Author

Xingtan Zhang

Agricultural Genomics Institute at ShenzhenORCID 0000-0002-5207-0882Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Genetics· 2 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Organism:plant (other)· 3 Assay:whole-genome sequencing· 3 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Research Focus:genome assembly· 2 Research Focus:clustering· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Dongna MaiD· 2 shared Yibin WangiD· 2 shared Agusto Luzuriaga-NeiraiD· 1 shared Annaliese S. MasoniD· 1 shared Ben M. SaddiD· 1 shared Benedict PateniD· 1 shared Caowen SuniD· 1 shared Chang N. KimiD· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersGenetics

Dongna MaORCID

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5 papers

Recent·Most cited

Histology-informed spatial domain identification through multi-view graph convolutional networks

Huihui Zhang, Jiaxing Chang, Yue Sun, Pinli Hu, Jing Liu, Jiuju Luo, Hang Yang, Yonglin Ren, Xingtan Zhang, Zehua Chen, Kok Wai Wong, Haojing Shao

This paper introduces STESH, a spatial transcriptomics clustering method that integrates gene expression, spatial location, and histology, achieving superior clustering accuracy across multiple tissue types.

PLoS Computational Biology · Jun 1, 2026Peer-reviewedBioinformatics

Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

Xiaofei Zeng, Zili Yi, Xingtan Zhang, Yuhui Du, Yu Li, Zhiqing Zhou, Sijie Chen, Huijie Zhao, Sai Yang, Yibin Wang, Guoan Chen

This paper introduces HapHiC, a reference-independent allele-aware scaffolding tool that improves chromosome assignment and contig ordering, and applies it to construct a haplotype-resolved allotriploid genome.

Nature Plants · Aug 5, 2024Peer-reviewedBioinformatics

Whole-genome duplication reshaped adaptive evolution in a relict plant species, Cyclocarya paliurus

Yinquan Qu, Xulan Shang, Ziyan Zeng, Yanhao Yu, Guoliang Bian, Wenling Wang, Li Liu, Tian Li, Shengcheng Zhang, Qian Wang, Dejin Xie, Xuequn Chen, Zhenyang Liao, Yibin Wang, Jian Qin, , Shengzuo Fang

This study presents three genomes of Cyclocarya paliurus, identifies recent whole-genome duplications, and links dosage-effect genes to adaptive traits like photosynthesis and triterpenoid accumulation.

Genomics Proteomics & Bioinformatics · Feb 10, 2023Peer-reviewedGenetics

The last missing piece of the Triangle of U: the evolution of the tetraploid Brassica carinata genome

Won Cheol Yim, Mia Swain, Dongna Ma, Hong An, Kevin A. Bird, David D. Curdie, Samuel Wang, Hyun Don Ham, Agusto Luzuriaga-Neira, Jay S. Kirkwood, Manhoi Hur, Juan K. Q. Solomon, Jeffrey F. Harper, Dylan K. Kosma, David Alvarez‐Ponce, , Xingtan Zhang

This study completes the Triangle of U by sequencing the genome of Brassica carinata, revealing genomic features and gene family expansions linked to its agronomic traits.

bioRxiv · Jan 3, 2022 · PreprintGenetics

Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators

Cheng Sun, Jiaxing Huang, Yun Wang, Xiaomeng Zhao, Long Su, Gregg W.C. Thomas, Mengya Zhao, Xingtan Zhang, Irwin Jungreis, M Kellis, Saverio Vicario, Igor V. Sharakhov, Semen M. Bondarenko, Martin Hasselmann, Chang N. Kim, , Rachel Lockridge Mueller

The paper characterizes bumblebee genomes across 17 species to identify genetic variation linked to ecological and behavioral traits, revealing insights into genome structure, evolution, and adaptation.

Molecular Biology and Evolution · Sep 17, 2020Peer-reviewedGenomics