Research / 研究

We study single-cell and spatial omics, gene regulatory networks, and mechanisms of development and disease.

我们聚焦单细胞与空间多组学、基因调控网络，以及发育与疾病机制研究。

Highlighted

RegVelo: gene-regulatory-informed dynamics of single cells

Weixu Wang, Zhiyuan Hu, Philipp Weiler, Sarah Mayes, Marius Lange, …, Julianna O. Haug, Jingye Wang, Zhengyuan Xue, Tatjana Sauka-Spengler, Fabian J. Theis

Cell · 11 May 2026 · doi:10.1016/j.cell.2026.04.022

RegVelo; Cell (2026).

Code

Docs

The Repertoire of Serous Ovarian Cancer Non-genetic Heterogeneity Revealed by Single-Cell Sequencing of Normal Fallopian Tube Epithelial Cells

Zhiyuan Hu, Mara Artibani, Abdulkhaliq Alsaadi, Nina Wietek, Matteo Morotti, …, Stephanie Jones, Vincenzo Cerundolo, Tatjana Sauka-Spengler, Christopher Yau, Ahmed Ashour Ahmed

Cancer Cell · 01 Feb 2020 · doi:10.1016/j.ccell.2020.01.003

Single-cell profiling of normal fallopian tube epithelial cells; Cancer Cell (2020).

single-cell cancer ovarian-cancer heterogeneity

All Publications / 全部论文

RegVelo: gene-regulatory-informed dynamics of single cells

Weixu Wang, Zhiyuan Hu, Philipp Weiler, Sarah Mayes, Marius Lange, …, Julianna O. Haug, Jingye Wang, Zhengyuan Xue, Tatjana Sauka-Spengler, Fabian J. Theis

Cell · 11 May 2026 · doi:10.1016/j.cell.2026.04.022

RegVelo; Cell (2026).

Code

Docs

software single-cell rna-velocity grn method

Endothelial regulatory circuits control cranial neural crest migration and plasticity

Zhiyuan Hu, Sarah Mayes, Weixu Wang, José M. Santos-Pereira, Fabian Theis, Tatjana Sauka-Spengler

bioRxiv · 17 Sep 2024 · doi:10.1101/2024.09.17.613303

Cranial neural crest regulatory circuits.

Code

development neural-crest multiome perturb-seq grn

Whole-genome methylation profiling of extracellular vesicle DNA in gastric cancer identifies intercellular communication features

Bingqian Lin, Zhenna Jiao, Shouquan Dong, Weikai Yan, Jinting Jiang, …, Xiaocheng Weng, Hongling Wang, Zhiyuan Hu, Yibin Liu, Xiang Zhou

Nature Communications · 29 Aug 2025 · doi:10.1038/s41467-025-63435-w

TEMPT; Nature Communications (2025).

Code

epigenomics methylation ev-dna liquid-biopsy method

FINE-EM-seq: a rapid isothermal amplification method enabling comprehensive methylome profiling of zebrafish early embryos

Chenyang Ding, Qifeng Zhang, Jing Wang, Yanbo Xu, Tiantian Huang, Yanfang Du, Junjie Zhang, Xiang Zhou, Yibin Liu, Zhiyuan Hu

Cell Insight · 01 Jun 2026 · doi:10.1016/j.cellin.2026.100324

FINE-EM-seq; Cell Insight (2026).

Code

epigenomics methylation zebrafish embryo method

CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation

Zhiyuan Hu, Ahmed A. Ahmed, Christopher Yau

Genome Biology · 01 Dec 2021 · doi:10.1186/s13059-021-02561-2

CIDER; Genome Biology (2021).

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Docs

software single-cell integration clustering method

Single-cell transcriptomics identifies a WNT7A-FZD5 signaling axis that maintains fallopian tube stem cells in patient-derived organoids

Abdulkhaliq Alsaadi, Mara Artibani, Zhiyuan Hu, Nina Wietek, Matteo Morotti, …, Jarret Adams, Francesca Silvestri, Sachdev S. Sidhu, Joan S. Brugge, Ahmed Ashour Ahmed

Cell Reports · 01 Nov 2023 · doi:10.1016/j.celrep.2023.113354

WNT7A-FZD5 organoid work; Cell Reports (2023).

organoid fallopian-tube stem-cell single-cell cancer

The Repertoire of Serous Ovarian Cancer Non-genetic Heterogeneity Revealed by Single-Cell Sequencing of Normal Fallopian Tube Epithelial Cells

Zhiyuan Hu, Mara Artibani, Abdulkhaliq Alsaadi, Nina Wietek, Matteo Morotti, …, Stephanie Jones, Vincenzo Cerundolo, Tatjana Sauka-Spengler, Christopher Yau, Ahmed Ashour Ahmed

Cancer Cell · 01 Feb 2020 · doi:10.1016/j.ccell.2020.01.003

Single-cell profiling of normal fallopian tube epithelial cells; Cancer Cell (2020).

single-cell cancer ovarian-cancer heterogeneity

The Oxford Classic Links Epithelial-to-Mesenchymal Transition to Immunosuppression in Poor Prognosis Ovarian Cancers

Zhiyuan Hu, Paula Cunnea, Zhe Zhong, Haonan Lu, Oloruntoba I. Osagie, …, Joanna Hester, Ashwag Albukhari, Eric O. Aboagye, Christina Fotopoulou, Ahmed Ahmed

Clinical Cancer Research · 01 Mar 2021 · doi:10.1158/1078-0432.CCR-20-2782

The Oxford Classic links epithelial-mesenchymal transition to immunosuppression in poor prognosis ovarian cancers; Clinical Cancer Research (2021).

Code

ovarian-cancer emt immunosuppression cancer-genomics transcriptomics

Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution

Yibin Liu, Zhiyuan Hu, Jingfei Cheng, Paulina Siejka-Zielińska, Jinfeng Chen, Masato Inoue, Ahmed Ashour Ahmed, Chun-Xiao Song

Nature Communications · 27 Jan 2021 · doi:10.1038/s41467-021-20920-2

Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution; Nature Communications (2021).

Code

epigenomics methylation sequencing 5mc method