Lightnews — Scholar-powered news

Jay Shendure @jshendure.bsky.social · 15h

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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Jay Shendure @jshendure.bsky.social · 5d

There is also no space bar 😢

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the Node @the-node.bsky.social · 8d

Developmental Biology and Disability.

“Developmental biology is fundamentally beautiful. We are no less beautiful for our variation. Instead, perhaps we are more so. Perhaps we are remarkable. Perhaps we are full of wonder.”

Insightful post by Bethan ⬇️👀
thenode.biologists.com/developmenta...

Developmental Biology and Disability - the Node

Hopeful monsters. Morphospace. Mutation. Natural variation. Mutagenesis screens. Polymorphism. Deformity. Phenotype. Disease. Adaptation. Anomaly.

thenode.biologists.com

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Benoit Bruneau @benoitbruneau.bsky.social · 12d

awesome new work by my @gladstoneinst.bsky.social and @ucsanfrancisco.bsky.social colleagues incl @vram142.bsky.social on how chromatin remodelers affect mesoscale chromatin organization www.science.org/doi/10.1126/...

ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes

Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

www.science.org

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Nobu Hamazaki @nobuhamazaki.bsky.social · 18d

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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Greg Findlay @gregfindlay.bsky.social · Sep 4

Hugely thankful for this 🙏. We will do our best to make the most of it. @erc.europa.eu!

The Francis Crick Institute @crick.ac.uk · Sep 4

Congratulations to @gregfindlay.bsky.social on being awarded a €1.5 million Starting Grant from the @erc.europa.eu to take a closer look at possible disease variants hiding in the dark genome.

www.crick.ac.uk/news/2025-09...

€1.5 million to uncover disease risk hiding in non-coding DNA

Greg Findlay, Group Leader of the Genome Function Laboratory at the Francis Crick Institute, has been awarded a Starting Grant from the European Research Council for €1.5 million to take a deep dive i...

www.crick.ac.uk

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Greg Findlay @gregfindlay.bsky.social · Aug 18

Our latest research is out today on ‪@medrxivpreprint.bsky.social:

www.medrxiv.org/content/10.1...

Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk.

Led by the amazing Phoebe Dace. This one’s packed full of data, so check out the paper. Quick highlights… 🧵 1/n

Saturation genome editing of BRCA1 across cell types accurately resolves cancer risk

Germline pathogenic BRCA1 variants predispose women to breast and ovarian cancer. Despite accumulation of functional evidence for variants in BRCA1 , over half of reported single-nucleotide variants (...

www.medrxiv.org

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Jay Shendure @jshendure.bsky.social · Aug 7

Thrilled at the news of @10xgenomics.bsky.social ' acquisition of Scale Bio which I co-founded with Frank Steemers (ex-Illumina), @coletrapnell.bsky.social and Garry Nolan . Further thrilled to joining 10X Genomics as an scientific advisor and for the synergies that lie ahead!

10x Genomics @10xgenomics.bsky.social · Aug 7

This acquisition will bring together two pioneering companies with a shared vision: to make single cell analysis more powerful, affordable and accessible to researchers worldwide.

Learn more: bit.ly/4mAWAS8

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Alfonso Martinez Arias @amartinezarias.bsky.social · Jul 15

Two new preprints from the @arjunraj.bsky.social‬ on #gastruloids. Both excellent. Exploring the relationship between macroscopic reproducibility v microscopic heterogeneity. Stunning experiments and much to think about
biorxiv.org/content/earl...
biorxiv.org/content/earl...

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Sriram Pendyala @treependyala.bsky.social · Jul 7

🚨 Most variant screens measure growth or abundance. What do they miss? That variants impact a spectrum of protein and cellular phenotypes. Variant in situ sequencing (VIS-seq) finds what’s missing: image cells 🔬 first, decode later, revealing multi-scale phenotypes for thousands of variants.👇

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Anshul Kundaje @anshulkundaje.bsky.social · Jun 28

One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/

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Kevin Mitchell @wiringthebrain.bsky.social · Jun 20

Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae | Science www.science.org/doi/10.1126/... 😍

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 ...

www.science.org

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EPIGENETIC HULK @epigenetichulk.bsky.social · Jun 13

EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!

