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Sudarshan Pinglay

@sudpinglay.bsky.social
322 followers 210 following 66 posts

Scientist at UW Genome Sciences and the Seattle Hub for Synthetic Biology. pinglay-lab.com synBio/genomics/soccer/heavy metal/food

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Sudarshan Pinglay @sudpinglay.bsky.social · 6h
Big congrats Mo!!!
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Sudarshan Pinglay @sudpinglay.bsky.social · 8h
Excited to share Shotgun Genetic Engineering, developed by @julietrolle.bsky.social out now @natbiotech.nature.com! Read on to learn how Julie enabled mammalian cells to grow without 2 essential amino acids for the first time in >500 million years using highly multiplexed metabolic engineering!
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Sudarshan Pinglay @sudpinglay.bsky.social · 16/06/2026
congrats Priya!! so excited for you :)
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
huge thank you to all the co-authors and in particular, @jonaskoeppel.bsky.social and @jshendure.bsky.social for helping to lead this effort! also big thanks to @brotmanbaty.bsky.social, @biohub.org, NIH @genometdcc.org, NIH Common Fund and DARPA for funding!
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
Looking forward to engaging further with the community on these ideas. If you're excited about working in these areas, we are hiring! www.pinglay-lab.com
pinglay-lab.com
Pinglay Lab
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
3. Genome synthesis: smaller genomes are cheaper and easier to synthesize. The first minimal genome built becomes the foundation every future synthetic genome can be built from, bringing the cost of every subsequent project down with it.
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
2. Bio-manufacturing/bio-medicine: the vast majority of a CHO cell or CAR-T cell genome is not an asset but a liability: silenced viruses that can reactivate, transposons that drive instability, unexpressed DNA to maintain and the pull towards unwanted cellular states.
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
1. Fundamental biology: minimizing genomes reveals which combinations of genetic elements are sufficient to support the function of any cell. Importantly, any minimization is useful! We don't have to build the entire genome to learn something. We learn at each step.
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
DNA synthesis, long-read sequencing, AI models for DNA design, and programmable methods for DNA delivery and integration, all of which are critical for genome design and synthesis have all come a long way since 2016. A minimal genome is the right target for a few reasons:
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
In a Nature World View, I mark the ten-year anniversary of GP-write, a project that set out to synthesize a human genome in cells. I argue that the conditions are right to try again, with a sharper target: a minimal human genome. www.nature.com/articles/d41...
nature.com
Why a synthetic human genome is still worth building
A decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
We're excited to scale Shred-seq to saturating coverage, genome-wide and across multiple cell states, to fully map essentiality in the human genome. Knowing what's essential is the first step toward knowing what we'd actually need to build, which brings us to the second piece.
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
We demonstrate that Shred-seq is compatible with single-cell RNA-seq readout, enabling deletions to be linked to more complex phenotypes across thousands of cells. This could provide the kind of training data for genomic AI models that Perturb-seq has for coding regions.
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
Surviving deletions are depleted not just for known essential genes, but some non-coding regions as well, giving us a direct, annotation-agnostic measure of what's essential in the genome of one human cell line. We are able to put empirical bounds on dispensability of 50-96%!
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
Shred-seq, led by the incredible @jonaskoeppel.bsky.social, couples CRISPR-Cas3 with phage polymerase genotyping to enable gigabase-scale deletion scans. We generated >36,000 overlapping deletions ranging from 100bp to 500kb, covering ~14% of the genome! bsky.app/profile/jona...
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
How much of the human genome is essential? Two pieces out today from our lab: 1) a method to map essential genomic intervals at gigabase scale, and 2) an argument that it's time to consider synthesizing a minimal human genome. biorxiv.org/content/10.6... nature.com/articles/d41...
nature.com
Why a synthetic human genome is still worth building
A decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.
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Sudarshan Pinglay @sudpinglay.bsky.social · 04/06/2026
Thanks for the feedback! We do mention the Wellcome project, though it had to be brief for length: "UK researchers are aiming to build the first fully synthetic human chromosome through a £10-million (US$13-million) project launched in 2025."
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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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Sudarshan Pinglay @sudpinglay.bsky.social · 06/02/2026
We are hiring a staff member to support various projects in our lab. Please reach out with questions! wd5.myworkdaysite.com/recruiting/u...
wd5.myworkdaysite.com
Research Scientist/Engineer 2, SeaHub
Job Description The Department of Genome Sciences has an outstanding opportunity for a Research Scientist Engineer 2 to join the team. About this Opportunity Reporting to the Principal Investigator, t...
