Robert Lafyatis

Suppression of interferon signaling via small molecule modulation of TFAM

This study identifies small molecule modulators of TFAM that increase its levels and mtDNA copy number, reducing mtDNA stress and inflammation in disease models.

HALO: Hierarchical Causal Modeling for Single Cell Multi-Omics Data

HALO models temporal causal relations in single-cell multi-omics data by distinguishing coupled and decoupled latent representations, revealing lineage specification dynamics in AT2 cells.

Genetic regulation and targeted reversal of lysosomal dysfunction and inflammatory sterol metabolism in pulmonary arterial hypertension

The paper identifies NCOA7's role in lysosomal function and inflammatory sterol metabolism in PAH, showing its deficiency exacerbates disease through oxysterol/bile acid generation.

SenSet, a novel human lung senescence cell gene signature, identifies cell-specific senescence mechanisms

The paper develops SenSet, a gene signature for human lung senescence, validated in 3D culture models and identifies cell-type specific senescence mechanisms in aging and disease.

Altered AP-1, RUNX, and EGR chromatin dynamics drive fibrotic lung disease

The paper identifies transcription factor networks driving fibrotic lung disease using multiomic single-cell data from SSc-ILD and control lungs.

SLIDE: Significant Latent Factor Interaction Discovery and Exploration across biological domains

SLIDE identifies significant interacting latent factors in multi-omic datasets, revealing biological insights in systemic sclerosis, spatial transcriptomics, and T1D models.

LEF1 isoforms regulate cellular senescence and aging

The paper identifies LEF1 isoforms as key regulators of cellular senescence and aging through transcriptomic analysis and validation in human and mouse models.

Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity

The paper identifies TWIST1 as a critical regulator of myofibroblast activity in IPF using single-nucleus ATAC-seq and scRNA-seq integration.

Loss of Protein Kinase D2 Activity Protects Against Bleomycin-induced Dermal Fibrosis in Mice

This study shows that reducing PKD2 activity in mice prevents bleomycin-induced dermal fibrosis by decreasing collagen and inflammatory markers.

SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics

SECANT improves clustering and annotation of single-cell multi-omics data by integrating surface protein and RNA information with biology-guided semi-supervised learning.

Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis

The paper identifies early fibroblast transitions to a profibrotic state in IPF using scRNA-seq and validates MOXD1 as an early marker.

BAMM-SC: A Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies

BAMM-SC clusters droplet-based scRNA-seq data from multiple individuals by accounting for batch effects and heterogeneity, improving accuracy over existing methods.