Testbed

Basic formatting

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

External link

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italic text

bold text

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Text with extra blank lines above and below

• list item a
• list item b
• list item c

1. ordered list item 1
2. ordered list item 2
3. ordered list item 3

1. top level list item
   • nested list item
     1. even deeper nested list item

Plain image:

Heading 1

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Heading 2

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Heading 3

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Heading 4

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Heading 5

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Heading 6

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It was the best of times it was the worst of times. It was the age of wisdom, it was the age of foolishness. It was the spring of hope, it was the winter of despair.

// some code with syntax highlighting
const popup = document.querySelector("#popup");
popup.style.width = "100%";
popup.innerText =
  "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.";

This sentence has inline code, useful for making references to variables, packages, versions, etc. within a sentence.

Lorem ipsum dolor sit amet.

Consectetur adipiscing elit.

Sed do eiusmod tempor incididunt.

Jekyll Spaceship

$ a * b = c ^ b $

$ 2^{\frac{n-1}{3}} $

$ \int_a^b f(x)\,dx. $

Components

Section

Section, background

Section, dark=true

Section, background dark=true

Section, size=wide

Section, size=full w/ figure

Figure

Button

Icon

Lorem Ipsum Dolor

Feature

Title

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Title

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

List

List citations

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

List projects

RegVelo Gene-regulatory-informed dynamics of single cells

RegVelo connects single-cell dynamics with gene regulatory networks to predict how cells choose their future states and which genes drive those transitions. By simulating regulatory perturbations, it helps prioritize experimentally testable drivers of cell fate.

software method single-cell grn

Neural crest regulatory circuits Single-cell multi-omics, spatial transcriptomics and systematic perturbation

By integrating time-resolved single-cell multi-omics, spatial transcriptomics, and systematic Perturb-seq, this work maps the regulatory programs that guide cranial neural crest migration and fate decisions. It reveals how regulatory circuits control cell plasticity during development.

preprint resource development multiomics

TEMPT Whole-genome EV-DNA methylation profiling

TEMPT enables whole-genome methylation profiling of extracellular vesicle DNA from low-input samples. The method supports liquid biopsy studies by revealing cancer-associated methylation patterns and intercellular communication features.

method epigenomics liquid-biopsy publication

FINE-EM-seq Rapid isothermal methylome profiling for early embryos

FINE-EM-seq is a rapid isothermal amplification strategy for low-input methylome profiling. It enables high-coverage methylation analysis of early embryos and helps resolve methylome dynamics during development.

method epigenomics zebrafish publication

CIDER Interpretable meta-clustering for scRNA-seq integration and evaluation

CIDER is an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation. It helps identify consistent cell populations across complex datasets while assessing whether integration preserves meaningful biological structure.

software single-cell integration resource

List team members

王静 / Jing Wang 硕士研究生 / Master Student 医学研究院
Medical Research Institute

王梦君 / Mengjun Wang 硕士研究生 / Master Student 医学研究院
Medical Research Institute

张崎峰 / Qifeng Zhang 博士研究生 / PhD Student 医学研究院
Medical Research Institute

张廷苏 硕士研究生 / Master Student 医学研究院
Medical Research Institute

徐彦博 / Yanbo Xu 硕士研究生 / Master Student 医学研究院
Medical Research Institute

卢云浩 / Yunhao Lu 本科生 / Undergraduate Student 化学与分子科学学院
College of Chemistry and Molecular Sciences

李雨晴 / Yuqing Li 硕士研究生 / Master Student 医学研究院
Medical Research Institute

焦振娜 / Zhenna Jiao 博士研究生 / PhD Student 医学研究院
Medical Research Institute

胡致远 / Zhiyuan Hu 课题组长 / Principal Investigator 医学研究院
Medical Research Institute

List blog posts

2023

Example post 3

john-doe February 23, 2023 June 24, 2026

biology medicine

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2021

2019

Citation

[no title info]

[no publisher info]  ·  [no date info]  ·  [no id info]

Card

A Large Card A cool card

A cool description

manual-tag

A Small Card A cool card

Lorem ipsum

manual-tag

Portrait

Manual name

Post Excerpt

Alert

Tags

Float

Figures

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Code

const test = "Lorem ipsum dolor sit amet, consectetur adipiscing elit.";

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Nulla facilisi etiam dignissim diam quis. Id aliquet lectus proin nibh nisl condimentum id venenatis a. Tristique magna sit amet purus gravida quis blandit turpis cursus. Ultrices eros in cursus turpis massa tincidunt dui ut ornare. A cras semper auctor neque vitae tempus quam pellentesque nec. At tellus at urna condimentum mattis pellentesque. Ipsum consequat nisl vel pretium. Ultrices mi tempus imperdiet nulla malesuada pellentesque elit eget gravida. Integer vitae justo eget magna fermentum iaculis eu non diam. Mus mauris vitae ultricies leo integer malesuada nunc vel. Leo integer malesuada nunc vel risus. Ornare arcu odio ut sem nulla pharetra. Purus semper eget duis at tellus at urna condimentum. Enim neque volutpat ac tincidunt vitae semper quis lectus.

Grid

Regular

With Markdown images

Square

With figure components

Grid of citations

2026

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

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

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

2025

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

2024

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

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

2023

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

2022

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

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

2021

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

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

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

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

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

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

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

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

2020

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

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

2019

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

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

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

2018

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

2017

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

Grid of blog posts

2023

Example post 3

john-doe February 23, 2023 June 24, 2026

biology medicine

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2021

Example post 2

jane-smith September 30, 2021 June 24, 2026

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2019

Example post 1

sarah-johnson January 07, 2019 June 24, 2026

biology medicine big-data

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Cols

Text

Images

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Code

const test = "Lorem ipsum dolor sit amet";

const test = "Lorem ipsum dolor sit amet";

const test = "Lorem ipsum dolor sit amet";

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