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Troy McDiarmid

@troymcdiarmid.bsky.social
187 followers 251 following 23 posts

Assistant Professor, School of Biomedical Engineering & Centre for Brain Health University of British Columbia @sbmeubc.bsky.social @dmcbrainhealth.bsky.social mcdiarmid-lab.sbme.ubc.ca

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Reposted by Troy McDiarmid
Jay Shendure @jshendure.bsky.social · 31/07/2026
Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n
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John Doench @johndoench.bsky.social · 06/07/2026
New preprint from the group, comparing CRISPRko and CRISPRi via a Perturb-seq readout: www.biorxiv.org/content/10.6...
biorxiv.org
Direct comparison of CRISPR knockout and interference with Perturb-seq
CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) are two workhorse technologies for loss-of-function studies, yet direct comparisons between the two are scant relative to their widespread ...
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Reposted by Troy McDiarmid
Djavad Mowafaghian Centre for Brain Health (DMCBH) @dmcbrainhealth.bsky.social · 18/06/2026
Meet @troymcdiarmid.bsky.social, an Assistant Professor in UBC's School of Biomedical Engineering. Dr. McDiarmid is focused on bridging neuroscience and bioengineering to understand brain function. At the core of his work is a powerful idea: what if cells could record their own history?
centreforbrainhealth.ca
From blueprint to black box: Dr. Troy McDiarmid is turning DNA into a record of brain health - Djavad Mowafaghian Centre for Brain Health | DMCBH
Dr. Troy McDiarmid grew up in rural Ontario watching people he loved change in ways nobody could explain. Multiple family members experienced dementia and
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Troy McDiarmid @troymcdiarmid.bsky.social · 30/04/2026
Congrats George!
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Troy McDiarmid @troymcdiarmid.bsky.social · 10/04/2026
Beautiful work @cxqiu.bsky.social @jshendure.bsky.social and co.!
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Troy McDiarmid @troymcdiarmid.bsky.social · 02/04/2026
Thank you!
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Troy McDiarmid @troymcdiarmid.bsky.social · 02/04/2026
@sbmeubc.bsky.social @dmcbrainhealth.bsky.social
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Troy McDiarmid @troymcdiarmid.bsky.social · 02/04/2026
Stoked to announce that I’m starting a lab as an Assistant Professor in the School of Biomedical Engineering and Centre for Brain Health at UBC! mcdiarmid-lab.sbme.ubc.ca Recruiting at all levels - please share the word! Cheers and happy long weekend all!
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Carl de Boer @carldeboer.bsky.social · 18/03/2026
New preprint from our lab where we learn some interesting things about the context specificity of TFs in their regulation of gene expression by dissecting MPRA-trained sequence-expression models. Surprising guest appearance from RNA Pol III(!) Thread from 1st author @sambean12.bsky.social 👇
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Reposted by Troy McDiarmid
Nika Shakiba @nikashakiba.bsky.social · 27/02/2026
[Plz 📢] A little late to the party, but check out our perspective on how cellular heterogeneity can be your friend😊 or foe😠 in cell therapy manufacturing🧫. Shout out to Yeganeh, Hourieh, Enzo, Ali, Yonatan: www.cell.com/cell-systems... @sbmeubc.bsky.social
cell.com
Harnessing heterogeneity for the rational design of cell manufacturing
Dorri Nokoorani et al. argue that heterogeneity can be harnessed as a design feature in the quality-by-design toolkit to optimize the yield, quality, and robustness of bioprocesses for manufacturing s...
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Reposted by Troy McDiarmid
Carl de Boer @carldeboer.bsky.social · 25/02/2026
We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here: journals.biologists.com/dev/article/...
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Will Chen @chenomics.bsky.social · 13/02/2026
We have significantly improved the protocol for recording CRE activities and orders with ENGRAM. We also designed new plasmids for easier cloning. Great work with @jennynathans.bsky.social, @troymcdiarmid.bsky.social and @jshendure.bsky.social . Happy recording!!
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Troy McDiarmid @troymcdiarmid.bsky.social · 15/02/2026
Check out our new protocol paper on molecular recording of transcriptional events in genomic DNA! Super fun pulling this together with @jennynathans.bsky.social @chenomics.bsky.social and @jshendure.bsky.social
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Reposted by Troy McDiarmid
Jenny Nathans @jennynathans.bsky.social · 13/02/2026
Super happy to share our protocol for ENGRAM is out in Nature Protocols! This was fun to write with @chenomics.bsky.social @troymcdiarmid.bsky.social @jshendure.bsky.social. In it we describe how to record CRE identity, activity, and order in mammalian cells.
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Emma Dann @emmamarydann.bsky.social · 05/01/2026
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
tinyurl.com
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
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Troy McDiarmid @troymcdiarmid.bsky.social · 12/11/2025
We added several additional experiments using the parts to target alternate loci, measure both transcription and editing, and more. Great experience working on this with Megan Taylor , @jshendure.bsky.social and co. and very rewarding to see the rapid uptake by the community. Cheers!
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Troy McDiarmid @troymcdiarmid.bsky.social · 12/11/2025
Our work developing a parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording is now out @natbiotech.nature.com
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Reposted by Troy McDiarmid
Nick Page @nicholaspage.bsky.social · 06/11/2025
🚀 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...
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
Thanks Sreeparna!
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
Thanks to all co-authors on and off bluesky, especially @nadavahituv.bsky.social and @jshendure.bsky.social, as well as the funders and families. Cheers!
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
