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

Internal link

italic text

bold text

strike-through text

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

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

Heading 2

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

Heading 3

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

Heading 4

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

Heading 5

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

Heading 6

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

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

2024

2023

2022

2021

2020

2019

2018

2017

2016

2011

List projects

List team members

Bocheng Li (李泊成) PhD Student

Danni Hong (洪丹妮) Postdoctoral Researcher

Feiyang Wang (王飞扬) Research Assistant

Juan Zhang (张娟) Research Assistant Professor

Kai Zhang (张垲) Principal Investigator

Kunpeng Liu (刘鲲鹏) Visiting Student

Mengjiao Li (李梦娇) PhD Student

Xiaowan Quan (权筱婉) Research Assistant

Yue Dai (戴玥) PhD Student

Yue Liu (刘悦) Postdoctoral Researcher

List blog posts

2023

Example post 3

john-doe February 23, 2023 January 14, 2025

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

2024

A fast, scalable and versatile tool for analysis of single-cell omics data

Kai Zhang, Nathan R. Zemke, Ethan J. Armand, Bing Ren

Nature Methods  ·  08 Jan 2024  ·  doi:10.1038/s41592-023-02139-9

Website

Code

2023

Single-cell analysis of chromatin accessibility in the adult mouse brain

Songpeng Zu, Yang Eric Li, Kangli Wang, Ethan J. Armand, Sainath Mamde, …, M. Margarita Behrens, Joseph R. Ecker, Allen Wang, Sebastian Preissl, Bing Ren

Nature  ·  13 Dec 2023  ·  doi:10.1038/s41586-023-06824-9

Integrated analysis of single-cell chromatin state and transcriptome identified common vulnerability despite glioblastoma heterogeneity

Ramya Raviram, Anugraha Raman, Sebastian Preissl, Jiangfang Ning, Shaoping Wu, …, Paul S. Mischel, Vineet Bafna, Laure Escoubet, Bing Ren, Clark C. Chen

Proceedings of the National Academy of Sciences  ·  08 May 2023  ·  doi:10.1073/pnas.2210991120

2022

Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation

Poshen B. Chen, Patrick C. Fiaux, Kai Zhang, Bin Li, Naoki Kubo, …, Mengchi Wang, Wei Wang, Graham McVicker, Paul S. Mischel, Bing Ren

Cell Reports  ·  01 Nov 2022  ·  doi:10.1016/j.celrep.2022.111630

Systems-biology analysis of rheumatoid arthritis fibroblast-like synoviocytes implicates cell line-specific transcription factor function

Richard I. Ainsworth, Deepa Hammaker, Gyrid Nygaard, Cecilia Ansalone, Camilla Machado, …, Amanda Kuhs, Mattias N. D. Svensson, David L. Boyle, Gary S. Firestein, Wei Wang

Nature Communications  ·  20 Oct 2022  ·  doi:10.1038/s41467-022-33785-w

2021

A single-cell atlas of chromatin accessibility in the human genome

Kai Zhang, James D. Hocker, Michael Miller, Xiaomeng Hou, Joshua Chiou, …, Yang E. Li, Kyle J. Gaulton, Allen Wang, Sebastian Preissl, Bing Ren

Cell  ·  01 Nov 2021  ·  doi:10.1016/j.cell.2021.10.024

Website

Code

Data

An atlas of gene regulatory elements in adult mouse cerebrum

Yang Eric Li, Sebastian Preissl, Xiaomeng Hou, Ziyang Zhang, Kai Zhang, …, Michael Nunn, Eran A. Mukamel, M. Margarita Behrens, Joseph R. Ecker, Bing Ren

Nature  ·  06 Oct 2021  ·  doi:10.1038/s41586-021-03604-1

Cardiac cell type–specific gene regulatory programs and disease risk association

James D. Hocker, Olivier B. Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang, …, Andrew D. McCulloch, Kyle J. Gaulton, Bing Ren, Neil C. Chi, Sebastian Preissl

Science Advances  ·  14 May 2021  ·  doi:10.1126/sciadv.abf1444

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

Rongxin Fang, Sebastian Preissl, Yang Li, Xiaomeng Hou, Jacinta Lucero, …, Kai Zhang, Yanxiao Zhang, M. Margarita Behrens, Joseph R. Ecker, Bing Ren

