Dr. Jean Fan
@jef.works
Associate prof @JHUBME. Doing #spatialtranscriptomics #compbio #dataviz #rstats. Founder @cuSTEMized. Editor @PLOSCompBio. Alum @HarvardDBMI @mbhsmagnet.
In this journal club commentary, I reflect on an older paper from the Campbell group @sangerinstitute.bsky.social showing how normal skin is full cancer mutations yet stays healthy to highlight the opportunity to revisit this question using new spatial omics tech: www.nature.com/articles/s41...
Revisiting the somatic mutation theory of cancer pathogenesis - Nature Reviews Genetics
Jean Fan recounts a 2015 paper by Martincorena et al. that revealed oncogenic mutations in normal tissues, also highlighting how the latest spatial technologies can now be used to study the spatial co...
www.nature.com
October 22, 2025 at 8:41 PM
In this journal club commentary, I reflect on an older paper from the Campbell group @sangerinstitute.bsky.social showing how normal skin is full cancer mutations yet stays healthy to highlight the opportunity to revisit this question using new spatial omics tech: www.nature.com/articles/s41...
What is RNA velocity in situ? ChatGPT kept getting it wrong...
So I made this video explaining how RNA velocity in situ infers gene expression dynamics by distinguishing nuclear vs. cytoplasmic expression in spatial transcriptomics data: youtu.be/z9Oxf1hvum0
#AcademicSky
So I made this video explaining how RNA velocity in situ infers gene expression dynamics by distinguishing nuclear vs. cytoplasmic expression in spatial transcriptomics data: youtu.be/z9Oxf1hvum0
#AcademicSky
RNA velocity in situ infers gene expression dynamics using spatial transcriptomics data
YouTube video by Prof. Jean Fan
youtu.be
October 13, 2025 at 7:09 PM
What is RNA velocity in situ? ChatGPT kept getting it wrong...
So I made this video explaining how RNA velocity in situ infers gene expression dynamics by distinguishing nuclear vs. cytoplasmic expression in spatial transcriptomics data: youtu.be/z9Oxf1hvum0
#AcademicSky
So I made this video explaining how RNA velocity in situ infers gene expression dynamics by distinguishing nuclear vs. cytoplasmic expression in spatial transcriptomics data: youtu.be/z9Oxf1hvum0
#AcademicSky
Looking to prep for faculty job interviews? Try my Academic Interview Simulator: Faculty Edition. About as realistic as dating sims are to real dating 🤣: www.youtube.com/watch?v=dzv-...
(I'm tinkering w/ AI. Inspired by the Rising Stars workshop for post-docs I just served on. Real advice 👇)
(I'm tinkering w/ AI. Inspired by the Rising Stars workshop for post-docs I just served on. Real advice 👇)
Academic Interview Simulation: Faculty Edition (mockup gameplay) #datingsim #parody #aivideo
YouTube video by Prof. Jean Fan
www.youtube.com
October 6, 2025 at 1:47 PM
Looking to prep for faculty job interviews? Try my Academic Interview Simulator: Faculty Edition. About as realistic as dating sims are to real dating 🤣: www.youtube.com/watch?v=dzv-...
(I'm tinkering w/ AI. Inspired by the Rising Stars workshop for post-docs I just served on. Real advice 👇)
(I'm tinkering w/ AI. Inspired by the Rising Stars workshop for post-docs I just served on. Real advice 👇)
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
Reposted by Dr. Jean Fan
Wrapping up AI in Molecular Biology, we celebrate 3 Future of Science Fund Award winners: @ryantheshark.bsky.social (@ucberkeleyofficial.bsky.social), Lucy Luo (@nufeinbergmed.bsky.social) & Reet Mishra. Their work shows the bright future of science! 🌟
#KSAIBio26 @drkbio.bsky.social @jef.works
#KSAIBio26 @drkbio.bsky.social @jef.works
September 18, 2025 at 5:42 PM
Wrapping up AI in Molecular Biology, we celebrate 3 Future of Science Fund Award winners: @ryantheshark.bsky.social (@ucberkeleyofficial.bsky.social), Lucy Luo (@nufeinbergmed.bsky.social) & Reet Mishra. Their work shows the bright future of science! 🌟
#KSAIBio26 @drkbio.bsky.social @jef.works
#KSAIBio26 @drkbio.bsky.social @jef.works
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 👋
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!
In this interview, I explain how university research, when funded by independent #NIH #NSF federal grants, brings oversight to biotech to fuel innovation while keeping science transparent, reliable, and in service of the public good: hub.jhu.edu/2025/07/30/j...
