Brendan F. Miller

I am pleased to announce that STdeconvolve, the newest tool out of the @JEFworks Lab, is finally out in @NatureComms! nature.com/articles/s4146… Huge thanks to my co-authors @JEFworks, Feiyang Huang, @lylaatta, and @arpansahoo16! 🧵👇

Learning how to share my scientific talks from home (v4)! Check out this abbreviated version of my talk on reference-free cell type deconvolution of #spatialtranscriptomics data w/ STdeconvolve 📽️ youtu.be/aYyD7OHNDLo #bioinformatics #dataanalysis #RStats #AcademicTwitter

Let's solve this y'all. 🦾 Biotech/pharma companies are in a crisis as they hemorrhage their best talent to cushy academic positions at universities located in cheaper and more vibrant cities. To right the ship, industry leaders should:

Big new release (v2.1.5) for Cenote-Taker 2, my tool for virus discovery and in-depth gene annotation. MUCH easier/more reliable installation. Turn your meaningless ATCGs into well-ordered virus genome maps. ✅bacteriophage ✅eukaryotic viruses ✅RNA ✅DNA github.com/mtisza1/Cenote…

Michael Lichten (@lichtenmj) of @NIH has been elected to the National Academy of Sciences for outstanding contributions to the field of meiotic recombination. #NAS159 Read more: ow.ly/zjLB50IYEtj #cancerresearch #molecularbiology

In this blog post, I compare deconvolution analysis using STdeconvolve to clustering analysis on multi-cellular pixel-resolution #spatialtranscriptomics data: jef.works/blog/2022/05/0… What do you think? Try it out for yourself! #RStats #Bioinformatics #dataanalysis #dataviz

STdeconvolve is currently available as an #R package on github.com/JEFworks-Lab/S… or #bioconductor (bioconductor.org/packages/devel…) with tutorials at jef.works/STdeconvolve/. We would love for you to try it out and report any feedback on the Issues page!

One cool example is the mouse olfactory bulb, in which STdeconvolve detected a cell-type that appears to correspond to the rostral migratory stream but was not detected with standard transcriptional clustering of the ST dataset pixels.

I am pleased to announce that STdeconvolve, the newest tool out of the @JEFworks Lab, is finally out in @NatureComms! nature.com/articles/s4146… Huge thanks to my co-authors @JEFworks, Feiyang Huang, @lylaatta, and @arpansahoo16! 🧵👇

As I prepare to participate in a faculty search committee, I reflect on what it takes to retain talent in academia: jean.fan/2022/02/07/ret… In short: Stop telling young scientists "Don't give up" + Start telling yourself to work harder to retain them. #AcademicChatter #phdlife

Amazing to see how this project has developed over the past year. A huge thanks to @JEFworks Feiyang Huang @lylaatta @arpansahoo16 and the rest of the lab for their help! Please check it out and let me know how it can be improved at github.com/JEFworks-Lab/S…

Check out this amazing recorded talk by my mentor Dr. Jean Fan @JEFworks! Wish all scientific talks were like this!

I'm learning how to give + record my scientific talks from home (take 3)! This video is based on a series of invited scientific talks I gave on characterizing subcellular RNA compartmentalization w/ #spatialtranscriptomics #bioinformatics #dataanalysis youtube.com/watch?v=4oSEo1…

Excited to share VeloViz, my first PhD work in the JEFworks lab! We asked if using information on cells’ future transcriptional states predicted via RNA velocity could help create more informative low dimensional embeddings of single cell data. doi.org/10.1093/bioinf… (1/5)