Dr. Jean Fan
@jef.works
Associate prof @JHUBME. Doing #spatialtranscriptomics #compbio #dataviz #rstats. Founder @cuSTEMized. Editor @PLOSCompBio. Alum @HarvardDBMI @mbhsmagnet.
In this blog post, I use #RStats to explore publicly available ICE arrest data. #Dataviz shows recent trend where ICE are primarily targeting/locating people without criminal records in communities.
Code along and take a look for yourself: jef.works/blog/2025/09... #CodeTutorial
Code along and take a look for yourself: jef.works/blog/2025/09... #CodeTutorial
September 27, 2025 at 3:56 PM
In this blog post, I use #RStats to explore publicly available ICE arrest data. #Dataviz shows recent trend where ICE are primarily targeting/locating people without criminal records in communities.
Code along and take a look for yourself: jef.works/blog/2025/09... #CodeTutorial
Code along and take a look for yourself: jef.works/blog/2025/09... #CodeTutorial
Greetings from beautiful Sante Fe for the AI in Molecular Biology @keystonesymposia.bsky.social #KSAIBio26
Excited to bring together academic and industry leaders in this emerging field to organize, shape trends, influence policy, discuss challenges
If you're around, please come say hi 👋
Excited to bring together academic and industry leaders in this emerging field to organize, shape trends, influence policy, discuss challenges
If you're around, please come say hi 👋
September 16, 2025 at 2:48 AM
Greetings from beautiful Sante Fe for the AI in Molecular Biology @keystonesymposia.bsky.social #KSAIBio26
Excited to bring together academic and industry leaders in this emerging field to organize, shape trends, influence policy, discuss challenges
If you're around, please come say hi 👋
Excited to bring together academic and industry leaders in this emerging field to organize, shape trends, influence policy, discuss challenges
If you're around, please come say hi 👋
Likewise, to pinpoint what imaging data quality factors may drive these performance differences, we simulated lower-resolution images by applying Gaussian blur to the H&E images to demonstrate that image resolution has a measurable impact on performance and interpretability. 6/n
September 9, 2025 at 2:25 PM
Likewise, to pinpoint what imaging data quality factors may drive these performance differences, we simulated lower-resolution images by applying Gaussian blur to the H&E images to demonstrate that image resolution has a measurable impact on performance and interpretability. 6/n
Further, we demonstrate how imputation methods intended to rescue sparsity and noise boost performance when evaluated on the held-out test set but decreases performance when evaluated on an independent replicate, suggesting overfitting that limit robustness and generalizability. 5/n
September 9, 2025 at 2:24 PM
Further, we demonstrate how imputation methods intended to rescue sparsity and noise boost performance when evaluated on the held-out test set but decreases performance when evaluated on an independent replicate, suggesting overfitting that limit robustness and generalizability. 5/n
To pinpoint what molecular data quality factors may drive these performance differences, we performed a series of in silico ablation experiments in which we systematically decrease molecular data to show sparsity and noise as drivers of decreased performance. 4/n
September 9, 2025 at 2:24 PM
To pinpoint what molecular data quality factors may drive these performance differences, we performed a series of in silico ablation experiments in which we systematically decrease molecular data to show sparsity and noise as drivers of decreased performance. 4/n
We train identical models using matched ST datasets from different technologies (Visium vs Xenium) with unique technical constraints that impact data quality. We find that the predictive performance across genes is 38% higher when trained on Xenium data compared to Visium data. 3/n
September 9, 2025 at 2:22 PM
We train identical models using matched ST datasets from different technologies (Visium vs Xenium) with unique technical constraints that impact data quality. We find that the predictive performance across genes is 38% higher when trained on Xenium data compared to Visium data. 3/n
High costs motivate efforts to predict spatial transcriptomics from H&E images w/ deep learning. In our recent preprint, we show that noise, sparsity & resolution in ST data impact performance, highlighting the importance of training data quality: www.biorxiv.org/content/10.1...
🧵1/n
🧵1/n
September 9, 2025 at 2:20 PM
High costs motivate efforts to predict spatial transcriptomics from H&E images w/ deep learning. In our recent preprint, we show that noise, sparsity & resolution in ST data impact performance, highlighting the importance of training data quality: www.biorxiv.org/content/10.1...
🧵1/n
🧵1/n
Our paper identifying evidence of off-target probe binding in the 10x Genomics Xenium Breast Gene Panel is now available as a reviewed preprint at #eLife
elifesciences.org/reviewed-pre...
