Computational Biologist, Associate Professor at U. Michigan
Joined July 2019
- Tweets 616
- Following 547
- Followers 1,565
- Likes 2,229
96 Photos and videos
Jun 13
We are very excited that our CytoSignal paper is featured on the cover of the June 2026 issue of Nature Genetics! The image is a stylized version of data from our figures, showing groups of cells that signal to each other by ligand/receptor interactions.
nature.com/ng/volumes/58/iss…
Jun 12
Our CytoSignal paper is now published in @NatureGenet! During revision, we generated a one-of-a-kind dataset with direct measurements of ligand-receptor protein interactions in situ in the mouse embryo, along with Visium HD spatial transcriptomics. nature.com/articles/s41588-0…
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Jun 12
Our CytoSignal paper is now published in @NatureGenet! During revision, we generated a one-of-a-kind dataset with direct measurements of ligand-receptor protein interactions in situ in the mouse embryo, along with Visium HD spatial transcriptomics. nature.com/articles/s41588-0…
15 Mar 2024
How can you use RNA velocity to infer the dynamics of cell signaling from spatial transcriptomic data? Check out our new preprint!
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Jun 12
We hope this tool and our benchmarking data will be a useful community resource. We have provided processed data and notebooks to reproduce our analyses: github.com/welch-lab/cytosig…
@JialinLiuSKP and several others did a fantastic job of building a useful tool
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Jun 12
And finally, we are very grateful to @ChanZuckerberg initiative for funding this work, which would not have been possible without their support.
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Jun 8
Excited to attend and speak at AI x Bio! It's my first time to visit the Wellcome Genome Campus--beautiful campus. coursesandconferences.wellco…
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May 5
Excited to share tomorrow about our work linking live imaging, CRISPR screening, and spatial transcriptomics using the 10X Xenium platform:
biorxiv.org/content/10.1101/…
You can register here: 10xgen.com/1YC
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Mar 14
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…
6 Nov 2025
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 🧵
biorxiv.org/content/10.1101/…
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Josh Welch retweeted
Feb 22
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.
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15 Dec 2025
The Welch lab just got our very own 10X Genomics Chromium X instrument! So excited to start generating our own data.
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9 Dec 2025
Excited to speak in the UK Gen AI Hub seminar series!
genai.ac.uk/events/gen-biolo…
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Josh Welch retweeted
1 Dec 2025
MultiVeloVAE infers differential dynamics from multi-lineage, multi-omic, and multi-sample single-cell data. #BiotechNatureComms
@NatureComms
@LabWelch
nature.com/articles/s41467-0…
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29 Nov 2025
The kids and I made our own hype video for the big football game today!
sora.chatgpt.com/p/s_692b14d…
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26 Nov 2025
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…
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26 Nov 2025
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.
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26 Nov 2025
The intrepid @cwen777 did a great job putting this review together, particularly making nice diagrams to illustrate some complex molecular mechanisms.
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