胡致远课题组 | Hu Lab Single-cell & Spatial Omics · Regulatory Genomics · Development & Disease

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

FINE-EM-seq: a rapid isothermal amplification method enabling comprehensive methylome profiling of zebrafish early embryos
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
Genome-Wide Single-Nucleotide Resolution Mapping of DNA Damage by Dual Enzyme Cleavage-Assisted Sequencing
Genome-Wide Single-Nucleotide Resolution Mapping of DNA Damage by Dual Enzyme Cleavage-Assisted Sequencing
Tong-Tong Ji, Neng-Bin Xie, Yong Zhu, Jun Xiong, Yao-Hua Gu, …, Shan Zhang, Fang-Yin Gang, Zhiyuan Hu, Yibin Liu, Bi-Feng Yuan
Analytical Chemistry  ·  06 May 2026  ·  doi:10.1021/acs.analchem.6c00913
RegVelo: gene-regulatory-informed dynamics of single cells
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
Whole-genome methylation profiling of extracellular vesicle DNA in gastric cancer identifies intercellular communication features
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
Endothelial regulatory circuits control cranial neural crest migration and plasticity
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
RegVelo: gene-regulatory-informed dynamics of single cells
RegVelo: gene-regulatory-informed dynamics of single cells
Weixu Wang, Zhiyuan Hu, Philipp Weiler, Sarah Mayes, Marius Lange, Jingye Wang, Zhengyuan Xue, Tatjana Sauka-Spengler, Fabian J. Theis
bioRxiv  ·  11 Dec 2024  ·  doi:10.1101/2024.12.11.627935
Single-cell transcriptomics identifies a WNT7A-FZD5 signaling axis that maintains fallopian tube stem cells in patient-derived organoids
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
Cellular plasticity in the neural crest and cancer
Cellular plasticity in the neural crest and cancer
Zhiyuan Hu, Tatjana Sauka-Spengler
Current Opinion in Genetics & Development  ·  01 Aug 2022  ·  doi:10.1016/j.gde.2022.101928
Single Cell Transcriptomics identifies a WNT7A-FZD5 Signaling Axis that maintains Fallopian Tube Stem Cells in Patient-derived Organoids
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
bioRxiv  ·  03 Aug 2022  ·  doi:10.1101/2022.08.02.502319
CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation
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).
Code
Docs
software single-cell integration clustering method
Promises and challenges of adoptive T-cell therapies for solid tumours.
Promises and challenges of adoptive T-cell therapies for solid tumours.
Matteo Morotti, Ashwag Albukhari, Abdulkhaliq Alsaadi, Mara Artibani, James D Brenton, …, Helen White, Nina Wietek, David N Church, David C Wedge, Ahmed A Ahmed
British journal of cancer  ·  29 Mar 2021  ·  pmid:33782566
Adipocyte-like signature in ovarian cancer minimal residual disease identifies metabolic vulnerabilities of tumor initiating cells
Adipocyte-like signature in ovarian cancer minimal residual disease identifies metabolic vulnerabilities of tumor initiating cells
Mara Artibani, Kenta Masuda, Zhiyuan Hu, Pascal C. Rauher, Garry Mallett, …, Christer S. Ejsing, Robin W. Klemm, Christopher Yau, Tatjana Sauka-Spengler, Ahmed A. Ahmed
JCI Insight  ·  04 May 2021  ·  doi:10.1172/jci.insight.147929
An interpretable meta-clustering framework for single-cell RNA-Seq data integration and evaluation
An interpretable meta-clustering framework for single-cell RNA-Seq data integration and evaluation
Zhiyuan Hu, Ahmed A. Ahmed, Christopher Yau
bioRxiv  ·  30 Mar 2021  ·  doi:10.1101/2021.03.29.437525
Eating disorders treatment experiences and social support: Perspectives from service seekers in mainland China
Eating disorders treatment experiences and social support: Perspectives from service seekers in mainland China
Ruofan Ma, Manning Zhang, Jonathan M. Oakman, Jiping Wang, Siqi Zhu, Chendi Zhao, Zhiyuan Hu, NiCole T. Buchanan
International Journal of Eating Disorders  ·  08 Jun 2021  ·  doi:10.1002/EAT.23565
