Author

Tong Ye

State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystemsORCID 0000-0003-1017-6969Unclaimed ORCID profile · follow to get notified of new preprints

Additional preprints under this name without ORCID

Tong Ye1 paper · University of Science and Technology of China

Biology Disciplines

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Bioinformatics· 1 Evolutionary Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Assay:DNA methylation· 2 Research Focus:phylogenetics / evolution· 2 Approach:statistical model· 2 Approach:Bayesian inference· 1 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Approach:deep learning· 1 Research Focus:dimensionality reduction· 1

Frequent Co-Authors

Dong ZhangiD· 2 shared Hong ZouiD· 2 shared Ivan JakovlićiD· 2 shared Rui SongiD· 2 shared Bing Wang· 1 shared Chuan‐Yu XiangiD· 1 shared Feng YaniD· 1 shared Gui-Tang Wang· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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2 shared papersEvolutionary Biology

Dong ZhangORCID

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Author profile →

3 papers

Recent·Most cited

MINT infers the latent single-cell spatial transcriptome from paired histology

Liying Chen, Zhongmin Zhang, Bing Wang, Wenle Ren, Hongke Peng, Shihong Lu, Mengyuan Xu, Yunhe Zhou, Xiongjian Luo, Tong Ye, Qi Zhu, Feng Yan, Luyi Tian

MINT infers cell-resolved spatial transcriptomes from paired histology and Slide-tags data, improving alignment and expression recovery in lung adenocarcinoma.

bioRxiv · Sep 22, 2026 · PreprintBioinformatics

The Phylogeny and the Evolution of Parasitic Strategies in Trematoda

Chuan‐Yu Xiang, Y Hu, Tong Ye, Rui Song, Hong Zou, Gui-Tang Wang, Dong Zhang, Wen-Xiang Li, Ivan Jakovlić

This study reconstructs the evolutionary history of trematode parasitic strategies using mitogenomic and nuclear genomic data, finding that ancestral trematodes had direct life cycles with no intermediate hosts.

Current Zoology · Mar 2, 2026Peer-reviewedEvolutionary Biology

Mitochondrial Genome-Based Phylogeny of Turbellarians and Evidence for Accelerated Mitochondrial Evolution in Symbiotic Species

Jiaqi Wang, Rui Song, Ming-Dian Liu, Tong Ye, Hong Zou, Guitang Wang, Wenxiang Li, Ivan Jakovlić, Dong Zhang

This study presents the first complete mitochondrial genome of the ectosymbiont Craspedella pedum, confirms the paraphyly of the Neoophora clade, and finds accelerated mitochondrial evolution in symbiotic turbellarians.

bioRxiv · Jul 1, 2025 · PreprintGenomics