Author

Manfei Xie

Vanderbilt University

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

Biology Disciplines

Click to filter author papers

Bioinformatics· 3

Signature Assays, Organisms & Methods

Click to filter · or open tag

Assay:spatial transcriptomics· 3 Research Focus:benchmarking· 2 Approach:benchmark study· 1 Research Focus:database / resource· 1 Research Focus:dimensionality reduction· 1 Approach:graph neural network· 1 Approach:optimal transport· 1 Approach:simulation· 1

Frequent Co-Authors

Xin ZhouiD· 3 shared Lu ZhangiD· 2 shared Mingxing Rao· 2 shared Weiman Yuan· 2 shared Wenjun SheniD· 2 shared Yikang LiiD· 2 shared Bingshan LiiD· 1 shared Can LuoiD· 1 shared

Activity by Year

2024-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 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

3 shared papersBioinformatics

Xin ZhouORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

From features to slice: parameter-cloud modeling of spatial transcriptomics for simulation and 3D interpolatory augmentation

Yiru Chen, Manfei Xie, Yunfei Hu, Weiman Yuan, Hirak Sarkar, Bingshan Li, Lu Zhang, Xin Zhou

FEAST generates synthetic spatial transcriptomics data with tunable spatial and transcriptional variation for benchmarking and 3D reconstruction.

bioRxiv · Dec 8, 2025 · PreprintBioinformatics

Benchmarking clustering, alignment, and integration methods for spatial transcriptomics

Yunfei Hu, Yikang Li, Manfei Xie, Mingxing Rao, Wenjun Shen, Can Luo, Haoran Qin, Jihoon Baek, Xin Zhou

This paper benchmarks clustering, alignment, and integration methods for spatial transcriptomics using real and simulated datasets, providing recommendations and code for reproducibility.

bioRxiv · Mar 12, 2024 · PreprintBioinformatics

MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics

Yunfei Hu, Zhenhan Lin, Manfei Xie, Weiman Yuan, Yikang Li, Mingxing Rao, Yichen Henry Liu, Wenjun Shen, Lu Zhang, Xin Zhou

MaskGraphene integrates multi-slice, multi-condition spatial transcriptomics data using a graph neural network to generate interpretable joint embeddings with preserved geometric information, improving downstream analyses.

bioRxiv · Feb 21, 2024 · PreprintBioinformatics