#ResearchMatters
#ResearchMatters
University labs help power America's biotech innovation ecosystem
Hopkins researcher Jean Fan and her team create open-source tools that help bridge the gap between academic discoveries and life-saving treatments. Cuts to federal funding threaten to break this criti...
hub.jhu.edu
July 31, 2025 at 2:07 PM
In this interview, I explain how university research, when funded by independent #NIH #NSF federal grants, brings oversight to biotech to fuel innovation while keeping science transparent, reliable, and in service of the public good: hub.jhu.edu/2025/07/30/j...
#ResearchMatters
#ResearchMatters
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
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
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
To supplement my students' learning, I made this brief explanation + demo on how to analyze #spatialtranscriptomics data to identify spatially variable genes using Moran's I #dataanalysis #Rstats
Code along: www.youtube.com/watch?v=aaAN...
#AcademicSky #codetutorials #Bioinformatics
Code along: www.youtube.com/watch?v=aaAN...
#AcademicSky #codetutorials #Bioinformatics
May 12, 2025 at 4:15 PM
To supplement my students' learning, I made this brief explanation + demo on how to analyze #spatialtranscriptomics data to identify spatially variable genes using Moran's I #dataanalysis #Rstats
Code along: www.youtube.com/watch?v=aaAN...
#AcademicSky #codetutorials #Bioinformatics
Code along: www.youtube.com/watch?v=aaAN...
#AcademicSky #codetutorials #Bioinformatics
Another semester done 🥳🥂
In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i...
#AcademicSky
In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i...
#AcademicSky
Jean Fan | Personal site
Personal website of Prof. Jean Fan
jean.fan
May 5, 2025 at 8:00 PM
Another semester done 🥳🥂
In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i...
#AcademicSky
In this blog post, I reflect on how I chose to accommodate a student who wanted to miss class to attend a political rally, and how I promote the ideologies of freedom of speech and democracy through my teaching of computer science: jean.fan/2025/05/05/i...
#AcademicSky
Are you interested in learning about the intersection of #AI and molecular #biology? Come to our @keystonesymposia.bsky.social this September in beautiful Santa Fe! keysym.us/KSAIBio26 #KSAIBio26
Scholarship + short talk deadline May 20 so apply soon! Look forward to seeing you there!
#AcademicSky
Scholarship + short talk deadline May 20 so apply soon! Look forward to seeing you there!
#AcademicSky
April 28, 2025 at 12:29 AM
Are you interested in learning about the intersection of #AI and molecular #biology? Come to our @keystonesymposia.bsky.social this September in beautiful Santa Fe! keysym.us/KSAIBio26 #KSAIBio26
Scholarship + short talk deadline May 20 so apply soon! Look forward to seeing you there!
#AcademicSky
Scholarship + short talk deadline May 20 so apply soon! Look forward to seeing you there!
#AcademicSky
In this #codetutorial blog post, I demonstrate a multi-sample integrative #dataanalysis of VisiumHD #spatialtranscriptomics data using geometric sketching with Harmony in Seurat to identify transcriptionally similar tissue structures.
Try it out for yourself: jef.works/blog/2025/04...
#AcademicSky
Try it out for yourself: jef.works/blog/2025/04...
#AcademicSky
April 23, 2025 at 2:33 PM
In this #codetutorial blog post, I demonstrate a multi-sample integrative #dataanalysis of VisiumHD #spatialtranscriptomics data using geometric sketching with Harmony in Seurat to identify transcriptionally similar tissue structures.
Try it out for yourself: jef.works/blog/2025/04...
#AcademicSky
Try it out for yourself: jef.works/blog/2025/04...
#AcademicSky
Reposted by Dr. Jean Fan
👏 A huge thank-you to Jean Fan (@jef.works) from @jhu.edu @hopkinsengineer.bsky.social for an outstanding IICD Seminar on evidence of off-target probe binding.
Watch the recording here: youtu.be/OhYAFJ3o1mM?...
#CancerResearch #SpatialOmics #MathematicalOncology
Watch the recording here: youtu.be/OhYAFJ3o1mM?...
#CancerResearch #SpatialOmics #MathematicalOncology
April 10, 2025 at 4:11 PM
👏 A huge thank-you to Jean Fan (@jef.works) from @jhu.edu @hopkinsengineer.bsky.social for an outstanding IICD Seminar on evidence of off-target probe binding.
Watch the recording here: youtu.be/OhYAFJ3o1mM?...
#CancerResearch #SpatialOmics #MathematicalOncology
Watch the recording here: youtu.be/OhYAFJ3o1mM?...
#CancerResearch #SpatialOmics #MathematicalOncology