Troy McDiarmid
@troymcdiarmid.bsky.social
Banting Postdoc with @JShendure @uwgenome | Prev
@CIHR_IRSC UBC Neuro PhD | Genome engineering, molecular recording, neurodevelopment and its disorders | Mountains & skateboarding
@CIHR_IRSC UBC Neuro PhD | Genome engineering, molecular recording, neurodevelopment and its disorders | Mountains & skateboarding
Pinned
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - @jshendure.bsky.social @troymcdiarmid.bsky.social @uwgenome.bsky.social go.nature.com/49eTPCu
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - Nature Biotechnology
Prime editing in mammalian cells benefits from a comprehensive list of genetic parts.
go.nature.com
November 12, 2025 at 6:06 PM
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com
Reposted by Troy McDiarmid
🚀 Very excited to share the first major work from my PhD!!
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
November 6, 2025 at 11:57 PM
🚀 Very excited to share the first major work from my PhD!!
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
We combined MPRA and CRISPRa in excitatory neurons to test and validate cis-regulation therapies for hundreds of haploinsufficient neurodevelopmental disorder genes. 🧬🔬
www.biorxiv.org/content/10.1...
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
November 5, 2025 at 3:09 PM
Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
shorturl.at/H3Qww
This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.
Bluetorial below.
Reposted by Troy McDiarmid
Thrilled to share I’ve started my lab at Dartmouth’s Geisel School of Medicine! We focus on mapping cellular trajectories & TF networks in development and Mendelian disorders, exploring new therapies. Join us—postdocs, grads, and scientists welcome! sites.dartmouth.edu/qiulab/
November 4, 2025 at 3:10 PM
Thrilled to share I’ve started my lab at Dartmouth’s Geisel School of Medicine! We focus on mapping cellular trajectories & TF networks in development and Mendelian disorders, exploring new therapies. Join us—postdocs, grads, and scientists welcome! sites.dartmouth.edu/qiulab/
Reposted by Troy McDiarmid
Sometimes I think about how from 1935-1975ish, Bell Labs produced an insane amount of revolutionary science and technology, including 11 Nobel Prizes, the transistor, UNIX, C, the laser, the solar cell, information theory, etc. The secret? Provide scientists with ample, steady, no-strings funding.
sites.stat.columbia.edu
October 4, 2025 at 5:35 PM
Sometimes I think about how from 1935-1975ish, Bell Labs produced an insane amount of revolutionary science and technology, including 11 Nobel Prizes, the transistor, UNIX, C, the laser, the solar cell, information theory, etc. The secret? Provide scientists with ample, steady, no-strings funding.
Reposted by Troy McDiarmid
Check out MitoScribe in our new preprint led by Linhan Wang: www.biorxiv.org/content/10.1...
It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!
It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!
September 8, 2025 at 5:13 PM
Check out MitoScribe in our new preprint led by Linhan Wang: www.biorxiv.org/content/10.1...
It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!
It's an analog molecular recorder that uses neutral base edits to the mitochondrial genome to store information about historical signaling in a cell. Single cell resolution at scale (see next post)!
Reposted by Troy McDiarmid
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.
Read more: e11.bio/blog/prism
Read more: e11.bio/blog/prism
October 1, 2025 at 2:16 PM
E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.
Read more: e11.bio/blog/prism
Read more: e11.bio/blog/prism
Reposted by Troy McDiarmid
After 10 years of work, a complete telomere-to-telomere gap-free genome for C. elegans finally exists: it has 106 Mb rather than the textbook 100.3 Mb, and up to 366 additional genes.
genome.cshlp.org/content/35/8...
genome.cshlp.org/content/35/8...
August 1, 2025 at 9:55 PM
After 10 years of work, a complete telomere-to-telomere gap-free genome for C. elegans finally exists: it has 106 Mb rather than the textbook 100.3 Mb, and up to 366 additional genes.
genome.cshlp.org/content/35/8...
genome.cshlp.org/content/35/8...
Reposted by Troy McDiarmid
September 26, 2025 at 11:06 PM
Reposted by Troy McDiarmid
Well don't I feel stupid
September 26, 2025 at 11:02 PM
Well don't I feel stupid
Reposted by Troy McDiarmid
New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...
