Lily Wang

An Integrative Multi-Omics Random Forest Framework for Robust Biomarker Discovery

This paper introduces a multivariate random forest framework for multi-omics biomarker discovery, showing it outperforms existing methods in identifying biologically relevant biomarkers and pathways.

Integrating Tumor and Organoid DNA Methylation Profiles Reveals Robust Predictors of Chemotherapy Response in Rectal Cancer

This study integrates DNA methylation profiles from tumors and organoids to identify CpGs predictive of chemotherapy response in rectal cancer, finding a methylation risk score significantly predicts progression-free survival.

SERBP1 interacts with PARP1 and is present in PARylation-dependent protein complexes regulating splicing, cell division, and ribosome biogenesis

The paper identifies SERBP1 as a protein involved in PARylation-dependent complexes that regulate splicing, cell division, and ribosome biogenesis, with implications for neurodegenerative diseases.

The landscape of regional missense mutational intolerance quantified from 730,947 exomes

The paper quantifies regional missense mutational intolerance using 730,947 exomes to identify constrained gene regions and improve variant interpretation.

Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features

The paper identifies SMC3 loss-of-function variants associated with variable growth and developmental features, including some unexpected phenotypes like bone marrow failure and leukemia.

Exploring therapeutic strategies for Infantile Neuronal Axonal Dystrophy (INAD/PARK14)

The paper identifies ceramide accumulation, lysosomal expansion, and mitochondrial defects as root causes of INAD/PARK14 and tests therapeutic strategies including drugs and gene therapy.

Tissue and cell-type specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models

This study identifies molecular and functional changes in mouse and human models of 16p11.2 reciprocal genomic disorder, revealing context-specific disruptions in energy metabolism, RNA processing, and neuronal development.

FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources

FAIRshake evaluates the FAIRness of research digital resources through community-driven metrics, automated assessments, and visualization tools, revealing opportunities for improvement.

pathwayPCA: an R package for integrative pathway analysis with modern PCA methodology and gene selection

pathwayPCA is an R package that performs integrative pathway analysis with modern PCA methods and gene selection, enabling multi-omics data analysis and sample-specific pathway activity estimation.

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse

The paper develops ARCHS4, a resource that provides uniformly processed RNA-seq data from human and mouse, enabling easier integration and analysis.