Peter J. Castaldi

The paper identifies protein interactors of COPD GWAS genes using AP-MS and network analysis, revealing a disease network module involving 8 proteins.

RADIS enables comprehensive pre-mRNA structural analysis across intronic and intergenic regions, revealing structural patterns and relationships with splice-site strength and variant effects.

The paper analyzes expression and splicing quantitative trait loci (e/sQTL) across multiple tissues in the TOPMed dataset and finds that secondary e/sQTL signals are still discoverable, with many GWAS signals colocalizing with these e/sQTL.

The paper identifies smoking-associated miRNA regulatory networks in blood and tissue, revealing NDUFA12 as a key target linked to mitochondrial dysfunction in smokers.

This study identifies 38 COPD GWAS loci with evidence of sQTLs, showing that sQTL analysis in whole blood and lung tissue provides novel insights into COPD mechanisms.

This paper introduces SGTCCA-Net, a framework for multi-omics network inference that addresses limitations of existing methods by incorporating higher-order correlations and improving computational efficiency.

Biosurfer identifies sources of protein isoform diversity by analyzing long-read RNA-seq data, revealing common mechanisms like alternative transcription start sites and 'ragged codons'.

The paper identifies HHIP protein interactions in lung cells, revealing new connections to COPD GWAS genes and providing insights into COPD pathogenesis.

This study identifies LIFR as a master amplifier of fibroblast activation in IPF, showing that blocking LIFR reduces fibrosis in ex vivo tissue.

The paper introduces R2C2+UMI, a method combining concatemeric consensus sequencing with UMIs to achieve ultra-accurate sequencing of amplicons on Oxford Nanopore sequencers.

This study shows that common splice-regulatory variants can reduce the pathogenicity of rare exonic variants by modulating mRNA splicing.

The paper finds that somatic mutations in diseased lung tissue correlate with reduced lung function and cell type proportions in COPD and IPF.

The paper uses whole genome sequencing to identify genetic loci associated with platelet aggregation, including novel variants in RGS18, SVEP1, and PEAR1.

The paper identifies a genetic variant in NPNT associated with COPD risk and lung function through splicing analysis using long-read sequencing.

This study identifies peripheral blood microbial signatures associated with COPD and exacerbation phenotypes in smokers.

The paper uses SWIM software to analyze COPD transcriptomic networks, identifying key modules and switch genes associated with immune response, inflammation, and hypoxia.

The paper identifies FBXO38 as a novel COPD susceptibility gene by analyzing genetically driven alternative splicing and finding a protective exon associated with COPD risk.

The paper examines immune cell changes in COPD patients and finds associations between cell counts and lung function decline, suggesting immune response roles in disease progression.

The paper identifies ACVR1B as a candidate causal gene for emphysema distribution by integrating GWAS, eQTL, and epigenomic data.