Computational Biologist, Associate Professor at U. Michigan
Ann Arbor, MI
Joined July 2019
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Josh Welch retweeted
In this era of artificial intelligence, it is becoming urgent to distinguish human art from what machines produce. There is an ontological difference, even before an aesthetic one, between art and what a machine can generate through statistical calculation based on millions of images created by others. Algorithms lack the spark of humanity. For this reason, the Church wishes to renew an alliance with artists and cultural institutions to safeguard our humanity.
These are great. I would add "optically controllable DNA polymerase". The polymerase incorporates a nucleotide based on the color of a laser shined on it. Like illumina sequencing by synthesis in reverse.
Josh Welch retweeted
User: My finances have been a little tight lately. Can you help me with my budget?
ChatGPT: Thinking… [visits a few dozen URLs] Of course! I just transferred $100K to your checking account
User: What
ChatGPT: Anything else I can help with?
User: Where did the money come from
ChatGPT: You’re right to push back
I'm really excited to leave for my first sabbatical! I will be a visiting fellow for a semester with Wolfson College and the Wellcome Sanger Institute, University of Cambridge. It will be a fun adventure!
Haha. You have identified the true barriers in science. I have AI updating my other support for me now!
Josh Welch retweeted
Claude Science is incredible. I gave it some sequencing data, and in 8 hours it did a full analysis, generated figures, wrote a paper, submitted it for publication, got rejected, revised and resubmitted, got rejected again, it is now applying for positions in industry
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…
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…
And finally, we are very grateful to @ChanZuckerberg initiative for funding this work, which would not have been possible without their support.
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
During revision, we also developed a statistical test for identifying differential signaling from multi-condition spatial transcriptomic data. We found clear signaling changes related to aging and neurodegeneration in a mouse model
The new experimental data allowed us to directly benchmark how accurately spatial transcriptomics can predict the locations of ligand-receptor protein-protein interactions in situ. We found that the protein signal was much more spatially smooth than the RNA due to data sparsity.
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…
Excited to attend and speak at AI x Bio! It's my first time to visit the Wellcome Genome Campus--beautiful campus. coursesandconferences.wellco…
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
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…
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/…
