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---
title: Welcome to the JEFworks Lab
layout: default
sectionid: home
image: /assets/banners/bg.jpg
desc: <img src="/assets/logo/jefworks_lab_logo_hex.svg" width="128px"><br/><br/>Welcome to the JEFworks Lab, <br/>where Prof. Jean Fan and team work on statistical analysis approaches and machine learning tools for analyzing big spatially resolved omics data to better understand the molecular and spatial-contextual factors shaping cellular identity and heterogeneity in the context of human health and disease.
---
<div class="bg-light">
<div class="container page-pad" align="center">
<h2>We are a bioinformatics research lab in the <a href="https://ccb.jhu.edu/">Center for Computational Biology</a> and the <a href="https://www.bme.jhu.edu/">Department of Biomedical Engineering</a> at Johns Hopkins University. <a href="team">Meet our team!</a></h2>
<div class="row">
<div class="col-xs-3 col-md-2">
<a href="team">
<img src="/img/profile.jpg" class="img-responsive img-circle" alt="Prof. Jean Fan" style="padding: 15px 5px">
</a>
</div>
{% for pub in site.team %}
{% if pub.alumni == nil %}
{% if pub.name != 'Remy' %}
{% if pub.name != 'You!' %}
<div class="col-xs-3 col-md-2">
<a href="team">
<img src="{{ pub.profile }}" class="img-responsive img-circle" alt="{{ pub.name }}" style="padding: 15px 5px">
</a>
</div>
{% endif %}
{% endif %}
{% endif %}
{% endfor %}
<div class="col-xs-3 col-md-2">
<a href="team">
<img src="/img/remy.jpg" class="img-responsive img-circle" alt="Remy" style="padding: 15px 5px">
</a>
</div>
<div class="col-xs-3 col-md-2">
<a href="team">
<img src="/img/sample.jpg" class="img-responsive img-circle" alt="You! Aspiring Scientist" style="padding: 15px 5px">
</a>
</div>
</div>
<a href="join"><button type="button" class="btn btn-warning btn-block btn-lg">Learn how you can join us!</button></a>
</div>
</div>
<div class="container page-pad">
<div align="center"><h2>We develop bioinformatics methods for analyzing spatially resolved sequencing and imaging data.</h2></div>
<div class="row">
<div class="col-md-7">
<p>Spatial organization at both the subcellular-level within cells as well as the cellular-level within tissues play important roles in regulating cell identity and function. Recent technological advances have enabled high-throughput spatially resolved transcriptomic profiling at single-molecule and near-single-cell resolution. We develop machine learning and other statistical approaches as open-source computational software to take advantage of this new spatial information in deriving biological insights regarding how spatial organization plays a role in both healthy and diseased settings. </p>
<ul>
<li>
<a href="/publications#/papers/2024/06/20/seraster/">Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F Miller, Rahul Satija, John W Hickey, Jean Fan^. SEraster - a rasterization preprocessing framework for scalable spatial omics data analysis. Bioinformatics. June 20, 2024. doi.org/10.1093/bioinformatics/btae412</a>
</li>
<li>
<a href="/publications#/papers/2024/06/12/imsrt-normalization/">Lyla Atta, Kalen Clifton, Manjari Anant, Gohta Aihara, and Jean Fan^. Gene count normalization in single-cell imaging-based spatially resolved transcriptomics. Genome Biology. June 12, 2024. doi.org/10.1186/s13059-024-03303-w</a>
</li>
<li>
<a href="/publications#/papers/2023/12/08/stalign/">Kalen Clifton*, Manjari Anant*, Gohta Aihara, Lyla Atta, Osagie K Aimiuwu, Justus M Kebschull, Michael I Miller, Daniel Tward^, Jean Fan^. STalign - alignment of spatial transcriptomics data using diffeomorphic metric mapping. Nature Communications. December 8, 2023. doi.org/10.1038/s41467-023-43915-7</a>
</li>
<li>
<a href="/publications#/papers/2022/04/29/Miller_et_al-2022-Nature_Communications/">Brendan F Miller, Feiyang Huang, Lyla Atta, Arpan Sahoo, Jean Fan^. Reference-free cell type deconvolution of pixel-resolution spatially resolved transcriptomics data. Nature Communications. 2022. doi:/10.1038/s41467-022-30033-z</a>
</li>
<li>
<a href="/publications#/papers/2021/09/06/Atta_et_al-2021-Nature_Communications/">Lyla Atta, Jean Fan^. Computational challenges and opportunities in spatially resolved transcriptomic data analysis. Nature Communications. 2021. doi:10.1038/s41467-021-25557-9</a>
</li>
</ul>
</div>
<div class="col-md-5">
<img src="assets/papers/Atta_et_al-2021-Nature_Communications.png" width="100%">
</div>
</div>
