Sudarshan Pinglay
@sudpinglay.bsky.social
Scientist at UW Genome Sciences and the Seattle Hub for Synthetic Biology.
http://pinglay-lab.com/
synBio/genomics/soccer/heavy metal/food
http://pinglay-lab.com/
synBio/genomics/soccer/heavy metal/food
Pinned
Sudarshan Pinglay
@sudpinglay.bsky.social
· Jan 31
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
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/...
Reposted by Sudarshan Pinglay
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
Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions.
www.massivconference.com
Abstract deadline: Nov 14
October 25, 2025 at 4:21 PM
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
Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions.
www.massivconference.com
Abstract deadline: Nov 14
Reposted by Sudarshan Pinglay
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.
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.
October 18, 2025 at 5:50 PM
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.
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.
Reposted by Sudarshan Pinglay
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...
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!
Job posting below:
alleninstitute.org/careers/jobs...
Please reach out if you have any questions!
Jobs
We are working to solve the biggest mysteries in bioscience.
alleninstitute.org
August 13, 2025 at 7:03 PM
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!
Job posting below:
alleninstitute.org/careers/jobs...
Please reach out if you have any questions!
Reposted by Sudarshan Pinglay
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/...
www.molbiolcell.org/doi/10.1091/...
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. ...
www.molbiolcell.org
July 21, 2025 at 5:46 PM
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/...
www.molbiolcell.org/doi/10.1091/...
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...
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...
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...
doi.org
July 14, 2025 at 10:36 PM
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...
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...
Reposted by Sudarshan Pinglay
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/
Range extender mediates long-distance enhancer activity - Nature
The REX element is associated with long-range enhancer–promoter interactions.
www.nature.com
July 2, 2025 at 4:17 PM
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/
Reposted by Sudarshan Pinglay
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☺️
June 20, 2025 at 10:17 PM
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☺️
Reposted by Sudarshan Pinglay
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 Sudarshan Pinglay
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
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
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...
tinyurl.com
April 11, 2025 at 2:23 PM
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
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
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...
Link to apply:
alleninstitute.org/careers/jobs...
Jobs
We are working to solve the biggest mysteries in bioscience.
alleninstitute.org
March 28, 2025 at 7:17 PM
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...
Link to apply:
alleninstitute.org/careers/jobs...
Reposted by Sudarshan Pinglay
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_meeting/
CAGT: Cascadia Advanced Genomic Technologies
June 19-20 2025, Vancouver, BC, Canada
de-boer-lab.github.io
March 26, 2025 at 4:47 PM
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_meeting/
Join us at the Cascadia Advanced Genomic Technologies conference in beautiful Vancouver this summer.
Registration is FREE at the link below!
de-boer-lab.github.io/CAGT_meeting/
Registration is FREE at the link below!
de-boer-lab.github.io/CAGT_meeting/
CAGT: Cascadia Advanced Genomic Technologies
June 19-20 2025, Vancouver, BC, Canada
de-boer-lab.github.io
March 25, 2025 at 10:45 PM
Join us at the Cascadia Advanced Genomic Technologies conference in beautiful Vancouver this summer.
Registration is FREE at the link below!
de-boer-lab.github.io/CAGT_meeting/
Registration is FREE at the link below!
de-boer-lab.github.io/CAGT_meeting/
Check out this video explainer of our recent paper on shuffling mammalian genomes. Thanks to Jeremy @genometdcc.bsky.social for putting this together!
🧪🧬🖥️ #STS
@sudpinglay.bsky.social describes how Genome-Shuffle-seq enables multiplex generation, mapping, and characterization of structural variants by leveraging barcoded "shuffle cassettes" with site-specific recombination and novel barcode pairings for genome-wide mapping 📽️ 👇
youtu.be/rW8AFhq1Pys
@sudpinglay.bsky.social describes how Genome-Shuffle-seq enables multiplex generation, mapping, and characterization of structural variants by leveraging barcoded "shuffle cassettes" with site-specific recombination and novel barcode pairings for genome-wide mapping 📽️ 👇
youtu.be/rW8AFhq1Pys
Shuffling Mammalian Genomes
YouTube video by GenomeTDCC
youtu.be
February 24, 2025 at 4:57 PM
Check out this video explainer of our recent paper on shuffling mammalian genomes. Thanks to Jeremy @genometdcc.bsky.social for putting this together!
Reposted by Sudarshan Pinglay
@science.org Genome recombination on demand | Science www.science.org/doi/10.1126/... a Perspective by @seczmarta.bsky.social Lars Steinmetz @stanford.edu on two studies bit.ly/4hzFRMg + bit.ly/4jyT4Hf that generate large genome rearrangements in mammalian cells @ unprecedented scale #synbio #genome
Genome recombination on demand
Large genome rearrangements in mammalian cells can be generated at scale
www.science.org
February 1, 2025 at 6:58 PM
@science.org Genome recombination on demand | Science www.science.org/doi/10.1126/... a Perspective by @seczmarta.bsky.social Lars Steinmetz @stanford.edu on two studies bit.ly/4hzFRMg + bit.ly/4jyT4Hf that generate large genome rearrangements in mammalian cells @ unprecedented scale #synbio #genome
Read thread below, if you want more details on the personal side of this wonderful collaboration.
Great work and it's very nice to see the studies co-published. Can you say a bit more about how the two teams ended up knowing about each other's work and co-submitting? cc @jshendure.bsky.social @sudpinglay.bsky.social
January 31, 2025 at 7:58 PM
Read thread below, if you want more details on the personal side of this wonderful collaboration.
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/...
Reposted by Sudarshan Pinglay
The Chan Zuckerberg Initiative is awarding BBI researchers $1.5 million over two years to “democratize” access to synthetic DNA. We are envisoning complementary technologies that address shortcomings of current systems for manufacturing DNA.
brotmanbaty.org/news/chan-zu...
@sudpinglay.bsky.social
brotmanbaty.org/news/chan-zu...
@sudpinglay.bsky.social
January 29, 2025 at 10:39 PM
The Chan Zuckerberg Initiative is awarding BBI researchers $1.5 million over two years to “democratize” access to synthetic DNA. We are envisoning complementary technologies that address shortcomings of current systems for manufacturing DNA.
brotmanbaty.org/news/chan-zu...
@sudpinglay.bsky.social
brotmanbaty.org/news/chan-zu...
@sudpinglay.bsky.social
Reposted by Sudarshan Pinglay
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
Redirecting
doi.org
December 2, 2024 at 4:44 PM
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
Reposted by Sudarshan Pinglay
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 4:13 AM
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...