We look forward to revising the paper to incorporate reviewer recommendations and other updates 🧵👇
elifesciences.org/reviewed-pre...
We look forward to revising the paper to incorporate reviewer recommendations and other updates 🧵👇
August 29, 2025 at 4:36 PM
Our paper identifying evidence of off-target probe binding in the 10x Genomics Xenium Breast Gene Panel is now available as a reviewed preprint at #eLife
elifesciences.org/reviewed-pre...
We look forward to revising the paper to incorporate reviewer recommendations and other updates 🧵👇
elifesciences.org/reviewed-pre...
We look forward to revising the paper to incorporate reviewer recommendations and other updates 🧵👇
Final call for posters @keystonesymposia.bsky.social on AI in molecular biology. Deadline August 21
Beyond talks, our program also includes panel discussions on challenges + opportunities for innovation + responsibility in AI-driven biology: keysym.us/KSAIBio26
Hope u can join the conversation!
Beyond talks, our program also includes panel discussions on challenges + opportunities for innovation + responsibility in AI-driven biology: keysym.us/KSAIBio26
Hope u can join the conversation!
August 19, 2025 at 12:19 AM
Final call for posters @keystonesymposia.bsky.social on AI in molecular biology. Deadline August 21
Beyond talks, our program also includes panel discussions on challenges + opportunities for innovation + responsibility in AI-driven biology: keysym.us/KSAIBio26
Hope u can join the conversation!
Beyond talks, our program also includes panel discussions on challenges + opportunities for innovation + responsibility in AI-driven biology: keysym.us/KSAIBio26
Hope u can join the conversation!
People are being arrested by ICE. What countries are they from?
I analyze public data from deportationdata.org/data/ice.html to find increased arrests for immigrants from many countries #FirstTheyCame
Code so you can reproduce these trends for yourself: gist.github.com/JEFworks/1f0...
I analyze public data from deportationdata.org/data/ice.html to find increased arrests for immigrants from many countries #FirstTheyCame
Code so you can reproduce these trends for yourself: gist.github.com/JEFworks/1f0...
July 24, 2025 at 1:27 PM
People are being arrested by ICE. What countries are they from?
I analyze public data from deportationdata.org/data/ice.html to find increased arrests for immigrants from many countries #FirstTheyCame
Code so you can reproduce these trends for yourself: gist.github.com/JEFworks/1f0...
I analyze public data from deportationdata.org/data/ice.html to find increased arrests for immigrants from many countries #FirstTheyCame
Code so you can reproduce these trends for yourself: gist.github.com/JEFworks/1f0...
I visualize trends in #ICE #immigration arrests and encounters over time and across select US cities using public data from deportationdata.org/data/ice.html
Here is the #RStats #ggplot code so you can visualize the #dataviz trends in your own city: gist.github.com/JEFworks/0c7...
#codetutorial
Here is the #RStats #ggplot code so you can visualize the #dataviz trends in your own city: gist.github.com/JEFworks/0c7...
#codetutorial
July 20, 2025 at 8:27 PM
I visualize trends in #ICE #immigration arrests and encounters over time and across select US cities using public data from deportationdata.org/data/ice.html
Here is the #RStats #ggplot code so you can visualize the #dataviz trends in your own city: gist.github.com/JEFworks/0c7...
#codetutorial
Here is the #RStats #ggplot code so you can visualize the #dataviz trends in your own city: gist.github.com/JEFworks/0c7...
#codetutorial
I received some old microscopy slides from the 1800s, when at-home microscopes made it possible to look at hidden worlds of diatoms, polycystina, and other teeny tiny things.
I made this website so people today can take a look too: microspeci.men
Enjoy! #scienceisforeveryone #microscopy #HistSci
I made this website so people today can take a look too: microspeci.men
Enjoy! #scienceisforeveryone #microscopy #HistSci
July 17, 2025 at 12:02 AM
I received some old microscopy slides from the 1800s, when at-home microscopes made it possible to look at hidden worlds of diatoms, polycystina, and other teeny tiny things.
I made this website so people today can take a look too: microspeci.men
Enjoy! #scienceisforeveryone #microscopy #HistSci
I made this website so people today can take a look too: microspeci.men
Enjoy! #scienceisforeveryone #microscopy #HistSci
I use #ggplot #gganimate #Rstats to visualize spatiotemporal trends in public ICE detention data.
Watch ICE detention increase over time: more detainees (bigger dots), more non-criminals (blue → red), and more jails far from the border in 2025.
Code #gist: gist.github.com/JEFworks/899...
