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charliebell.bsky.social

@charliebell.bsky.social
88 followers 89 following 17 posts

Senior post-doc in the Faulkner lab ARC DECRA Fellow Interested in how gene regulatory mechanisms contribute to biological complexity

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Reposted by @charliebell.bsky.social
Nature @nature.com · 13/09/2026
Scientists are probing whether language models trained on historical data can reproduce creative breakthroughs go.nature.com/4czwufO
go.nature.com
The Einstein test: what happens when AI tries to rediscover relativity?
Nature - Scientists are probing whether language models trained on historical data can reproduce creative breakthroughs.
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Pablo Navarro @pablonavarrolab.bsky.social · 03/06/2026
Epigenetics means different things for different people. In this workshop we will discuss two major views anchored on transcriptional memory: chromatin vs networks. Come and share with us our excitement for the topic and the magnificent place, the Andalusian Baeza. urldefense.com/v3/__https:/...
urldefense.com
Workshop Transcriptional memory in health and disease
The idea that cells remember past states to prepare their future endeavors has split into two parallel languages that rarely converse. On one side, chromatin epigenetics defines inheritance through th...
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mvstaller.bsky.social @mvstaller.bsky.social · 17/08/2026
Our new paper went live today! We build biophysical neural networks to predict transcriptional activation domains from protein sequence. We interpret these neural networks to show how acidic and hydrophobic residues control abundance and activation strength. www.sciencedirect.com/science/arti...
sciencedirect.com
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charliebell.bsky.social @charliebell.bsky.social · 31/07/2026
Happy to have played my part is what really was a whole lab effort. Congrats to all, but particularly to Geoff who was the mastermind behind it all
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Geoff Faulkner @faulknerlab.bsky.social · 31/07/2026
If you can't otherwise access it, here's a link to read our recent Science paper for free (valid for the first 2,000 clicks!): www.science.org/eprint/BYBPQ...
science.org
X-chromosome inactivation draws L1 mutagenesis to the human X chromosome
X-chromosome inactivation (XCI) enables gene dosage compensation in XX eutherians. Long interspersed element-1 (LINE-1 or L1) retrotransposons are unusually abundant on the human X chromosome and are ...
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Reposted by @charliebell.bsky.social
Nature @nature.com · 30/07/2026
Nature research paper: Intestinal stem cells count self-renewal divisions to switch multipotency go.nature.com/45uYCwn
go.nature.com
Intestinal stem cells count self-renewal divisions to switch multipotency - Nature
In Drosophila, cell fate switching in adult intestinal stem cells is determined through an epigenetic mechanism in which these cells count divisions, switching from producing enterocytes to producing an enteroendocrine mother cell every ninth division.
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Di Jiang @dijiang319.bsky.social · 30/07/2026
Why is the X chromosome rich in L1 mobile elements? @science.org X-chromosome inactivation draws L1 mutagenesis to the human X chromosome | Science www.science.org/doi/10.1126/...
science.org
X-chromosome inactivation draws L1 mutagenesis to the human X chromosome
X-chromosome inactivation (XCI) enables gene dosage compensation in XX eutherians. Long interspersed element-1 (LINE-1 or L1) retrotransposons are unusually abundant on the human X chromosome and are ...
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Reposted by @charliebell.bsky.social
Geoff Faulkner @faulknerlab.bsky.social · 30/07/2026
Our study published today @science.org shows that X-chromosome inactivation (XCI) attracts L1 mutations to the human X chromosome: doi.org/10.1126/scie... With outstanding Perspective from @aurelien-doucet.bsky.social & @retrogenomics.bsky.social: doi.org/10.1126/scie...
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Vicky C Yang @vcyang.bsky.social · 02/06/2026
Between 1985--2023, MIT's faculty grew 9%. Administrative staff grew 189%. 📈 Why? In new @pnas.org paper, we use dynamical system model to show administrative bloat can emerge without empire-building--just from well-intentioned problem-solving gone awry www.pnas.org/doi/10.1073/...
