Josh Welch

Computational Biologist, Associate Professor at U. Michigan

[Josh Welch @LabWelch]

Excited to share tomorrow about our work linking live imaging, CRISPR screening, and spatial transcriptomics using the 10X Xenium platform:
https://t.co/KGuhHdGtGC
You can register here: https://t.co/qdv0CcWHXd

[Josh Welch @LabWelch]

Excited to see that @10xGenomics named our VISTA-FISH platform one of the top 5 single cell and spatial innovations from 2025!
https://t.co/E1DGfkxOEF

[Josh Welch @LabWelch]

What if we could record single-cell RNA levels and videos in the same cells? Our new VISTA-FISH assay links gene expression with neuron firing, lysosome movement, and neuron morphology. VISTA-FISH also detects sgRNAs, enabling live-cell CRISPR screens 🧵
https://t.co/KGuhHdGtGC

[Doug @DHaggie42]

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.

[Josh Welch @LabWelch]

@ChangyangLinghu @Richard_She @Nature Amazing work! Congratulations!

[Josh Welch @LabWelch]

@jmuiuc Congratulations! Well deserved!

[Josh Welch @LabWelch]

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

[Josh Welch @LabWelch]

Excited to speak in the UK Gen AI Hub seminar series!
https://t.co/R3lOf5fDr0

[Qian Cheng @sgqcheng]

MultiVeloVAE infers differential dynamics from multi-lineage, multi-omic, and multi-sample single-cell data. #BiotechNatureComms
@NatureComms
@LabWelch

https://t.co/CFg85zdBKr

[Josh Welch @LabWelch]

The kids and I made our own hype video for the big football game today!
https://t.co/rF31fE72nD

[Josh Welch @LabWelch]

@_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.

[Josh Welch @LabWelch]

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

[Josh Welch @LabWelch]

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.
https://t.co/NMjK7skZDU

[Josh Welch @LabWelch]

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.

[Josh Welch @LabWelch]

Our paper is now out in @NatureComms!

[Josh Welch @LabWelch]

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. 🧵
https://t.co/OPCSMn3y4q

[Josh Welch @LabWelch]

This work was led by the fearless Chen Li. Check out our package on github, including notebooks to reproduce the analyses from the paper: https://t.co/2eZxhZ1miF
This paper is also a big milestone for Welch lab--our first in-house 10X multiome dataset (great work, @therealjklee)!

[Josh Welch @LabWelch]

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. 🧵
https://t.co/OPCSMn3y4q

[Josh Welch @LabWelch]

@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).