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Silvia Domcke @sdomcke.bsky.social · May 25

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. 🧵 www.biorxiv.org/content/10.1...

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...

www.biorxiv.org

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Junhong Choi @choijunhong.bsky.social · May 27

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)

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...

www.biorxiv.org

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Nozomu Yachie @nzmyachie.bsky.social · May 21

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...

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

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Reposted by Jay Shendure

Nadav Ahituv @nadavahituv.bsky.social · May 9

Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others.
www.nature.com/articles/s41...

Massively parallel jumping assay decodes Alu retrotransposition activity - Nature Communications

Here, the authors develop a high-throughput assay to measure the jumping potential of thousands of transposons in parallel.

www.nature.com

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Junhong Choi @choijunhong.bsky.social · May 6

Very grateful to receive the Searle Scholars Award, especially during this challenging time! This support will help our lab realize our vision of genomic recording for reconstructing the mammalian cell fate decision. searlescholars.org/2025/04/14/s...

SEARLE SCHOLARS PROGRAM NAMES 15 SCIENTISTS AS SEARLE SCHOLARS FOR 2025

Members of the new class of Searle Scholars pursue ground-breaking research in chemistry and the biomedical sciences. Each receives an award of $300,000 in flexible funding to support his, her, or …

searlescholars.org

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Junhong Choi @choijunhong.bsky.social · May 6

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)

Trends in Genetics @cp-trendsgenetics.bsky.social · May 6

Online now -- a new Review:

"Molecular circuits for genomic recording of cellular events"
by Wei Chen & Junhong Choi (@choijunhong.bsky.social)

FREE to read till June 25th using this link:
authors.elsevier.com/a/1l2gMcQbJF...

Figure 1. Reconstructing cell signaling history with genomic recording circuits.

(A) Concept overview: cellular signals (e.g., environmental changes, signaling molecules, or cell–cell interactions) are converted into genomic recordings via event sensors in each cell. Recorded information is retrieved through sequencing assays to reconstruct each cell’s signaling history and its role in cell fate decisions. (B) Key advancements enabling genomic recording: the discovery of CRISPR-Cas9 provided precise, programmable genome editing. Single-cell profiling methods facilitated the accurate retrieval of genomic recordings. Advances in protein design and synthetic biology are transforming the development of cellular event sensors for genomic recording.

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Seungsoo Kim @seungsookim.bsky.social · Apr 25

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

Junior / Assistant Specialist: Kim Lab, Developmental & Cell Biology

University of California, Irvine is hiring. Apply now!

recruit.ap.uci.edu

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Stein Aerts @steinaerts.bsky.social · Apr 4

Very proud of two new preprints from the lab:
1) CREsted: to train sequence-to-function deep learning models on scATAC-seq atlases, and use them to decipher enhancer logic and design synthetic enhancers. This has been a wonderful lab-wide collaborative effort. www.biorxiv.org/content/10.1...

CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species

Sequence-based deep learning models have become the state of the art for the analysis of the genomic regulatory code. Particularly for transcriptional enhancers, deep learning models excel at decipher...

www.biorxiv.org

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Shelly Sakiyama-Elbert @drsakiyama.bsky.social · Mar 14

‘With the current turmoil, China could surpass the U.S. in the near future,’ Nobel Prize winner David Baker warns
www.wsj.com/articles/bio...

Bioscience Funding Confusion Threatens U.S. Innovation

‘With the current turmoil, China could surpass the U.S. in the near future,’ Nobel Prize winner David Baker warns.

www.wsj.com

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Richard Sever @richardsever.bsky.social · Mar 11

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

Homepage - openRxiv

openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.

openrxiv.org

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Washington State Department of Health @doh.wa.gov · Feb 12

We're expediting sex designation change requests on birth certificates. People born in WA who want to change the sex designation on their birth certificate can do so by filing a request with us. . doh.wa.gov/DesignationC...

Sex Designation Change on a Birth Certificate

We are currently processing requests in three (3) business days. Please allow up to two (2) weeks for delivery and mail time for ordered certificates.

doh.wa.gov

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Sri Kosuri @srikosuri.bsky.social · Feb 8

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

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