Our results provide a comprehensive resource of active, target-linked human neural enhancers for NDD genes and gRNA reagents for CRT development. More broadly, this work establishes a generalizable strategy for discovering CRT gRNA candidates across cell types and haploinsufficient disorders.
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
Finally, we confirmed that several of the CRISPRa gRNAs identified here demonstrated selective and therapeutically relevant upregulation of SCN2A, CHD8, CTNND2 and TCF4 when delivered virally to patient cell lines, human cerebral organoids, and a humanized mouse model of hTcf4.
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
We identified hundreds of promoter- and enhancer-targeting CRISPRa gRNAs that upregulated 200 of the 337 NDD genes in human neurons, including 91 novel enhancer-gene pairs.
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
Next, we applied multiplex single-cell CRISPRa screening with 15,643 gRNAs to test all MPRA-prioritized cCREs and 761 promoters of NDD genes in their endogenous genomic contexts.
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
We then tested all 5,425 candidate neuronal enhancers with MPRA, identifying 2,422 that are active in human neurons.
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
We first prioritized 337 haploinsufficient NDD risk genes from 42,320 cases. We then nominated 5,425 candidate enhancers for these 337 genes leveraging multiple datasets characterizing the regulatory landscape of the developing human brain, together with various enhancer-gene mapping strategies.
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
Here, we combined Massively Parallel Reporter Assays (MPRAs) and a multiplex single cell CRISPRa screen to discover functional human neural enhancers whose CRISPRa targeting yields specific upregulation of NDD risk genes.
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
However, scaling this cis-regulatory therapy (CRT) paradigm requires pinpointing which candidate cis-regulatory elements (i.e. promoters and enhancers) are active in human neurons, and which can be targeted with CRISPRa to yield specific and therapeutic levels of target gene upregulation.
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
Many neurodevelopmental disorders are caused by haploinsufficiency - where functional loss of one gene copy leaves insufficient expression from the other. CRISPR-based gene activation (CRISPRa) has emerged as a promising therapeutic approach for NDD caused by haploinsufficiency.
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Troy McDiarmid @troymcdiarmid.bsky.social · 05/11/2025
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.
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cxqiu.bsky.social @cxqiu.bsky.social · 04/11/2025
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/
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Kevin J. Kircher @kevinjkircher.com · 04/10/2025
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
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Reposted by Troy McDiarmid
Seth Shipman @seth-shipman.bsky.social · 08/09/2025
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)!
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Andrew Payne @andrewcpayne.bsky.social · 01/10/2025
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
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Erich M. Schwarz @erichmschwarz.bsky.social · 01/08/2025
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...
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Michael Hendricks 🇨🇦 @michaelhendricks.bsky.social · 27/09/2025
I'll never get tired of these. (courtesy of Sebasitan Wittekindt doi.org/10.1101/2025...)
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Troy McDiarmid @troymcdiarmid.bsky.social · 27/09/2025
Beautiful!
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Reposted by Troy McDiarmid
Glen @vaguebiscuit.bsky.social · 27/09/2025
Well don't I feel stupid
A headline about the James Webb Telescope potentially finding a new stellar object dubbed a black hole star
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Nobu Hamazaki @nobuhamazaki.bsky.social · 26/09/2025
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...
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mathiaseder.bsky.social @mathiaseder.bsky.social · 19/09/2025
✨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/...
science.org
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...
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Jesse Engreitz @jengreitz.bsky.social · 19/09/2025
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/
bioRxiv - An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq
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John Ray @jraylab.bsky.social · 18/09/2025
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...
nature.com
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 ...
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Kevin Bender @neurobender.bsky.social · 17/09/2025
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
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...
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Janel Comeau 🍁 @verybadllama.bsky.social · 10/06/2025
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
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Nozomu Yachie @nzmyachie.bsky.social · 21/05/2025
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...
nature.com
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.
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Troy McDiarmid @troymcdiarmid.bsky.social · 21/05/2025
Congrats @nzmyachie.bsky.social and co.! Beautiful work.
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Carl de Boer @carldeboer.bsky.social · 28/04/2025
⏰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/
CAGT Poster featuring Keynote, Dr. Calin Plesa, of DropSynth fame!
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Vikram Agarwal @vagar.bsky.social · 13/03/2025
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 😉
nature.com
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.
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Jeremy Berg @jeremymberg.bsky.social · 22/02/2025
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.
media.tenor.com
the word irony is written on a white background
ALT: the word irony is written on a white background
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Harmit Singh Malik @harmitmalik.bsky.social · 23/02/2025
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/
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