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

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 👇)

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

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

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 👋

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

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 🧵👇

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!

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

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 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

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 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

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

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

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

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...

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

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

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

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

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

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

👏 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

We identify evidence of off-target probe binding in the 10x Genomics #Xenium v1 Human Breast Gene Expression Panel, compromising the accuracy of resulting #singlecell #spatialtranscriptomics profiles See our preprint for more details: www.biorxiv.org/content/10.1... #AcademicSky 🧵👇 1/n

Our #bionformatics #dataviz #Rstats package scatterbar for visualizing cell-type proportions in spot-resolution #spatialtranscriptomics data is now published! Try it out! Paper: academic.oup.com/bioinformati... Code: cran.r-project.org/web/packages... Tutorials: jef.works/scatterbar/ #AcademicSky

Honored to receive the Presidential Early Career Award for Scientists and Engineers (PECASE): www.whitehouse.gov/ostp/news-up... #NSFfunded #AcademicSky #womeninSTEM For aspiring young scientists and engineers #PhDLife looking for guidance/advice, I wanted to offer a 🧵 on what I did:

Yeah I'm on sab[ #brat ]ical Made a Guess/Technologic #parody for #PhDlife 📽️ Academique: youtube.com/shorts/hvJ4X... "Write it, read it, fix it, save it, Send it to reviewers, quick, rewrite it. Trash it, change it, pay it, print it. Send it to your friends, yeah I think they'll cite it."

Made a #short about my internal conflicts on academic publishing #AcademicSky #PhDlife "Stop asking me where I want to publish our paper. I don't care...I just want people to read it. And maybe learn from it. Even build on it. Ok?" Is this #hopecore or #hopelesscore youtube.com/shorts/GV7NJ...

Our #bionformatics #Rstats method CRAWDAD for quantifying cell-type spatial relationships across length scales in #singlecell #spatialomics data is now published! Paper: www.nature.com/articles/s41... Code: github.com/JEFworks-Lab... 🥳🥂 #AcademicSky Previous 🧵 summary: bsky.app/profile/jef....

Every year, I give my lab (and myself) a "mini-sabbatical" to pursue creative endeavors outside of regular work/studies. So I spent some time reflecting on my thoughts on #AI + the role of professors in this AI transformation via a short film 📽️: www.youtube.com/watch?v=6MPs... #AcademicSky

In this student-requested video, I demo the process of making a high quality publication-ready figure (from making a mockup to enhancing visual similarity in Illustrator) and narrate my general process. Follow along and try it out for yourself: www.youtube.com/watch?v=L9qo... #phdlife #AcademicSky

Every year, I spend some time trying to figure out how to access #healthcareinamerica using the shoppable medical services info that hospitals have to make available now due to the CMS Transparency in Coverage Final Rule. This year, I made a video of my experience: www.youtube.com/watch?v=6mC9...

Updated our lab website: jef.works Still using #jekyll hosted on #Github But now with: - a #lightbox image gallery (jekyllcodex.org/without-plug...) - client side full-text blog search via #lunrjs (learn.cloudcannon.com/jekyll/jekyl...) - (most importantly) new banner pics! 🥳 #JustAcademicThings

Check out our updated scatterbar package for visualizing proportional data across spatial coordinates like deconvolved cell types in #spatialtranscriptomics using stacked bar plots (alternative to scatterpies)! Preprint: www.biorxiv.org/content/10.1... Code: github.com/JEFworks-Lab... #dataviz

We developed STalign for alignment of #spatialtranscriptomics data but we can apply the same mathematical framework to align images as well. In this blog post, I align fluorescence and histological images from the same tissue section at #singlecell resolution. Try it out: jef.works/blog/2024/04...

Just finished teaching another semester of my class on Genomic Data Visualization 🥳 Discover the awesome #dataviz made by students in the class for various #singlecell #spatialtranscriptomics data Check out the course notes + #Rstats code to explore for yourself: jef.works/genomic-data...

In this #codetutorial, I quickly identify spatially variable genes in a #spatialtranscriptomic dataset w/ 377,985 cells by combining our recently developed preprocessing tool SEraster with our existing tool MERINGUE. Try it out for yourself: jef.works/blog/2024/03... #AcademicSky #Rstats

Has the scientific literature been flooded with papers containing AI-generated text? I use rvest to scrape Google Scholar to quantify the number of publications containing obviously LLM-generated phrases over time (and compare to other phrases). Try it out for yourself! jef.works/blog/2024/03...

I record myself coding a spatial-omics data analysis to structurally align a single-cell spatial transcriptomics Xenium dataset to a spot-resolution Visium dataset for serial breast cancer sections using our lab's recently published tool STalign Code along: www.youtube.com/watch?v=qZLh...

Every year, I give my lab (and myself) a "mini-sabbatical" to travel, decompress, and/or pursue creative endeavors outside of their regular work/studies. I spent some time learning filming/editing videos/audio and made a short film about my thoughts on teaching. www.youtube.com/watch?v=Jco1...

In this blog post, I use our #Bioinformatics #Python tool STalign to align two 10X Visium #SpatialTranscriptomics datasets. I prefer working in #Rstats so I show how I use reticulate to interface with Python from within RStudio. Code along: jef.works/blog/2023/11... #AcademicChatter #codetutorials

Check out our new #bioinformatics tool to characterize cell-type spatial relationships across length scales in #singlecell #spatialomics data Preprint: www.biorxiv.org/content/10.1... Software: github.com/JEFworks-Lab... Led by Rafael dos Santos Peixoto + Brendan Miller w/ Maigan Brusko + team 🧵