#DataViz
Watch ICE detention increase over time: more detainees (bigger dots), more non-criminals (blue → red), and more jails far from the border in 2025.
Code #gist: gist.github.com/JEFworks/899...
#DataViz
July 12, 2025 at 12:15 AM
I use #ggplot #gganimate #Rstats to visualize spatiotemporal trends in public ICE detention data.
Watch ICE detention increase over time: more detainees (bigger dots), more non-criminals (blue → red), and more jails far from the border in 2025.
Code #gist: gist.github.com/JEFworks/899...
#DataViz
Watch ICE detention increase over time: more detainees (bigger dots), more non-criminals (blue → red), and more jails far from the border in 2025.
Code #gist: gist.github.com/JEFworks/899...
#DataViz
Some ICE facilities have >4x non-criminal vs criminal detainees + are more likely to be owned by private companies, including publicly-traded corporations.
Stock data highlights how positive jumps in stock prices for these publicly-traded corporations have coincided with the November elections.
Stock data highlights how positive jumps in stock prices for these publicly-traded corporations have coincided with the November elections.
July 10, 2025 at 7:41 PM
Some ICE facilities have >4x non-criminal vs criminal detainees + are more likely to be owned by private companies, including publicly-traded corporations.
Stock data highlights how positive jumps in stock prices for these publicly-traded corporations have coincided with the November elections.
Stock data highlights how positive jumps in stock prices for these publicly-traded corporations have coincided with the November elections.
In this blog post, I use #RStats to analyze ICE detention data. #Datavisualization shows record numbers of detainees without any criminal records. Further more/bigger ICE facilities are popping up far from the border.
Code along and take a look for yourself: jef.works/blog/2025/07...
#CodeTutorial
Code along and take a look for yourself: jef.works/blog/2025/07...
#CodeTutorial
July 10, 2025 at 7:20 PM
In this blog post, I use #RStats to analyze ICE detention data. #Datavisualization shows record numbers of detainees without any criminal records. Further more/bigger ICE facilities are popping up far from the border.
Code along and take a look for yourself: jef.works/blog/2025/07...
#CodeTutorial
Code along and take a look for yourself: jef.works/blog/2025/07...
#CodeTutorial
How it started vs. How it's going #Tenured
Grateful to all those who've been a part of this journey so far. But the fun is just getting started 💪
Curious to find out just what this privilege of tenure can enable. Let's see how we can put it to the test. Feel free to share ideas 😉
#AcademicSky
Grateful to all those who've been a part of this journey so far. But the fun is just getting started 💪
Curious to find out just what this privilege of tenure can enable. Let's see how we can put it to the test. Feel free to share ideas 😉
#AcademicSky
July 8, 2025 at 1:14 AM
How it started vs. How it's going #Tenured
Grateful to all those who've been a part of this journey so far. But the fun is just getting started 💪
Curious to find out just what this privilege of tenure can enable. Let's see how we can put it to the test. Feel free to share ideas 😉
#AcademicSky
Grateful to all those who've been a part of this journey so far. But the fun is just getting started 💪
Curious to find out just what this privilege of tenure can enable. Let's see how we can put it to the test. Feel free to share ideas 😉
#AcademicSky
I received this Victorian (~1850s) #microscope slide of a butterfly as a gift and was inspired to make a little video about it #sciart #microscopy
📽️ youtube.com/shorts/vVKCk...
Apparently back then, people had microscopes at home as a form of entertainment! #scienceisforeveryone
📽️ youtube.com/shorts/vVKCk...
Apparently back then, people had microscopes at home as a form of entertainment! #scienceisforeveryone
June 24, 2025 at 2:05 AM
I received this Victorian (~1850s) #microscope slide of a butterfly as a gift and was inspired to make a little video about it #sciart #microscopy
📽️ youtube.com/shorts/vVKCk...
Apparently back then, people had microscopes at home as a form of entertainment! #scienceisforeveryone
📽️ youtube.com/shorts/vVKCk...
Apparently back then, people had microscopes at home as a form of entertainment! #scienceisforeveryone
I got a used Nikon Labophot #microscope to do some fun #scienceathome! Check out this video of bird bath water I was able to take through the microscope with my phone. Still learning to identify protozoan microorganisms though! #scienceisforeveryone
📽️ www.youtube.com/shorts/0X0nt...
📽️ www.youtube.com/shorts/0X0nt...