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Sudarshan Pinglay @sudpinglay.bsky.social · 23/01/2026
if you are excited about these areas, come join our lab @uwgenome.bsky.social and the Seattle Hub for Synthetic Biology! We are hiring at all levels. t.co/wAehoBsJ5F
t.co
https://www.pinglay-lab.com/
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Sudarshan Pinglay @sudpinglay.bsky.social · 23/01/2026
We also discuss current bottlenecks for mammalian genome writing (mainly throughput and size), mechanisms to address them, and future directions for the technology. We think it is particularly poised to revolutionize generating training data for genomic AI models.
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Sudarshan Pinglay @sudpinglay.bsky.social · 23/01/2026
Engineering mammalian cells with large synthetic DNA payloads promises to be highly enabling for understanding mammalian gene regulation, dissecting GWAS haplotypes, engineering better animal models for human disease, and encoding multi-gene functions for cell therapy and biotech
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Sudarshan Pinglay @sudpinglay.bsky.social · 23/01/2026
Happy to share that our review on mammalian genome writing with Jack Atwater, Ran Brosh, Jef Boeke, @jshendure.bsky.social and Matt Maurano is now out in @cellpress.bsky.social! www.sciencedirect.com/science/arti...
sciencedirect.com
Mammalian genome writing: Unlocking new length scales for genome engineering
The ability to design and engineer mammalian genomes across arbitrary length scales would transform biology and medicine. Such capabilities would enab…
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Nozomu Yachie @nzmyachie.bsky.social · 25/10/2025
Please 🔁! #MASSIV will be held in Vancouver from January 19-22, 2026. 4-day meeting on #synbio x #tissueengineering. Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions. www.massivconference.com Abstract deadline: Nov 14
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Nozomu Yachie @nzmyachie.bsky.social · 18/10/2025
Please RP! A 4-day synbio and tissue engineering conference #MASSIV to transform biology and medicine together. Couldn't list all amazing speakers, so please check out this 👉https://www.massivconference.com/ Poster due is Nov 7, but will be extended. With @stemcellnetwork.ca and JST.
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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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Sudarshan Pinglay @sudpinglay.bsky.social · 13/08/2025
We are hiring a scientist to lead our 'Build' team at the Seattle Hub for Synthetic Biology. @alleninstitute.org Job posting below: alleninstitute.org/careers/jobs... Please reach out if you have any questions!
alleninstitute.org
Jobs
We are working to solve the biggest mysteries in bioscience.
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Abby Buchwalter @abbybuch.bsky.social · 21/07/2025
The nuclear lamina strengthens the nucleus and organizes the genome. So what happens when you acutely degrade it in living cells? Not what we thought! (1/n) www.molbiolcell.org/doi/10.1091/...
molbiolcell.org
Lamin B1 and LAP2β resist cytoskeletal force to maintain lamin A/C meshwork organization and preserve nuclear integrity | Molecular Biology of the Cell
The nuclear lamins are extremely long-lived proteins in most cell types. As a consequence, lamin function cannot be effectively dissected with temporal precision using standard knock-down approaches. ...
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
Here's a link to the preprint if you made it this far: www.biorxiv.org/content/10.1... any feedback would be highly appreciated!
biorxiv.org
A shotgun approach for highly multiplexed mammalian metabolic engineering
Mammalian metabolic engineering is critical to advancing basic biology, bioproduction, and cell therapy. However, as pathway complexity increases, so does the size of both the combinatorial design spa...
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
A big thank you to all co-authors - looking forward to seeing where we can take this approach. If you are interested in joining us on this effort, check out our website: www.pinglay-lab.com
pinglay-lab.com
Pinglay Lab
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
Finally, we demonstrate that data resulting from SGE is compatible with training predictive machine learning models. We are very excited about using SGE to generate the synthetic data needed to train the next generation of models for biological design.
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
SGE is generalizable across cell types. We engineer T-cells (Jurkat) to grow without valine. We believe a similar strategy could help create more resilient T-cells for therapy, capable of surviving and functioning in the metabolically depleted environments of tumors. Hopefully more here soon!
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
Here's a link to the preprint if you made it this far: doi.org/10.1101/2025... any feedback would be highly appreciated!
doi.org
A shotgun approach for highly multiplexed mammalian metabolic engineering
Mammalian metabolic engineering is critical to advancing basic biology, bioproduction, and cell therapy. However, as pathway complexity increases, so does the size of both the combinatorial design spa...
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
A big thank you to all co-authors - looking forward to seeing where we can take this approach. If you are interested in joining us on this effort, check out our website: www.pinglay-lab.com
pinglay-lab.com
Pinglay Lab
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
Finally, we demonstrate that data resulting from SGE is compatible with training predictive machine learning models. We are very excited about using SGE to generate the synthetic data needed to train the next generation of models for biological design.
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
We then used SGE to engineer CHO cells to grow without isoleucine, a feat we could not achieve via rational design and delivery of entire synthetic pathways. Again, mitochondrial localization was favored, with individual clones reflecting ~40-50kb of integrated DNA!
