Publications

2025

1. scMultiSim

   scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell–cell interactions

   Hechen Li, Ziqi Zhang, Michael Squires, and 2 more authors

   Nature Methods, 2025

   Bib

   @article{li2025scmultisim,
     title = {scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell--cell interactions},
     author = {Li, Hechen and Zhang, Ziqi and Squires, Michael and Chen, Xi and Zhang, Xiuwei},
     journal = {Nature Methods},
     pages = {1--12},
     year = {2025},
     publisher = {Nature Publishing Group US New York},
   }

2024

1. Data-driven batch detection enhances single-cell omics data analysis

   Ziqi Zhang and Xiuwei Zhang

   Cell Systems, 2024

   Bib

   @article{zhang2024data,
     title = {Data-driven batch detection enhances single-cell omics data analysis},
     author = {Zhang, Ziqi and Zhang, Xiuwei},
     journal = {Cell Systems},
     volume = {15},
     number = {10},
     pages = {893--894},
     year = {2024},
     publisher = {Elsevier},
   }

2. scDisInFact

   scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data

   Ziqi Zhang, Xinye Zhao, Mehak Bindra, and 2 more authors

   Nature Communications, 2024

   Bib

   @article{zhang2024scdisinfact,
     title = {scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data},
     author = {Zhang, Ziqi and Zhao, Xinye and Bindra, Mehak and Qiu, Peng and Zhang, Xiuwei},
     journal = {Nature Communications},
     volume = {15},
     number = {1},
     pages = {912},
     year = {2024},
     publisher = {Nature Publishing Group UK London},
   }

2023

1. scMoMaT

   scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection

   Ziqi Zhang, Haoran Sun, Ragunathan Mariappan, and 7 more authors

   Nature Communications, 2023

   Bib

   @article{zhang2023scmomat,
     title = {scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection},
     author = {Zhang, Ziqi and Sun, Haoran and Mariappan, Ragunathan and Chen, Xi and Chen, Xinyu and Jain, Mika S and Efremova, Mirjana and Teichmann, Sarah A and Rajan, Vaibhav and Zhang, Xiuwei},
     journal = {Nature Communications},
     volume = {14},
     number = {1},
     pages = {384},
     year = {2023},
     publisher = {Nature Publishing Group UK London},
   }

2022

1. CeSpGRN

   Inferring cell-specific gene regulatory networks from single cell gene expression data

   Ziqi Zhang, Jongseok Han, Le Song, and 1 more author

   BioRxiv, 2022

   Bib

   @article{zhang2022GRN,
     title = {Inferring cell-specific gene regulatory networks from single cell gene expression data},
     author = {Zhang, Ziqi and Han, Jongseok and Song, Le and Zhang, Xiuwei},
     journal = {BioRxiv},
     year = {2022},
     publisher = {Cold Spring Harbor Laboratory},
   }

2. scDART

   scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously

   Ziqi Zhang, Chengkai Yang, and Xiuwei Zhang

   Genome Biology, Jun 2022

   DOI Bib

   @article{Zhang2022scDART,
     title = {scDART: integrating unmatched scRNA-seq and scATAC-seq data and learning cross-modality relationship simultaneously},
     author = {Zhang, Ziqi and Yang, Chengkai and Zhang, Xiuwei},
     journal = {Genome Biology},
     year = {2022},
     month = jun,
     day = {27},
     volume = {23},
     number = {1},
     pages = {139},
     issn = {1474-760X},
     doi = {10.1186/s13059-022-02706-x},
     url = {https://doi.org/10.1186/s13059-022-02706-x},
   }

2021

1. CellPath

   Inference of high-resolution trajectories in single-cell RNA-seq data by using RNA velocity

   Ziqi Zhang and Xiuwei Zhang

   Cell Reports Methods, Jun 2021

   Bib

   @article{zhang2021inference,
     title = {Inference of high-resolution trajectories in single-cell RNA-seq data by using RNA velocity},
     author = {Zhang, Ziqi and Zhang, Xiuwei},
     journal = {Cell Reports Methods},
     volume = {1},
     number = {6},
     pages = {100095},
     year = {2021},
     publisher = {Elsevier},
   }

2. VeloSim

   VeloSim: Simulating single cell gene-expression and RNA velocity

   Ziqi Zhang and Xiuwei Zhang

   BioRxiv, Jun 2021

   Bib

   @article{zhang2021velosim,
     title = {VeloSim: Simulating single cell gene-expression and RNA velocity},
     author = {Zhang, Ziqi and Zhang, Xiuwei},
     journal = {BioRxiv},
     year = {2021},
     publisher = {Cold Spring Harbor Laboratory},
   }

3. Maximum likelihood reconstruction of ancestral networks by integer linear programming

   Vaibhav Rajan, Ziqi Zhang, Carl Kingsford, and 1 more author

   Bioinformatics, Jun 2021

   Bib

   @article{rajan2021maximum,
     title = {Maximum likelihood reconstruction of ancestral networks by integer linear programming},
     author = {Rajan, Vaibhav and Zhang, Ziqi and Kingsford, Carl and Zhang, Xiuwei},
     journal = {Bioinformatics},
     volume = {37},
     number = {8},
     pages = {1083--1092},
     year = {2021},
     publisher = {Oxford University Press}
   }

4. Integrating unpaired scRNA-seq and scATAC-seq with unequal cell type compositions

   Ziqi Zhang, Haoran Sun, Ragunathan Mariappan, and 6 more authors

   ICML workshop on Computational Biology, Jun 2021