September 26, 2025 at 6:06 PM
New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...
Reposted by Troy McDiarmid
✨Exciting news: the main story of my PhD is out in Science!
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
www.science.org
September 19, 2025 at 2:09 PM
✨Exciting news: the main story of my PhD is out in Science!
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Reposted by Troy McDiarmid
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
September 19, 2025 at 3:03 AM
New preprint from our lab!
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?
Find out here: www.biorxiv.org/content/10.1...
👇
1/
Reposted by Troy McDiarmid
Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks - Nature Genetics
Massively parallel reporter assay in primary human CD4+ T cells and bulk and single-cell CRISPR-interference screens identify candidate causal variants linked to autoimmune disease risk that modulate ...
www.nature.com
September 18, 2025 at 8:50 PM
Excited to finally present the lab's latest work in defining candidate causal genetic variants that drive autoimmune diseases and their effects on primary human T cell expression and function! www.nature.com/articles/s41...
Reposted by Troy McDiarmid
SCN2A loss is strongly linked to neurodevelopmental delays and, at times, seizure. In an amazing collaboration with @nadavahituv.bsky.social, led by Serena Tamura, Andrew Nelson, and Perry Spratt, we leveraged CRISPR activator approaches to rescue this loss.
rdcu.be/eGU0W
rdcu.be/eGU0W
CRISPR activation for SCN2A-related neurodevelopmental disorders
Nature - Using SCN2A haploinsufficiency as a proof-of-concept, upregulation of the existing functional gene copy through CRISPR activation was able to rescue neurological-associated phenotypes in...
rdcu.be
September 17, 2025 at 6:27 PM
SCN2A loss is strongly linked to neurodevelopmental delays and, at times, seizure. In an amazing collaboration with @nadavahituv.bsky.social, led by Serena Tamura, Andrew Nelson, and Perry Spratt, we leveraged CRISPR activator approaches to rescue this loss.
rdcu.be/eGU0W
rdcu.be/eGU0W
Reposted by Troy McDiarmid
Google and Meta search both report that Cape Breton Island has its own time zone 12 minutes ahead of mainland Nova Scotia time because they are both drawing that information from a Beaverton article I wrote in 2024
June 10, 2025 at 12:50 AM
Google and Meta search both report that Cape Breton Island has its own time zone 12 minutes ahead of mainland Nova Scotia time because they are both drawing that information from a Beaverton article I wrote in 2024
Reposted by Troy McDiarmid
CloneSelect published in Nature Biotechnology
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
A multi-kingdom genetic barcoding system for precise clone isolation - Nature Biotechnology
A barcoded CRISPR base editing system isolates target clones from complex mammalian, yeast and bacterial populations.
www.nature.com
May 21, 2025 at 1:56 PM
CloneSelect published in Nature Biotechnology
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
@natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...
Reposted by Troy McDiarmid
⏰Abstract deadline for the Cascadia Advanced Genomic Technologies Meeting is April 30!⚠️ We're hoping this will be the first of many, catalyzing collaboration and leveraging our regional strength in advanced genomics technologies! See you there!
de-boer-lab.github.io/CAGT_meeting/
de-boer-lab.github.io/CAGT_meeting/
April 28, 2025 at 6:05 PM
⏰Abstract deadline for the Cascadia Advanced Genomic Technologies Meeting is April 30!⚠️ We're hoping this will be the first of many, catalyzing collaboration and leveraging our regional strength in advanced genomics technologies! See you there!