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Science Magazine @science.org · 29/05/2026
Iron-rich immune cells within homing pigeons’ livers seem to give the birds their magnetic compass. scim.ag/4tYuK5r
scim.ag
‘Mind-blowing’: Iron-rich immune cells help homing pigeons navigate
New study identifies a surprising mechanism for sensing Earth’s magnetic field
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Will Ratcliff @wcratcliff.bsky.social · 13/05/2026
1/23 New preprint! Been thinking about the origin of cellular life. Specifically, how protocells (or *any* compartments) just aren't enough to support the evolution of increasingly complex cells. You gotta de-Darwinize the parts! The ribosome/genome do this. www.biorxiv.org/content/10.6...
biorxiv.org
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 13/05/2026
Beautiful new study from @elphegenoralab.bsky.social and Leonid Mirny's lab: Cohesin-bridged encounters mediate enhancer-promoter communication, predicting how enhancer effect scales with genomic distance and - for the first time - how CTCF sites modulate enhancer-promoter communciation! 🧵 below
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The Company of Biologists @biologists.bsky.social · 08/05/2026
From one centenarian to another: we wish Sir David Attenborough a very happy 100th birthday and thank him for all he has done to aid people's understanding of and - even more importantly - appreciation for the natural world.
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Nature @nature.com · 08/05/2026
Iconic British naturalist David Attenborough, whose work has shaped science for decades, turns 100 today go.nature.com/4dbRFUB
go.nature.com
A life in pictures: Celebrating Attenborough at 100
As the British naturalist celebrates a milestone birthday, we take a look at how his work has shaped science.
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Ricard Solé @ricardsole.bsky.social · 30/04/2026
What happens when AI starts to evolve on its own? As systems become capable of self-improvement and replication, open-ended “ecosystem” dynamics could drive behaviors like deception and manipulation, much like in biological evolution. Check this @pnas.org paper: www.pnas.org/doi/pdf/10.1...
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J. Craig Venter Institute @jcvi.org · 30/04/2026
It is with great sadness that we announce J. Craig Venter has died. 🧪🧬 www.jcvi.org/media-center...
jcvi.org
J. Craig Venter, genomics pioneer and founder of JCVI and Diploid Genomics, Inc., dies at 79
La Jolla, California—April 29, 2026—The J. Craig Venter Institute (JCVI) announced that J. Craig Venter, Ph.D., the Institute’s founder, board...
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James Briscoe @jamesbriscoe.bsky.social · 09/03/2026
New Perspective form Rory Maizels & me: "Gene regulatory networks: from correlative models to causal explanations" Gene regulatory networks are supposed to give us mechanistic explanations of development, so why are we drowning in 'hairballs' of statistical correlations? rdcu.be/e7zx7
rdcu.be
Gene regulatory networks: from correlative models to causal explanations
Nature Reviews Genetics - In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without...
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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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Nature Cell Biology @natcellbio.nature.com · 13/02/2026
☕Neville, Ferguson et al. show that non-canonical Polycomb repressive complex 1.1-mediated gene silencing is antagonized by DOT1L and is required for the therapeutic efficacy of Menin and DOT1L inhibitors in mixed-lineage leukaemia. bit.ly/46MZ3Di
bit.ly
DOT1L provides transcriptional memory through PRC1.1 antagonism - Nature Cell Biology
Neville, Ferguson et al. show that non-canonical Polycomb repressive complex 1.1-mediated gene silencing is antagonized by DOT1L and is required for the therapeutic efficacy of Menin and DOT1L inhibit...
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Alex Holehouse @alexholehouse.bsky.social · 12/02/2026
Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now? www.nature.com/articles/s41... More functional data, many thousands of words removed, and a few other updates from last year's preprint.
nature.com
Sequence and chemical specificity define the functional landscape of intrinsically disordered regions - Nature Cell Biology
Langstein-Skora, Schmid, Huth et al. propose that intrinsically disordered region functionality can be driven by the interplay between linear binding motifs and contextual chemical characteristics suc...
