@cxqiu.bsky.social
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📥 73
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https://sites.dartmouth.edu/qiulab/
reposted by
Junyue Cao
10 days ago
Excited to share our new paper
@nature.com
! We developed PerturbFate, a scalable single-cell platform to discover how diverse genetic perturbations converge on a shared drug-resistant cell state, and key programs driving it, led by our incredible Zihan Xu from
@rockefeller.edu
rdcu.be/fdC14
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reposted by
Niklas Kempynck
17 days ago
CREsted is finally out! You can find the article, together with a summarizing Research Briefing, in thread. 🦎
add a skeleton here at some point
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reposted by
Jay Shendure
16 days ago
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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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...
16 days ago
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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/
6 months ago
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reposted by
Nobu Hamazaki
7 months ago
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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reposted by
Junhong Choi
11 months ago
New preprint with the Shendure lab
@jshendure.bsky.social
! We apply the DNA Typewriter lineage recorder to mouse 3D gastruloids, a powerful model of early mammalian development. Led by Sam Regalado and CX Qiu
@cxqiu.bsky.social
:
www.biorxiv.org/content/10.1...
(1/13)
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Lineage recording in monoclonal gastruloids reveals heritable modes of early development
Mammalian stem cells possess a remarkable capacity for self-organization, a property that underlies increasingly sophisticated in vitro models of early development. However, even under carefully contr...
https://www.biorxiv.org/content/10.1101/2025.05.23.655664v1
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reposted by
Silvia Domcke
11 months ago
Big thanks to Sam Regalado, @‪cxqiu.bsky.social‬,
@jshendure.bsky.social
and all co-authors for sharing this journey. Also check out the accompanying preprint applying barcoded monoclonals for lineage recording with
@choijunhong.bsky.social
.
www.biorxiv.org/content/10.1...
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Lineage recording in monoclonal gastruloids reveals heritable modes of early development
Mammalian stem cells possess a remarkable capacity for self-organization, a property that underlies increasingly sophisticated in vitro models of early development. However, even under carefully contr...
https://www.biorxiv.org/content/10.1101/2025.05.23.655664v1
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reposted by
Silvia Domcke
11 months ago
Expanding Perturb-seq-like screens to multicellular systems also increases the complexity of confounding effects. We encountered this when we perturbed all TFs in mosaic embryoid bodies (EBs) and develop a scalable solution by barcoding monoclonal individuals. đź§µ
www.biorxiv.org/content/10.1...
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Barcoded monoclonal embryoids are a potential solution to confounding bottlenecks in mosaic organoid screens
Genetic screens in organoids hold tremendous promise for accelerating discoveries at the intersection of genomics and developmental biology. Embryoid bodies (EBs) are self-organizing multicellular str...
https://www.biorxiv.org/content/10.1101/2025.05.23.655669v1
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