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 . See our preprint for more details: #AcademicTwitter. 🧵👇 1/n.

How it started vs. How it's going #Tenured. Grateful to all those who've been a part of this journey so far. The fun is just getting started 💪. Curious to find out what this privilege of tenure can enable. Let's put it to the test. Feel free to share ideas 😉. #AcademicTwitter

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. 📽️ 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 . 📽️

Just got my Presidential Early Career Award #PECASE certificate in the mail! 🎉. Grateful for #NSF grants that power our #BiomedicalResearch. Reminder that federally funded research creates valuable public goods that help us reach our full potential. #ScienceMatters #FundResearch

Thanks to our amazing team led by post-doc @Sami2wits with @dee_velazquez_ @JHUBME + Hamid Rabb et al @HopkinsMedicine for their hard work and dedication. These efforts help us all improve care for kidney transplant patients. 7/7 #TeamScience #TransplantResearch #AcademicTwitter.

We also created an interactive website so doctors and scientists can easily explore our #spatialtranscriptomics research data and use it to advance patient care and discoveries. 6/n . Try it out for yourself: #datavisualization #javascript #react

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

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

Kidney transplants save lives, but deceased donor kidneys need to be kept on ice before surgery, which can cause cold ischemia injury + lead to poorer outcomes. Our #NIH #NSF federally funded research is helping uncover why this happens + how to improve transplant success. 2/n.

In our latest study, we look at how storing kidneys on ice before transplant can cause damage over time. We use #spatialtranscriptomics to characterize cold ischemia injury at multiple time points to reveal compartment-specific changes. Preprint: 🧵👇 1/n

Interested in learning more about #AI in molecular #biology? Students can apply for a scholarship and short talk at our @KeystoneSymp this September: #KSAIBio26 Deadline June 3, 2025. Check out our speakers lineup with academic and industry leaders! 🥳🥂

To supplement my students' learning, in this #bioinformatics #dataanalysis #codetutorial, I walk through how to analyze #spatialtranscriptomics data to identify spatially variable genes using the Moran’s I statistic #Rstats. Code along: #AcademicTwitter

Another semester done 🥳 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: . #AcademicTwitter.

Are you interested in the intersection of #AI and molecular #biology? Come to our @KeystoneSymp this September in beautiful Santa Fe! #KSAIBio26. Scholarship and short talk deadline May 20 so apply soon! Look forward to seeing you there!. #AcademicTwitter

@caleb_hallinan @StevenSalzberg1 If you're interested in following our research, #codetutorials, and other #singlecell #spatialtranscriptomics #bioinformatics #computationalbiology #machinelearning #ai #dataviz resources, please come find me where the sky is blue

By shedding light on off-target probe binding + providing a tool to enable prediction, we hope this work will enhance the quality of #spatialtranscriptomics data + improve reproducibility in #spatialtranscriptomics research (fin). 🙌Team @caleb_hallinan Hayden Ji @StevenSalzberg1.

We are not the first to identify + provide evidence of demonstrable issues w/ probe design in a commercial platform. This underscore the complementarity between industry + #academia in fostering a reliable scientific process to the benefit of consumers and the public (12/n).

Given this putative off-target binding, we provide many #dataanalysis recommendations to handle existing data as well as experimental design recommendation for future data generation. So please check out our preprint for more details: . (11/n).