June 12, 2025 at 3:30 PM
I got a used Nikon Labophot #microscope to do some fun #scienceathome! Check out this video of bird bath water I was able to take through the microscope with my phone. Still learning to identify protozoan microorganisms though! #scienceisforeveryone
📽️ www.youtube.com/shorts/0X0nt...
📽️ www.youtube.com/shorts/0X0nt...
Just got my Presidential Early Career Award #PECASE certificate in the mail! 🎉
Grateful for #NSF grants that power our #BiomedicalResearch. Words remind us that federally funded research creates valuable public goods that help us reach our full potential.
#ScienceMatters #FundResearch #AcademicSky
Grateful for #NSF grants that power our #BiomedicalResearch. Words remind us that federally funded research creates valuable public goods that help us reach our full potential.
#ScienceMatters #FundResearch #AcademicSky
June 3, 2025 at 1:52 PM
Just got my Presidential Early Career Award #PECASE certificate in the mail! 🎉
Grateful for #NSF grants that power our #BiomedicalResearch. Words remind us that federally funded research creates valuable public goods that help us reach our full potential.
#ScienceMatters #FundResearch #AcademicSky
Grateful for #NSF grants that power our #BiomedicalResearch. Words remind us that federally funded research creates valuable public goods that help us reach our full potential.
#ScienceMatters #FundResearch #AcademicSky
We also created an interactive website so doctors and scientists can easily explore our research data and use it to advance care and discovery.
Try it out for yourself: jef.works/vitessce-col...
Work led by post-doc Sami Singh with Hamid Rabb + team 🎉 7/7
Try it out for yourself: jef.works/vitessce-col...
Work led by post-doc Sami Singh with Hamid Rabb + team 🎉 7/7
May 29, 2025 at 1:17 PM
We also created an interactive website so doctors and scientists can easily explore our research data and use it to advance care and discovery.
Try it out for yourself: jef.works/vitessce-col...
Work led by post-doc Sami Singh with Hamid Rabb + team 🎉 7/7
Try it out for yourself: jef.works/vitessce-col...
Work led by post-doc Sami Singh with Hamid Rabb + team 🎉 7/7
Altogether, these systems-level biological insights enabled by our spatiotemporal characterization suggests metabolic reprogramming, particularly within the kidney inner medulla, as a molecular feature of cold ischemia injury. 6/n
May 29, 2025 at 12:55 PM
Altogether, these systems-level biological insights enabled by our spatiotemporal characterization suggests metabolic reprogramming, particularly within the kidney inner medulla, as a molecular feature of cold ischemia injury. 6/n
We compared our cold ischemia model to a warm ischemia model to find commonalities in injury response, including induction of an anti-viral like immune response throughout the renal tissue. 5/n
May 29, 2025 at 12:54 PM
We compared our cold ischemia model to a warm ischemia model to find commonalities in injury response, including induction of an anti-viral like immune response throughout the renal tissue. 5/n
We identified compartment-specific temporally upregulated and downregulated genes with increasing cold ischemia time impacting a variety of pathways, including many involved in metabolic processes such as oxidative phosphorylation, TCA cycle, etc, further validated by qPCR. 4/n
May 29, 2025 at 12:53 PM
We identified compartment-specific temporally upregulated and downregulated genes with increasing cold ischemia time impacting a variety of pathways, including many involved in metabolic processes such as oxidative phosphorylation, TCA cycle, etc, further validated by qPCR. 4/n
We leveraged #spatialtranscriptomics to perform full transcriptome characterization of cold ischemia injury (0-48 hours) using a murine model and identified spatiotemporal transcriptomic changes that accompany the injury pathophysiology in a compartment-specific manner. 3/n
May 29, 2025 at 12:50 PM
We leveraged #spatialtranscriptomics to perform full transcriptome characterization of cold ischemia injury (0-48 hours) using a murine model and identified spatiotemporal transcriptomic changes that accompany the injury pathophysiology in a compartment-specific manner. 3/n
In our latest study, we use #spatialtranscriptomics to characterize cold ischemic injury at multiple time points modeling a kidney transplant setting to reveal compartment-specific changes
Check out the preprint: www.biorxiv.org/content/10.1...
🧵👇 1/n
Check out the preprint: www.biorxiv.org/content/10.1...
🧵👇 1/n
May 29, 2025 at 12:47 PM
In our latest study, we use #spatialtranscriptomics to characterize cold ischemic injury at multiple time points modeling a kidney transplant setting to reveal compartment-specific changes
Check out the preprint: www.biorxiv.org/content/10.1...
🧵👇 1/n
Check out the preprint: www.biorxiv.org/content/10.1...
🧵👇 1/n