PARROT detects change-points in dynamic gene regulatory networks using Stochastic Block Models, identifying module reassignments and connection changes in human and mouse data.

bioRxiv · Jun 28, 2026 · PreprintBioinformatics

Identifying Sex Differences in Lung Adenocarcinoma Using Multi-Omics Integrative Protein Signaling Networks

Chen Chen, Enakshi Saha, Jonas Fischer, Marouen Ben Guebila, Viola Fanfani, Katherine Hoff Shutta, Megha Padi, Kimberly Glass, Dawn Lisa DeMeo, Camila M. Lopes‐Ramos, John F Quackenbush

The paper identifies sex differences in lung adenocarcinoma by integrating multi-omics data to discover sex-biased signaling pathways and potential sex-specific therapies.

bioRxiv · Feb 3, 2025 · PreprintCancer Biology

Reproducible processing of TCGA regulatory networks

Viola Fanfani, Katherine Hoff Shutta, Panagiotis Mandros, Jonas Fischer, Enakshi Saha, Soel Micheletti, Chen Chen, Marouen Ben Guebila, Camila M. Lopes‐Ramos, John F Quackenbush

The paper develops a Nextflow workflow for reproducibly inferring regulatory networks from TCGA data, showing its application to colon cancer subtypes.

GigaScience · Jan 1, 2025Peer-reviewedBioinformatics

Selective loss of Y chromosomes in lung adenocarcinoma modulates the tumor immune environment through cancer/testis antigens

Jonas Fischer, Katherine Hoff Shutta, Chen Chen, Viola Fanfani, Enakshi Saha, Panagiotis Mandros, Marouen Ben Guebila, Joanne Xiu, Jorge J. Nieva, Stephen V. Liu, Dipesh Uprety, David B. Spetzler, Camila M. Lopes‐Ramos, Dawn Lisa DeMeo, John F Quackenbush

This study investigates how loss of the Y chromosome in lung adenocarcinoma affects the tumor immune environment and response to immunotherapy.

bioRxiv · Sep 19, 2024 · PreprintCancer Biology