The paper develops a classifier, DeCAF, to identify permissive and restraining cancer-associated fibroblast subtypes from bulk RNAseq data and validates its clinical relevance across multiple cancer types.

Cell Reports Medicine · Feb 1, 2026Peer-reviewedGenomics

RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species

David Kainer, Matthew J. Lane, Kyle A. Sullivan, J Izaak Miller, Mikaela Cashman, M. Morgan, Ashley M. Cliff, Jonathon Romero, Angelica M. Walker, D. Dakota Blair, Hari Bahadur Chhetri, Yongqin Wang, Mirko Pavicic, Anna Furches, Jaclyn M Noshay, , Daniel Jacobson

RWRtoolkit enables multi-omic network analysis using random walks on multiplex networks across any species, providing tools for topological analysis and statistical evaluation.

GigaScience · Jan 1, 2025Peer-reviewedBioinformatics

Digging deeper into GWAS signal using GRIN implicates additional genes contributing to suicidal behavior

Kyle A. Sullivan, Matthew J. Lane, Mikaela Cashman, J Izaak Miller, Mirko Pavicic, Angelica M. Walker, Ashley M. Cliff, Jonathon Romero, Xuejun Qin, Jennifer H. Lindquist, Niamh Mullins, Anna R. Docherty, Hilary H Coon, Douglas M. Ruderfer, VA Million Veteran Program, , David Kainer

This study relaxes GWAS significance thresholds and uses GRIN to identify additional genes linked to suicidal behavior, which replicate across cohorts and show stronger biological connections.

medRxiv · Apr 20, 2022 · PreprintGenetic & Genomic Medicine