Author

Ying Zhu

The University of Texas MD Anderson Cancer Center

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Same name, identified by ORCID

Biology Disciplines

Click to filter author papers

Bioinformatics· 4

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:benchmarking· 3 Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Organism:human· 2 Research Focus:batch correction / integration· 1 Research Focus:database / resource· 1 Research Focus:dimensionality reduction· 1 Approach:large language model· 1

Frequent Co-Authors

Vince D. CalhouniD· 2 shared Yuda BiiD· 2 shared Bai Jiang· 1 shared Bissan Al‐LazikaniiD· 1 shared Can YangiD· 1 shared Chenyu ZhangiD· 1 shared David S. MaxwelliD· 1 shared Hongyu ZhaoiD· 1 shared

Activity by Year

2016-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 11 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersBioinformatics

Vince D. CalhounORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

A Context-Aware Target Engagement and Pharmacodynamic Biomarker Resource to Accelerate Drug Discovery and Development

Yuntao Yang, Li Zhao, Seyedmehdi Orouji, Ying Zhu, Rebecca L Johnson, David S. Maxwell, Ioan L Mica, Kaitlyn P. Russell, Bissan Al‐Lazikani

The paper develops TargetTrace, a resource linking drug targets to pharmacodynamic biomarkers, compiling 71,323 target-biomarker relationships for oncology drug development.

bioRxiv · Apr 22, 2026 · PreprintBioinformatics

A residual-ratio framework for auditing transcriptomic gene signatures against background expression structure

Ying Zhu, Chenyu Zhang, Vince D. Calhoun, Yuda Bi

This paper introduces a residual-ratio framework to audit transcriptomic gene signatures by quantifying their independence from background expression structure, showing it discriminates biological signatures from random gene sets across multiple cancer types.

bioRxiv · Apr 14, 2026 · PreprintBioinformatics

Spectral Graph Features for Reference-free RNA 3D Quality Assessment

Ying Zhu, Huaiwen Zhang, Vince D Calhoun, Yuda Bi

This paper introduces SpecRNA-QA, a reference-free RNA 3D quality assessment method that outperforms local descriptors and statistical potentials by capturing global topological coherence.

bioRxiv · Apr 12, 2026 · PreprintBioinformatics

AC-PCA: simultaneous dimension reduction and adjustment for confounding variation

Zhixiang Lin, Can Yang, Ying Zhu, John C. Duchi, Yao Fu, Yong Wang, Bai Jiang, Mahdi Zamanighomi, Xuming Xu, Mingfeng Li, Nenad Sestan, Hongyu Zhao, Wing Hung Wong

AC-PCA reduces dimensionality and adjusts for confounding variation in biological datasets, recovering anatomical structure and shared variation across species.

bioRxiv · Apr 19, 2016Bioinformatics