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tony-li-sf.bsky.social

@tony-li-sf.bsky.social
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Beth Martin @bkmartin.bsky.social · 08/10/2026
Two teams map development of mammal embryos, cell by cell | Science | AAAS www.science.org/content/arti...
science.org
Two teams map development of mammal embryos, cell by cell
Using genome editing to trace cell lineages, researchers capture the early history of the mouse embryo in unprecedented detail
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Maitreya Dunham @maitreya.bsky.social · 06/10/2026
Here's the ad for the Genome Sciences faculty positions ap.washington.edu/ahr/position...
ap.washington.edu
Position Details - Academic Personnel & Faculty
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Maitreya Dunham @maitreya.bsky.social · 24/09/2026
Exciting news: @uwgenome.bsky.social will be hiring for two tenure-track faculty positions this year, one open rank and one assistant professor. Both are “Genome Sciences” interpreted broadly so we welcome applicants working in a variety of fields and methods. Ad will be out shortly.
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elena-romero.bsky.social @elena-romero.bsky.social · 15/09/2026
Happy to share this spotlight of our work studying how HIV can escape different broadly neutralizing antibodies in different ways. www.fredhutch.org/en/news/spot...
fredhutch.org
Recurring escape routes reveal patterns in HIV evolution
Researchers mapped how HIV evolves to escape broadly neutralizing antibodies, revealing recurring routes that could inform antibody combinations therapies.
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Shenzhi Chen @shenzhichen1999.bsky.social · 25/08/2026
Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41...
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Junhong Choi @choijunhong.bsky.social · 11/08/2026
Excited to share the first preprint from our lab! We combined a DNA Typewriter lineage recorder with clone-resolved founder profiling to find what makes metastatic potential heritable in lung cancer xenografts. 1/13 www.biorxiv.org/content/10.6...
biorxiv.org
Time-resolved lineage recording reveals a pre-existing, heritable cell state underlying metastatic potential
Metastasis causes most cancer deaths, yet no recurrent mutation specifically drives it, raising the possibility that metastatic potential is a non-genetic yet heritable cell state. Classic experiments...
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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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Jay Shendure @jshendure.bsky.social · 30/07/2026
New preprint from Shendure Lab on Locus-Scale aka Long-@$$ MPRAs led by the amazing Abby McGee & @carinabiar.bsky.social Most MPRAs test ~300 bp fragments next to a promoter. But real enhancers are bigger, act combinatorially and from a distance. 1/n www.biorxiv.org/content/10.6...
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Syd Sattler @sydsat.bsky.social · 29/06/2026
What if an embryo made immune cells before it finished building the tissue they usually come from? In our new preprint, we show that annual killifish embryos specify neutrophils before germ layers are fully resolved. www.biorxiv.org/content/10.6... Huge thanks to my PI, @ohnolog.bsky.social ! 🧵
biorxiv.org
Early immune cell development precedes gastrulation in annual killifish
During embryogenesis, cell types arise in a predictable order because developmental regulators act sequentially. But how evolutionary changes in morphogenesis reshape the signaling environments that a...
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Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...
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Jonas Koeppel @jonaskoeppel.bsky.social · 04/06/2026
22/n On a personal note, I’ll soon start an independent research group in the Genome Biology Unit at EMBL Heidelberg. If you enjoy this type of work and want to engineer genomes at the largest scale, please reach out! jonas-koeppel.github.io/koeppellab/ www.embl.org/groups/koepp...
jonas-koeppel.github.io
Koeppel Lab | Structural Variation and Genome Engineering
Genome engineering research led by Jonas Koeppel, developing scalable technologies to design structural variants and study mammalian genome function.
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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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Alison Feder @alisonfeder.bsky.social · 26/05/2026
I’m excited to share a new paper about HIV escape from broadly neutralizing antibody monotherapies! In it, we describe the most highly recurrent adaptation I have ever seen. A close collaboration with Lillian Cohn (FHCC) led jointly by Elena Romero and Abby Clyde. www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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cxqiu.bsky.social @cxqiu.bsky.social · 09/04/2026
New preprint @cxqiu.bsky.social @jshendure.bsky.social ! Can we learn regulatory grammars of human cell types — by training on mouse development and transferring across 241 mammalian genomes? Introducing STEAM & a whole-organism scATAC-seq atlas from E10 to birth. www.biorxiv.org/content/10.6...
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Jay Shendure @jshendure.bsky.social · 10/04/2026
Latest from Shendure & Qiu labs (@cxqiu.bsky.social) )! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).
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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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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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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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Nature Biotechnology @natbiotech.nature.com · 11/11/2025
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
go.nature.com
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.
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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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UW Genome Sciences @uwgenome.bsky.social · 28/10/2025
Jay Shendure elected to National Academy of Medicine newsroom.uw.edu/blog/jay-she...
newsroom.uw.edu
Jay Shendure elected to National Academy of Medicine - UW Medicine | Newsroom
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Jay Shendure @jshendure.bsky.social · 14/10/2025
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here: www.biorxiv.org/content/10.1...
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UW Genome Sciences @uwgenome.bsky.social · 21/08/2025
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae www.science.org/doi/10.1126/...
science.org
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
The constraints that govern the evolution of gene expression patterns across development remain unclear. Single-cell RNA sequencing can detail these constraints by systematically profiling homologous ...
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Maitreya Dunham @maitreya.bsky.social · 15/08/2025
So proud of my lab students Tiffany and Amanda for winning the Roman Scholarship from @uwgenome.bsky.social! I always love the story about how yeast genetics got its start at UW because corn wouldn’t grow in Seattle www.gs.washington.edu/about/histor...
gs.washington.edu
50 Years of Genetics at the UW
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Nadav Ahituv @nadavahituv.bsky.social · 15/06/2025
Capture C identifies promoter interacting sequences. MPRA tests sequences for regulatory activity. Here, we combined them both to test sequences with their target promoter. Amazing work by @colinearnould.bsky.social, Pia Keukeleire, Martin Kircher and many others. www.biorxiv.org/content/10.1...
biorxiv.org
Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity
Cis regulatory elements (CREs) interact with their target promoters over long genomic distances and can be identified using chromatin conformation capture (3C) assays. Their regulatory activity can be...
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Mitchell R. Vollger @mrvollger.bsky.social · 05/06/2025
Very excited to share I’ll be starting my own group at University of Utah in the Department of Human Genetics in the new year! Reach out if you are interested! vollgerlab.com
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Junhong Choi @choijunhong.bsky.social · 06/05/2025
Happy to share our new review on molecular circuits for genomic recording with @chenomics.bsky.social! Here, we present our views on the remaining challenges in the field of genomic recording for reconstructing cell-fate decisions. (1/2)
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Seungsoo Kim @seungsookim.bsky.social · 25/04/2025
I am hiring for a research technician role in my new lab at UC Irvine studying how transcription factors control cell identity. If you know any graduating undergrads or postbacs looking for a position, please spread the word! Apply by May 9 for full consideration. recruit.ap.uci.edu/JPF09594
recruit.ap.uci.edu
Junior / Assistant Specialist: Kim Lab, Developmental & Cell Biology
University of California, Irvine is hiring. Apply now!
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Beth Martin @bkmartin.bsky.social · 07/03/2025
I added the alt text for this very important message
Cardboard sign for the Stand Up for Science rally that says: HANDS OFF THE SCIENCE MONEY!! JUST TAX THE GODDAMNED BILLIONAIRES FOR FUCK'S SAKE!
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