Ivana V. Yang

Toll-Like-Receptor 5 protects against pulmonary fibrosis by reducing lung dysbiosis

TLR5 deficiency is linked to pulmonary fibrosis due to its role in preventing microbial dysbiosis following lung injury.

IPF AT2 cells are stuck in transition and biophysically dysfunctional

The paper identifies migratory non-canonical AT2 cells in IPF lung fibrosis, showing they are trapped in developmental transition states that drive fibrosis progression.

The MUC5B promoter variant results in proteomic changes in the non-fibrotic lung

This study identifies proteomic changes in non-fibrotic lung tissue associated with the MUC5B promoter variant, linking them to fibrosis progression.

Single Cell Transcriptome Signatures of Sarcoidosis in Lung Immune Cell Populations

The paper identifies cell-specific molecular changes in sarcoidosis by analyzing single-cell RNA-seq data from lung immune cells, revealing distinct macrophage subpopulations and altered gene expression patterns associated with disease progression.

Multi-Omic Signatures of Sarcoidosis and Progression in Bronchoalveolar Lavage Cells

The paper integrates DNA methylation, mRNA, and miRNA data from bronchoalveolar lavage cells to identify molecular signatures of sarcoidosis and disease progression.

Context-specific eQTLs reveal causal genes underlying shared genetic architecture of critically ill COVID-19 and idiopathic pulmonary fibrosis

The paper identifies shared genetic variants between critically ill COVID-19 and idiopathic pulmonary fibrosis by integrating GWAS with context-specific eQTLs and transcriptomics.

Epigenetic timing effects on child developmental outcomes: A longitudinal meta-regression of findings from the Pregnancy And Childhood Epigenetics Consortium

This study uses longitudinal meta-regression to examine how DNA methylation effects on child health outcomes vary by timing, finding larger effects in childhood but noisier associations and time-specific signals.

Integrative genetic and genomic networks identify microRNA associated with COPD and ILD

The paper identifies miRNAs and isomiRs associated with COPD and ILD through integrative network analysis of RNA-seq and SNP data from lung tissue samples.

Validation of human telomere length trans-ancestry meta-analysis association signals identifies POP5 and KBTBD6 as novel human telomere length regulation genes

The paper validates novel telomere length regulation genes POP5 and KBTBD6 identified through trans-ancestry GWAS using functional experiments in blood cells.

Novel genetic determinants of telomere length from a trans-ethnic analysis of 109,122 whole genome sequences in TOPMed

This study identifies 59 sentinel variants and two novel genes associated with telomere length using whole genome sequences from 109,122 trans-ethnic individuals.

Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes

The paper identifies germline genetic variants associated with clonal hematopoiesis of indeterminate potential (CHIP) using whole genome sequences from the TOPMed program.

Aligning sequence from molecular inversion probes

The paper introduces a tool for aligning sequences from molecular inversion probes, performing mapping, arm removal, and deduplication to produce SAM format alignments.