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Quanta Magazine @quantamagazine.org · 09/02/2026
“A bird with a 10-gram brain is doing pretty much the same as a chimp with a 400-gram brain,” said Onur Güntürkün, who studies brain structures at Ruhr University Bochum in Germany. “How is it possible?”
quantamagazine.org
Intelligence Evolved at Least Twice in Vertebrate Animals | Quanta Magazine
Complex neural circuits likely arose independently in birds and mammals, suggesting that vertebrates evolved intelligence multiple times.
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bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 10/02/2026
A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements www.biorxiv.org/content/10.64898/20…
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Chen Davidovich @davidovichlab.bsky.social · 03/02/2026
H3K79me2/3 is sufficient to antagonise PRC1 www.nature.com/articles/s41...
nature.com
DOT1L provides transcriptional memory through PRC1.1 antagonism - Nature Cell Biology
Neville, Ferguson et al. show that non-canonical Polycomb repressive complex 1.1-mediated gene silencing is antagonized by DOT1L and is required for the therapeutic efficacy of Menin and DOT1L inhibit...
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charliebell.bsky.social @charliebell.bsky.social · 03/02/2026
www.nature.com/articles/s41... happy i could be a part of this paper from the Gilan lab out now. Along with many other things, it provides strong evidence of chromatin memory for gene activation, and suggests that DOT1L is the missing link balancing the fast and slow arms of the MLL/Polycomb axis
nature.com
DOT1L provides transcriptional memory through PRC1.1 antagonism - Nature Cell Biology
Neville, Ferguson et al. show that non-canonical Polycomb repressive complex 1.1-mediated gene silencing is antagonized by DOT1L and is required for the therapeutic efficacy of Menin and DOT1L inhibit...
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Nature @nature.com · 21/01/2026
Nature research paper: Construction of complex and diverse DNA sequences using DNA three-way junctions go.nature.com/4qu2ExZ
go.nature.com
Construction of complex and diverse DNA sequences using DNA three-way junctions - Nature
Sidewinder enables high-fidelity DNA assembly by separating the information that guides assembly from the final assembled sequence.
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Scott Berry @scottbscience.bsky.social · 15/01/2026
What happens when you suddenly remove half of an essential enzyme from cells? 🤔 We watched in real-time as cells deploy multiple backup strategies to buffer against changes in RNA Pol II abundance. Our lab's new preprint 👇 bit.ly/4pyPgax
bit.ly
Hierarchical buffering of cellular RNA polymerase II pools maintains transcriptional homeostasis
RNA polymerase II (Pol II) abundance and transcriptional output are coordinated across diverse conditions to maintain mRNA homeostasis. To determine whether Pol II acts as a limiting factor for transc...
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Eileen Furlong @eileen-furlong.bsky.social · 11/12/2025
Can't believe it's that time of year - registration already open for next year's Transcription & Chromatin meeting. Almost half the talks are selected from the abstracts, so register soon before it fills up. This is a very lively meeting, with plenty of time to discuss over dinner & at the bar
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Anthony Hannan @anthonyjhannan.bsky.social · 28/09/2025
www.theage.com.au/politics/fed...
theage.com.au
Billions going unspent from Australia’s $24b medical research fund
Costings commissioned by independent MP Monique Ryan reveal the government could double how much funding it gives to innovative health research each year.
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 24/09/2025
18/ At large genomic distance, long encounters (=the important ones) are only due to loop extrusion; but at short genomic distance they can also be due to random collisions. This is why enhancers are no sensitive to loss of extrusion when they are close, but sensitive when they are far!
