

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.

High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0

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.

Genome-wide discovery of lupus genetic risk variant allelic regulatory activity

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

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

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.

Multi-study inference of regulatory networks for more accurate models of gene regulation

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

The impact of endogenous retroviruses on nuclear organization and gene expression

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

4C-ker: A method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments

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.