Jennifer Beane

Archetype analysis of lung adenocarcinoma premalignancy links heterogeneity in premalignant lesions to diverging features of invasive disease

This study identifies four molecular archetypes of lung adenocarcinoma premalignant lesions using bulk RNA and exome sequencing, linking proliferation-associated features to aggressive tumor outcomes.

FourierMIL: Fourier filtering-based multiple instance learning for whole slide image analysis

FourierMIL uses Fourier filtering and multiple instance learning to analyze whole-slide images, outperforming existing methods in tumor classification.

A gene program association study (GPAS) delineates novel patterns of lineage plasticity and aggressiveness in non-small cell lung cancer

The paper introduces GPAS to analyze gene co-expression modules in NSCLC, identifying lineage plasticity and aggressiveness patterns across different cancer subtypes.

Epithelial miR-149-5p up-regulation is associated with immune evasion in progressive bronchial premalignant lesions

This study identifies hsa-miR-149-5p as a regulator of immune evasion in progressive bronchial premalignant lesions through integrative analysis of RNA and miRNA sequencing data.

Identification of a gene expression signature of vascular invasion and recurrence in stage I lung adenocarcinoma via bulk and spatial transcriptomics

Graph attention-based fusion of pathology images and gene expression for prediction of cancer survival

This paper develops a graph attention-based framework that fuses pathology images and gene expression data to predict cancer survival, showing improved performance over existing methods.

A Lung Cancer Mouse Model Database

The paper establishes a database of lung cancer mouse models to improve data comparison and translational relevance by aligning mouse mutations with human lung cancer mutations.

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.

Interrogating the Precancerous Evolution of Pathway Dysfunction in Lung Squamous Cell Carcinoma Using XTABLE

The paper introduces XTABLE, an open-source tool for analyzing PML transcriptomic data, and uses it to study chromosomal instability as a biomarker for LUSC progression and pathway onset.

Differential Regulation Analysis Quantifies miRNA Regulatory Roles And Context-Specific Targets

The paper introduces a method to analyze differential miRNA regulation across multiple groups, identifying context-specific targets in immune cells and cancer subtypes.

Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution

This study uses single-cell RNA sequencing to analyze smoking effects on bronchial epithelial cell types, identifying molecular changes and a novel subpopulation linked to premalignant lesions.