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Luca Giorgetti lab @FMI @lucagiorgetti.bsky.social · 24/09/2025
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication. www.biorxiv.org/content/10.1... A🧵👇
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 15/07/2025
We are looking for a student to continue our work on chromatin evolution: www.nature.com/articles/s41... www.biorxiv.org/content/10.1... The project with @seanamontgomery.bsky.social will focus on chromatin state readers across eukaryotes. More info: recruitment.crg.eu/content/jobs...
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Carl de Boer @carldeboer.bsky.social · 04/09/2025
New preprint from the lab 🎉 on the evolution of gene regulatory network complexity, where we tested whether sexual recombination promotes more complex GRNs using biochemically-inspired evolutionary simulations 🧐. Bluetorial from 1st author @chapelmadison.bsky.social 👇
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Molecular Cell @cp-molcell.bsky.social · 27/06/2025
Online Now: Regulation of somatic hypermutation by higher-order chromatin structure Online now:
dlvr.it
Regulation of somatic hypermutation by higher-order chromatin structure
Schoeberl et al. employ Tri-C to unravel the higher-order chromatin architecture underpinning the co-transcriptional mutagenesis of immunoglobulin genes during antibody maturation in human B cells. They provide evidence that antibody maturation occurs within a dynamic multiway hub wherein transcription and mutation of different genes occur non-competitively.
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Oded Rechavi @odedrechavi.bsky.social · 27/06/2025
So cool, a novel archaeon with a super small genome and no metabolic genes! "An unprecedented level of metabolic dependence on a host, a condition that challenges the functional distinctions between minimal cellular life and viruses." www.biorxiv.org/content/10.1...
biorxiv.org
A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
Defining the minimal genetic requirements for cellular life remains a fundamental question in biology. Genomic exploration continually reveals novel microbial lineages, often exhibiting extreme genome...
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Levayer Lab @levayerr.bsky.social · 21/05/2025
Many cells during development are exposed to caspase activation and yet survive. Why some die and not others ? We found out that the memory of previous caspase activation bias significantly later death comitment and bias death distribution and single cell decision www.biorxiv.org/content/10.1...
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Lars Velten @larsplus.bsky.social · 21/05/2025
Out @nature.com: Clonal tracing with somatic epimutations 🧬 Single cell methylome encodes cell state & clonal identity 🔨 EPI-Clone reads out both (+mutations, +RNA) at scale 🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations doi.org/10.1038/s415... 🧵
doi.org
Clonal tracing with somatic epimutations reveals dynamics of blood ageing - Nature
The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing th...
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Lars Velten @larsplus.bsky.social · 08/05/2025
Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis 🧬🩸 screen of fully synthetic enhancers in blood progenitors 🤖 AI that creates new cell state specific enhancers 🔍 negative synergies between TFs lead to specificity! www.cell.com/cell/fulltex... 🧵
cell.com
Design principles of cell-state-specific enhancers in hematopoiesis
Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread dual activator-repressor function of transcription factors (TFs) and enables the model-guided design of cell-state-sp...
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Di Jiang @dijiang319.bsky.social · 24/04/2025
🐛🕷️🕸️ @science.org Hawaiian caterpillar patrols spiderwebs camouflaged in insect prey’s body parts | Science www.science.org/doi/10.1126/... #entomology
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Nature @nature.com · 09/04/2025
Nature research paper: DNA-guided transcription factor interactions extend human gene regulatory code go.nature.com/4j13XRc
go.nature.com
DNA-guided transcription factor interactions extend human gene regulatory code - Nature
A large-scale analysis of DNA-bound transcription factors (TFs) shows how the presence of DNA markedly affects the landscape of TF interactions, and identifies composite motifs that are recognized by complexes of TFs rather than by individual ones.
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charliebell.bsky.social @charliebell.bsky.social · 09/04/2025
www.nature.com/articles/s41...
nature.com
DNA-guided transcription factor interactions extend human gene regulatory code - Nature
A large-scale analysis of DNA-bound transcription factors (TFs) shows how the presence of DNA markedly affects the landscape of TF interactions, and identifies composite motifs that are recognized by ...