de-boer-lab.github.io/CAGT_meeting/
de-boer-lab.github.io/CAGT_meeting/
Reposted by Troy McDiarmid
Published in today's issue! OPEN ACCESS article, FREE massive dataset, FREE code, FREE pre-trained AI/ML model. #OpenScience was a mountain of work to make this happen: check it out if you haven't already 😉
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
www.nature.com
March 13, 2025 at 7:32 PM
Published in today's issue! OPEN ACCESS article, FREE massive dataset, FREE code, FREE pre-trained AI/ML model. #OpenScience was a mountain of work to make this happen: check it out if you haven't already 😉
Reposted by Troy McDiarmid
I have been trying to find the time to move away from the polical hellscape we find ourselves in to finish and share a bluetorial about science.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
the word irony is written on a white background
ALT: the word irony is written on a white background
media.tenor.com
February 22, 2025 at 10:19 AM
I have been trying to find the time to move away from the polical hellscape we find ourselves in to finish and share a bluetorial about science.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
Reposted by Troy McDiarmid
I think people both within science and outside science don’t fully appreciate the miracle that were the Covid-19 vaccines. How much courage it took to get the sequence out, how much work had already gone into figuring out the best viral antigen and how best to present it. 1/
February 23, 2025 at 7:23 AM
I think people both within science and outside science don’t fully appreciate the miracle that were the Covid-19 vaccines. How much courage it took to get the sequence out, how much work had already gone into figuring out the best viral antigen and how best to present it. 1/
Reposted by Troy McDiarmid
This was a really fun collaboration with @amarderstein.bsky.social where we explored some of the interesting relationships between context-specific non-coding variant effects, disease, and evolution using deep learning models of chromatin accessibility in the brain and heart.
New preprint w/ @soumyakundu.bsky.social @sbmontgom.bsky.social @anshulkundaje.bsky.social !
Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families.
doi.org/10.1101/2025...
Using deep learning & scATAC-seq, we studied context-specific variants in disease & evolution, and introduce FLARE for de novo mutations—w/ application to autism-affected families.
doi.org/10.1101/2025...
Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental contexts in the brain and heart
Whole genome sequencing has identified over a billion non-coding variants in humans, while GWAS has revealed the non-coding genome as a significant contributor to disease. However, prioritizing causal...
www.biorxiv.org
February 19, 2025 at 7:11 PM
This was a really fun collaboration with @amarderstein.bsky.social where we explored some of the interesting relationships between context-specific non-coding variant effects, disease, and evolution using deep learning models of chromatin accessibility in the brain and heart.
Reposted by Troy McDiarmid
Beware! AAV libraries prone to length & homology dependent chimerism! Our latest preprint, from the brilliant @jblalanne.bsky.social, was a true surprise as related phenomena are textbook for lentivirus (highly relevant to HIV & Perturb-seq) yet to our reading not known for AAV tinyurl.com/5amc562a
January 17, 2025 at 6:17 PM
Beware! AAV libraries prone to length & homology dependent chimerism! Our latest preprint, from the brilliant @jblalanne.bsky.social, was a true surprise as related phenomena are textbook for lentivirus (highly relevant to HIV & Perturb-seq) yet to our reading not known for AAV tinyurl.com/5amc562a
Reposted by Troy McDiarmid
Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Multiplex generation and single-cell analysis of structural variants in mammalian genomes
Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) ...
www.science.org
January 31, 2025 at 7:41 PM
Now out in @science.org w/ @jshendure.bsky.social we present 'Genome-shuffle-seq': a method to shuffle mammalian genomes and characterize the impact of structural variants (SVs) with single-cell resolution in one experiment.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Important PSA / technical note for any using AAVs for experiments that rely on linked elements/barcodes (e.g. multiplexed reporters, MPRAs, certain single cell CRISPR screens).
In work led by @jblalanne.bsky.social - we saw AAVs unlink/swap barcodes when packaged as a pool - design aware!
In work led by @jblalanne.bsky.social - we saw AAVs unlink/swap barcodes when packaged as a pool - design aware!
Brief PSA for the functional genomics community: if you are profiling complex libraries with >1 internal components (e.g., enhancer+barcodes in MPRAs) delivered via AAVs, be aware that there might be substantial unlinking within your libraries if you packaged as a pool! doi.org/10.1101/2025...
February 14, 2025 at 8:42 PM
Important PSA / technical note for any using AAVs for experiments that rely on linked elements/barcodes (e.g. multiplexed reporters, MPRAs, certain single cell CRISPR screens).
In work led by @jblalanne.bsky.social - we saw AAVs unlink/swap barcodes when packaged as a pool - design aware!
In work led by @jblalanne.bsky.social - we saw AAVs unlink/swap barcodes when packaged as a pool - design aware!