Nature Communications  ·  26 Feb 2021  ·  doi:10.1038/s41467-021-21583-9

2020

Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes

Allen Wang, Joshua Chiou, Olivier B Poirion, Justin Buchanan, Michael J Valdez, …, Gloria Pryhuber, Yan Xu, Kyle J Gaulton, Sebastian Preissl, Xin Sun

eLife  ·  09 Nov 2020  ·  doi:10.7554/elife.62522

Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss

Mengchi Wang, David Wang, Kai Zhang, Vu Ngo, Shicai Fan, Wei Wang

Genetics  ·  01 Oct 2020  ·  doi:10.1534/genetics.120.303597

2019

Identification of DNA motifs that regulate DNA methylation

Mengchi Wang, Kai Zhang, Vu Ngo, Chengyu Liu, Shicai Fan, …, Rizi Ai, Zhao Chen, Jun Wang, Lina Zheng, Wei Wang

Nucleic Acids Research  ·  25 Jun 2019  ·  doi:10.1093/nar/gkz483

Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development

Kai Zhang, Mengchi Wang, Ying Zhao, Wei Wang

Science Advances  ·  01 Mar 2019  ·  doi:10.1126/sciadv.aav3262

Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse

Vu Ngo, Zhao Chen, Kai Zhang, John W. Whitaker, Mengchi Wang, Wei Wang

Proceedings of the National Academy of Sciences  ·  12 Feb 2019  ·  doi:10.1073/pnas.1813565116

Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers

Shicai Fan, Jianxiong Tang, Nan Li, Ying Zhao, Rizi Ai, Kai Zhang, Mengchi Wang, Wei Du, Wei Wang

npj Genomic Medicine  ·  01 Feb 2019  ·  doi:10.1038/s41525-019-0077-8

2018

Bayesian Networks Predict Neuronal Transdifferentiation

Richard I Ainsworth, Rizi Ai, Bo Ding, Nan Li, Kai Zhang, Wei Wang

G3 Genes|Genomes|Genetics  ·  01 Jul 2018  ·  doi:10.1534/g3.118.200401

Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge

Wei Wei, Zhanglong Ji, Yupeng He, Kai Zhang, Yuanchi Ha, Qi Li, Lucila Ohno-Machado

Database  ·  01 Jan 2018  ·  doi:10.1093/database/bay017

2017

Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours

J. Justin Milner, Clara Toma, Bingfei Yu, Kai Zhang, Kyla Omilusik, …, Toan Nguyen, Shane Crotty, Wei Wang, Matthew E. Pipkin, Ananda W. Goldrath

Nature  ·  06 Dec 2017  ·  doi:10.1038/nature24993

Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation

Bingfei Yu, Kai Zhang, J Justin Milner, Clara Toma, Runqiang Chen, …, Shane Crotty, John T Chang, Matthew E Pipkin, Wei Wang, Ananda W Goldrath

Nature Immunology  ·  13 Mar 2017  ·  doi:10.1038/ni.3706

2016

Systematic identification of protein combinations mediating chromatin looping

Kai Zhang, Nan Li, Richard I. Ainsworth, Wei Wang

Nature Communications  ·  27 Jul 2016  ·  doi:10.1038/ncomms12249

Constructing 3D interaction maps from 1D epigenomes

Yun Zhu, Zhao Chen, Kai Zhang, Mengchi Wang, David Medovoy, John W. Whitaker, Bo Ding, Nan Li, Lina Zheng, Wei Wang

Nature Communications  ·  10 Mar 2016  ·  doi:10.1038/ncomms10812

2011

Signal-induced Brd4 release from chromatin is essential for its role transition from chromatin targeting to transcriptional regulation

Nanping Ai, Xiangming Hu, Feng Ding, Bingfei Yu, Huiping Wang, …, Yannan Li, Aidong Han, Wen Lin, Runzhong Liu, Ruichuan Chen

Nucleic Acids Research  ·  02 Sep 2011  ·  doi:10.1093/nar/gkr698

Isolation and functional characterization of P-TEFb-associated factors that control general and HIV-1 transcriptional elongation

Ruichuan Chen, Min Liu, Kai Zhang, Qiang Zhou

Methods  ·  01 Jan 2011  ·  doi:10.1016/j.ymeth.2010.04.005

Grid of blog posts

2023

Example post 3

john-doe February 23, 2023 January 14, 2025

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 January 14, 2025

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 January 14, 2025

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";

Search

Site Search