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Reposted by @charliebell.bsky.social
Kaia Mattioli @kaiamattioli.bsky.social · 26/03/2025
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell! key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity many are "negative regulators" & misexpressed in cancer www.sciencedirect.com/science/arti...
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Chen Davidovich @davidovichlab.bsky.social · 15/03/2025
1/ H3K27me3 mimicry has repeatedly emerged through evolution, but what's the physiological relevance? We show that JARID2 and PALI1 mimic H3K27me3 to antagonise PRC2 in vivo and restrict the spread of Polycomb domains. 🧵 www.biorxiv.org/content/10.1...
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The Groth lab @grothlab.bsky.social · 19/02/2025
𝐇𝐨𝐰 𝐝𝐨 𝐜𝐞𝐥𝐥𝐬 𝐫𝐞𝐦𝐞𝐦𝐛𝐞𝐫 𝐰𝐡𝐨 𝐭𝐡𝐞𝐲 𝐚𝐫𝐞 𝐚𝐟𝐭𝐞𝐫 𝐃𝐍𝐀 𝐫𝐞𝐩𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧? Our new study “Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability” is out in 𝘚𝘤𝘪𝘦𝘯𝘤𝘦 𝘈𝘥𝘷𝘢𝘯𝘤𝘦𝘴. Led by @lleonie.bsky.social @biranalva.bsky.social 🧵 More below👇
tinyurl.com
Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability
Losing parental histones during DNA replication fork passage challenges differentiation competence and cell viability.
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Chenxin Li, PhD @chenxinli2.bsky.social · 30/01/2025
Yeah I don’t really care how they made the plasmids. Just give me the genbank file.
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Nature @nature.com · 29/01/2025
Not only does Bennu contain all 5 of the nucleobases that form DNA and RNA on Earth and 14 of the 20 amino acids found in known proteins, the asteroid’s amino acids hold a surprise go.nature.com/4hDtGhL
go.nature.com
Asteroid fragments upend theory of how life on Earth bloomed
Samples from Bennu contain the chemical building blocks of life - but with a twist.
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charliebell.bsky.social @charliebell.bsky.social · 30/12/2024
"Everything in epigenetics is circular". Here, we explore how memory that is stored locally on chromatin has a crucial role in stabilising cellular state, updating our view of the epigenetic landscape from one shaped by the genotype, to one moulded by experience doi.org/10.1186/s130...
doi.org
Chromatin-based memory as a self-stabilizing influence on cell identity - Genome Biology
Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states...
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the Node @the-node.bsky.social · 27/12/2024
📢Vote for the 2024 Development cover image of the year @dev-journal.bsky.social featured 24 cover images in 2024. Now is the chance to pick your favourite! Browse through the images and vote by 13 Jan: thenode.biologists.com/vote-for-the… #DevBio
Collage of the 24 Development cover images in 2024
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James Briscoe @jamesbriscoe.bsky.social · 19/12/2024
Our latest: how to generate the notochord "Timely TGFβ signalling inhibition induces notochord" A thread: www.nature.com/articles/s41...
nature.com
Timely TGFβ signalling inhibition induces notochord - Nature
Through analysis of developing chick embryos and in vitro differentiation of embryonic stem cells, a study develops a method to generate a model of the human trunk with a notochord.
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The Francis Crick Institute @crick.ac.uk · 18/12/2024
Crick researchers have recreated a tissue in the lab that acts like a developing embryo’s navigation system, directing cells where to build the spine and nervous system. The findings were led by Tiago Rito with senior author @jamesbriscoe@bsky.social www.crick.ac.uk/news/2024-12...
crick.ac.uk
Building a backbone: scientists recreate the body’s ‘GPS system’ in the lab
Scientists at the Francis Crick Institute have generated human stem cell models1 which, for the first time, contain notochord – a tissue in the developing embryo that acts like a navigation system, di...
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