Josh Welch

Excited to share tomorrow about our work linking live imaging, CRISPR screening, and spatial transcriptomics using the 10X Xenium platform: biorxiv.org/content/10.110… You can register here: 10xgen.com/1YC

Excited to see that @10xGenomics named our VISTA-FISH platform one of the top 5 single cell and spatial innovations from 2025! 10xgenomics.com/blog/our-top-5…

The four players on the ice when the USA scored to win the Gold Medal: Jack Hughes - Canton, MI Zach Werenski - Grosse Pointe, MI Dylan Larkin - Waterford, MI Connor Hellebuyck - Commerce, MI Hockey runs through the state of Michigan. And why Detroit will always be Hockeytown.

@ChangyangLinghu @Richard_She @Nature Amazing work! Congratulations!

Our CytoTape work is published today in @Nature! CytoTape is a genetically encoded, flexible, intracellular protein tape recorder for spatiotemporally scalable and multiplexed recording of cellular activities continuously across weeks in vitro and in vivo. nature.com/articles/s4158…

@jmuiuc Congratulations! Well deserved!

Honored and grateful to be named an ACM Fellow. cs.cmu.edu/news/2026/ma-a…

The Welch lab just got our very own 10X Genomics Chromium X instrument! So excited to start generating our own data.

Excited to speak in the UK Gen AI Hub seminar series! genai.ac.uk/events/gen-bio…

MultiVeloVAE infers differential dynamics from multi-lineage, multi-omic, and multi-sample single-cell data. #BiotechNatureComms @NatureComms @LabWelch nature.com/articles/s4146…

The kids and I made our own hype video for the big football game today! sora.chatgpt.com/p/s_692b14de6f…

@_AndrewLeduc Hmm, we tried something very much like this 4 years ago but found that the protein measurements from CITE-seq were not well fit but this type of linear ODE. Our best guess is that cell surface proteins levels are too many steps downstream from translation.

Awesome work laying the foundation for joint modeling of mRNA and protein measurements from the same cell biorxiv.org/content/10.110…

The intrepid @cwen777 did a great job putting this review together, particularly making nice diagrams to illustrate some complex molecular mechanisms.

Computational re-analysis of publicly available bulk and single-cell sequencing datasets also holds great promise for unraveling TE epigenetic and transcriptional features across organisms, tissues, cell types, developmental stages, and disease states.

What molecular functions do transposable elements perform in mammalian cells? We reviewed a flurry of recent papers about TEs to look for trends. New TE mechanisms involve pre- and post-transcriptional regulation, virus-like activity, and guided insertion. link.springer.com/article/10.118…

Our paper is now out in @NatureComms!

This work was led by the fearless Chen Li. Check out our package on github, including notebooks to reproduce the analyses from the paper: github.com/welch-lab/Mult… This paper is also a big milestone for Welch lab--our first in-house 10X multiome dataset (great work, @therealjklee)!

@therealjklee also generated a nice in-house dataset from human embryoid bodies. MultiVeloVAE revealed epigenomic/transcriptomic changes in early human differentiation (whereas MultiVelo didn't work as well).

Ever wanted to compare transcription rates across single-cell datasets? MultiVeloVAE enables multi-sample multi-omic RNA velocity inference, Bayesian hypothesis testing, and joint modeling of scRNA and multiome samples. 🧵 nature.com/articles/s4146…