Author
David Brenes
Stanford MedicineORCID 0000-0003-1969-5386Unclaimed ORCID profile · follow to get notified of new preprints
Biology Disciplines
Click to filter author papersSignature Assays, Organisms & Methods
Click to filter · or open tagActivity by Year
2025-2026 · peak 4/yrCo-Author Collaboration Network
10 top collaborators · 45 mutual co-author links5 papers
Recent·Most cited
- PathologybioRxivPreprint
Scalable 3D cell-interaction analysis via supercell graphs for prostate cancer risk stratification
Yujie Zhao, Sarah S. L. Chow, Renao Yan…·Jonathan T.C. Liu
SCALE3D improves prostate cancer risk prediction by analyzing 3D cell interactions through supercell graphs, outperforming traditional features and reducing computational demands.
DOI 10.64898/2026.07.07.736891 - BioengineeringNature MethodsPeer-reviewed
3D pathology-guided microdissection
Huai-Ching Hsieh, Gan Gao, Qinghua Han…·Jonathan T.C. Liu
This paper introduces a 3D microdissection method combining CNC milling and light-sheet microscopy to study tumor evolution in complex 3D structures.
3 citationstop 4% - BioengineeringbioRxivPreprint
High-throughput, organ-scale 3D tubule tracking using TubuleMAP
Chetan Poudel, David Brenes, Wenhui Xie…·Joshua C. Vaughan
The paper introduces TubuleMAP, a semi-automated 3D tubule tracking pipeline for analyzing tubular networks, achieving high throughput and accuracy in reconstructing kidney and testis tubules.
- PathologybioRxivPreprint
Deep-learning triage of 3D pathology datasets for comprehensive and efficient pathologist assessments
Gan Gao, Renao Yan, Andrew H. Song…·Jonathan T.C. Liu
CARP3D uses deep learning to prioritize high-risk 2D sections in 3D pathology data, improving disease detection while reducing pathologist workload.
6 citations