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
Using SGE, we screened millions of pathway combinations in a single experiment to engineer CHO cells that grew at WT rate (~1.1 day/doubling) in valine-free medium. Intriguingly, the best clones all employed mitochondrial localization of pathway components, not cytoplasm as in our prev. design.
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
In collaboration with Harris Wang’s lab, we previously engineered cells to grow without valine by importing 4 genes from E.coli. However, the cells grew 4x slower than normal - and we could not extend this strategy to enable any other amino acid prototrophies. doi.org/10.7554/eLif...
doi.org
Resurrecting essential amino acid biosynthesis in mammalian cells
Mammalian cells were engineered to synthesize valine, a metabolic capacity that had been lost from the lineage of higher eukaryotes for >500 million years.
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
As a test case, we used SGE to engineer essential amino acid prototrophy in mammalian cells, a behavior last seen over 500 million years ago. Unlike E. coli, which can make all 20 proetinogenic amino acids, mammals lack the pathways for 9 “essential” ones and must obtain them through the diet.
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
In SGE, we clone and deliver a TU library at high MOI so that each cell gets a random mix, assembling a unique synthetic metabolic pathway per cell. Cells with the desired phenotype (e.g., survival or fluorescence) are selected, and TU barcodes are sequenced to identify functional combinations.
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
To address this, we developed Shotgun Genetic Engineering (SGE), which leverages the fact that building and delivering many small, barcoded transcription units - each with a gene, promoter and localization signal - is exponentially easier than delivering a single large construct to a mammalian cell.
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
Mammalian metabolic engineering is key to advancing bioproduction, cell therapy, and rejuvenation. But as pathway complexity grows, so does the combinatorial design space! However, delivering large DNA constructs to mammalian cells is inefficient, making large unbiased screens intractable.
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Sudarshan Pinglay @sudpinglay.bsky.social · 14/07/2025
Excited to share our work with @julietrolle.bsky.social & Jef Boeke. We developed a 'shotgun' method to screen millions of synthetic metabolic pathways to enable mammalian cells to grow without two essential nutrients for the first time in >500 million years! doi.org/10.1101/2025... Thread...
doi.org
A shotgun approach for highly multiplexed mammalian metabolic engineering
Mammalian metabolic engineering is critical to advancing basic biology, bioproduction, and cell therapy. However, as pathway complexity increases, so does the size of both the combinatorial design spa...
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Evgeny Kvon @evgenykvon.bsky.social · 02/07/2025
Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/
nature.com
Range extender mediates long-distance enhancer activity - Nature
The REX element is associated with long-range enhancer–promoter interactions.
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Nozomu Yachie @nzmyachie.bsky.social · 20/06/2025
CAGT was fun! Thanks @carldeboer.bsky.social @sudpinglay.bsky.social and the de Boer lab for organizing! Folks from Seattle, Oregon, and other places. Great community. Arman gave a usual super talk, and Sanchit and Dayag won poster prizes☺️
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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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Sudarshan Pinglay @sudpinglay.bsky.social · 25/04/2025
Such a cool story Maximus! Congrats
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Sudarshan Pinglay @sudpinglay.bsky.social · 11/04/2025
Let’s gooo! Congrats Dave and team - glad to see this out.
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Dave Truong @davidmtruong.bsky.social · 11/04/2025
Need a site-specific, dox-inducible system for human cells? Low leakage, silencing-resistant, and modular? It’s here in the first paper from my lab, led by Tomoki Yanagi MD, PhD. Bonus: forward programming of TEC-like cells from hiPSCs. tinyurl.com/trunod01
tinyurl.com
Termination sequence between an inducible promoter and ubiquitous chromatin opening element (UCOE) reduces gene expression leakage and silencing - Journal of Biological Engineering
Background Inducible gene expression circuits enable precise control over target gene activation and are widely used in direct reprogramming. However, their usability is often compromised by DNA methy...
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Sudarshan Pinglay @sudpinglay.bsky.social · 28/03/2025
We are hiring a person to join our team at the Seattle Hub for Synthetic Biology. Please share the word! Link to apply: alleninstitute.org/careers/jobs...
alleninstitute.org
Jobs
We are working to solve the biggest mysteries in bioscience.
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Carl de Boer @carldeboer.bsky.social · 26/03/2025
Join us June 19-20, 2025 in Vancouver BC for the Cascadia Advanced Genomic Technologies meeting! Featuring Keynote speaker Calin Plesa @calin.bsky.social Abstract deadline April 30🔔, but registration is capped so don't wait! 😱 de-boer-lab.github.io/CAGT_meeting/
de-boer-lab.github.io
CAGT: Cascadia Advanced Genomic Technologies
June 19-20 2025, Vancouver, BC, Canada
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