<div align="center"><h2>We apply these bioinformatics methods to better understand the role of cellular heterogeneity in disease.</h2></div>
<div class="row">
<div class="col-md-6">
<img src="img/main1.jpg" width="100%">
</div>
<div class="col-md-6">
<p>Advancements in high-throughput sequencing and imaging technologies have uncovered tremendous genetic, epigenetic, transcriptional, and spatial heterogeneity in various diseases but their impact on clinical outcomes is not well understood. We establish close collaborations with clinical collaborators to develop and apply bioinformatics methods that contribute to a more complete understanding of how cellular heterogeneity impacts disease progression and clinical prognosis.</p>
<ul>
<li>
<a href="/publications#/papers/2020/09/15/natureemm101038/"><u>Jean Fan^</u>, Kamil Slowikowski, Fan Zhang. Single-cell transcriptomics in cancer - computational challenges and opportunities. Nature Experimental and Molecular Medicine. 2020, doi.org:10.1038/s12276-020-0422-0</a>
</li>
<li>
<a href="/publications#/papers/2018/06/13/gr228080117/"><u>Jean Fan*</u>, Hae-Ock Lee*, Soohyun Lee, Da-eun Ryu, Semin Lee, et al. Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq. Genome Research. 2018. doi:10.1101/gr.228080.117</a>
</li>
<li>
<a href="/publications#/papers/2017/05/22/gr217331116/">Lili Wang*, <u>Jean Fan*</u>, Joshua M. Francis, George Georghiou, Sarah Hergert, et al. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Research. 2017. doi:10.1101/gr.217331.116</a>
</li>
</ul>
</div>
</div>
</div>
</div>
<div class="bg-light">
<div class="container page-pad">
<div class="row">
<div class="col-sm-4">
<h1 class="text-center"><i class="fa fa-book" aria-hidden="true"></i></h1>
<h2 class="text-center">Latest Publications</h2>
<ul class="post-list-container">
{% assign items = site.papers | reverse %}
{% for post in items limit:5 %}
<li><a href="{{ site.baseurl }}/publications#{{ post.url }}">{{ post.title }}</a> on {{ post.date | date_to_long_string }}</li>
{% endfor %}
</ul>
</div>
<div class="col-sm-4">
<h1 class="text-center"><i class="fa fa-rss-square" aria-hidden="true"></i></h1>
<h2 class="text-center">Latest News</h2>
<ul class="post-list-container">
{% assign items = site.news | reverse %}
{% for post in items limit:5 %}
<li><a href="{{ post.url | prepend: site.baseurl }}">{{ post.title }}</a> on {{ post.date | date_to_long_string}}</li>
{% endfor %}
</ul>
</div>
<div class="col-sm-4">
<h1 class="text-center"><i class="fa fa-pencil" aria-hidden="true"></i></h1>
<h2 class="text-center">Latest Blog Posts</h2>
<ul class="post-list-container">
{% for post in site.posts limit:5 %}
<li><a href="{{ post.url | prepend: site.baseurl }}">{{ post.title }}</a> on {{ post.date | date_to_long_string }}</li>
{% endfor %}
</ul>
</div>
</div>
<div class="row">
<div class="col-sm-4">
<a href="{{ site.baseurl }}/publications">
<button type="button" class="btn btn-primary btn-block">
More Publications
</button>
</a>
</div>
<div class="col-sm-4">
<a href="{{ site.baseurl }}/news">
<button type="button" class="btn btn-primary btn-block">
More News
</button>
</a>
</div>
<div class="col-sm-4">
<a href="{{ site.baseurl }}/blog">
<button type="button" class="btn btn-primary btn-block">
More Blog Posts
</button>
</a>
</div>
</div>
<br>
</div>
</div>
<div class="bg-dark"><div class="container page-pad" align="center">
<h3>Follow us on social media for the latest updates on our blog posts, code tutorials, software tools, and more!</h3>
<a href="https://www.twitter.com/jefworks" target="_blank"><li class="fa fa-fw fa-2x fa-twitter"></li></a>
<a href="https://bsky.app/profile/jef.works" target="_blank"><svg class="icon" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512"><path fill="#18BC9C" d="M111.8 62.2C170.2 105.9 233 194.7 256 242.4c23-47.6 85.8-136.4 144.2-180.2c42.1-31.6 110.3-56 110.3 21.8c0 15.5-8.9 130.5-14.1 149.2C478.2 298 412 314.6 353.1 304.5c102.9 17.5 129.1 75.5 72.5 133.5c-107.4 110.2-154.3-27.6-166.3-62.9l0 0c-1.7-4.9-2.6-7.8-3.3-7.8s-1.6 3-3.3 7.8l0 0c-12 35.3-59 173.1-166.3 62.9c-56.5-58-30.4-116 72.5-133.5C100 314.6 33.8 298 15.7 233.1C10.4 214.4 1.5 99.4 1.5 83.9c0-77.8 68.2-53.4 110.3-21.8z"/></svg></a>
<a href="https://www.youtube.com/JEFworks" target="_blank"><li class="fa fa-fw fa-2x fa-youtube"></li></a>
</div></div>
<div class="container page-pad">
<div class="row"><div align="center">
<h2>Latest Lab Fun</h2>
{% include image-gallery.html %}
</div></div>
</div>