Mechanistic Drivers of Müllerian Duct Development and Differentiation Into the Oviduct
Mechanistic Drivers of Müllerian Duct Development and Differentiation Into the Oviduct
Laura Santana Gonzalez, Ioanna A. Rota, Mara Artibani, Matteo Morotti, Zhiyuan Hu, Nina Wietek, Abdulkhaliq Alsaadi, Ashwag Albukhari, Tatjana Sauka-Spengler, Ahmed A. Ahmed
Frontiers in Cell and Developmental Biology  ·  08 Mar 2021  ·  doi:10.3389/fcell.2021.605301
Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution
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
The Oxford Classic Links Epithelial-to-Mesenchymal Transition to Immunosuppression in Poor Prognosis Ovarian Cancers
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
The Zinc Finger Protein Zbtb18 Represses Expression of Class I Phosphatidylinositol 3-Kinase Subunits and Inhibits Plasma Cell Differentiation
The Zinc Finger Protein Zbtb18 Represses Expression of Class I Phosphatidylinositol 3-Kinase Subunits and Inhibits Plasma Cell Differentiation
Bin Xie, Tariq E Khoyratty, Enas Abu-Shah, Pablo F Cespedes, Andrew J MacLean, …, Zhiyuan Hu, Ahmed A Ahmed, Michael L Dustin, Irina A Udalova, Tal I Arnon
The Journal of Immunology  ·  01 Apr 2021  ·  doi:10.4049/jimmunol.2000367
Enhanced Immunogenicity of Mitochondrial-Localized Proteins in Cancer Cells
Enhanced Immunogenicity of Mitochondrial-Localized Proteins in Cancer Cells
Gennaro Prota, Uzi Gileadi, Margarida Rei, Ana Victoria Lechuga-Vieco, Ji-Li Chen, …, Jan Rehwinkel, Jose A. Enríquez, Ahmed A. Ahmed, Ton N. Schumacher, Vincenzo Cerundolo
Cancer Immunology Research  ·  01 May 2020  ·  doi:10.1158/2326-6066.cir-19-0467
Etiologic and treatment conceptualizations of disordered eating symptoms among mainland Chinese therapists
Etiologic and treatment conceptualizations of disordered eating symptoms among mainland Chinese therapists
Ruofan Ma, Kevin P. Capobianco, NiCole T. Buchanan, Zhiyuan Hu, Jonathan M. Oakman
International Journal of Eating Disorders  ·  24 Nov 2019  ·  doi:10.1002/eat.23204
The Repertoire of Serous Ovarian Cancer Non-genetic Heterogeneity Revealed by Single-Cell Sequencing of Normal Fallopian Tube Epithelial Cells
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
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
Michael P. Menden, Dennis Wang, Mike J. Mason, Bence Szalai, Krishna C. Bulusu, …, Stephen Fawell, Gustavo Stolovitzky, Justin Guinney, Jonathan R. Dry, Julio Saez-Rodriguez
Nature Communications  ·  17 Jun 2019  ·  doi:10.1038/s41467-019-09799-2
An evolving story of the metastatic voyage of ovarian cancer cells: cellular and molecular orchestration of the adipose-rich metastatic microenvironment
An evolving story of the metastatic voyage of ovarian cancer cells: cellular and molecular orchestration of the adipose-rich metastatic microenvironment
Takeshi Motohara, Kenta Masuda, Matteo Morotti, Yiyan Zheng, Salma El-Sahhar, …, Mara Artibani, Laura Santana Gonzalez, Hidetaka Katabuchi, Hideyuki Saya, Ahmed Ashour Ahmed
Oncogene  ·  19 Dec 2018  ·  doi:10.1038/s41388-018-0637-x
The repertoire of serous ovarian cancer non-genetic heterogeneity revealed by single-cell sequencing of normal fallopian tube epithelial cells
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, …, Hooman Soleymani majd, Vincenzo Cerundolo, Tatjana Sauka-Spengler, Christopher Yau, Ahmed A. Ahmed
bioRxiv  ·  17 Jun 2019  ·  doi:10.1101/672626
A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay
A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay
Zhiyuan Hu, Christopher Yau, Ahmed Ashour Ahmed
Nature Communications  ·  26 Jun 2017  ·  doi:10.1038/ncomms15943
A pan-cancer genome-wide analysis reveals tumour dependencies by induction of nonsense-mediated decay; Nature Communications (2017).
Code
R package
cancer-genomics nonsense-mediated-decay pan-cancer tumour-dependency computational-biology