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Paul Geeleher

@pgeeleher.bsky.social
53 followers 70 following 18 posts

Compbio & precision medicine lab @stjude

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Reposted by Paul Geeleher
Ming Tommy Tang @tommytang.bsky.social · 19/12/2025
An open-source screening platform accelerates discovery of drug combinations www.nature.com/articles/s4...
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Reposted by Paul Geeleher
Dr. Jean Fan @jef.works · 29/08/2025
Our paper identifying evidence of off-target probe binding in the 10x Genomics Xenium Breast Gene Panel is now available as a reviewed preprint at #eLife elifesciences.org/reviewed-pre... We look forward to revising the paper to incorporate reviewer recommendations and other updates 🧵👇
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Reposted by Paul Geeleher
Science X / Phys.org @sciencex.bsky.social · 28/02/2025
Retinoic acid effectively treats metastasized neuroblastoma by exploiting the BMP signaling pathway in the bone marrow microenvironment, offering insights for future combination therapies. doi.org/g86pzp
medicalxpress.com
Scientists solve mystery of how the drug retinoic acid works to treat neuroblastoma
Neuroblastoma is a solid tumor that occurs in children. When high-risk, the disease has a poor prognosis. Decades ago, adding the drug retinoic acid to neuroblastoma treatment increased survival by 10–15%.
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Reposted by Paul Geeleher
Nature @nature.com · 10/04/2025
Nature research paper: An integrated large-scale photonic accelerator with ultralow latency go.nature.com/3R7tyvL
go.nature.com
An integrated large-scale photonic accelerator with ultralow latency - Nature
A large-scale photonic accelerator comprising more than 16,000 components integrated on a single chip to process MAC operations is described, demonstrating ultralow latency and reduced computing time compared with a commercially available GPU.
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Reposted by Paul Geeleher
Elizabeth McKenna @elizsmckenna.bsky.social · 02/04/2025
The April (and #AACR25) issue of Cancer Discovery is now online! The cover features work by Ling Cai, Nia Hammond, @faubert.bsky.social, @rjdlab.bsky.social & colleagues showing high glucose contribution to the TCA cycle is a feature of aggressive NSCLC - more here: aacrjournals.org/cancerdiscov...
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Reposted by Paul Geeleher
Nature @nature.com · 02/04/2025
Nature research paper: A natural experiment on the effect of herpes zoster vaccination on dementia go.nature.com/3XHRhq5
go.nature.com
A natural experiment on the effect of herpes zoster vaccination on dementia - Nature
Using a natural experiment that avoids common bias concerns, this study finds that the live-attenuated shingles vaccine reduced the probability of a new dementia diagnosis within a follow-up period of 7 years by approximately one-fifth.
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Reposted by Paul Geeleher
Petr Svoboda @svobodalab.bsky.social · 30/03/2025
Itai Yanai is now putting together with Oded Rechavi and others the Woodstock of Biology 2 & Night Science conference to integrate some of Itai's ideas into a scientific meeting. #theconferencetoendallconferences More info & registration here: woodstock.img.cas.cz
woodstock.img.cas.cz
Woodstock.Bio2 + Night Science 2025 | Courses & Meetings
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Reposted by Paul Geeleher
Science Magazine @science.org · 20/03/2025
In a new Science study, cryo–electron tomography captures the in-cell architecture of the mitochondrial respiratory chain, illuminating how the coordinated action of molecular machines drives life’s fundamental energy conversion. Learn more in this week's issue: scim.ag/3FA3Ygq
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Science Magazine @science.org · 23/03/2025
Polar bear fur remains ice-free in the Arctic cold thanks to the unique array of ingredients in its fur sebum, or hair grease, a #ScienceAdvances study finds. Learn more on #WorldBearDay:
scim.ag
Anti-icing properties of polar bear fur
Polar bears are able to minimize ice accumulation thanks to their hair oil.
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Reposted by Paul Geeleher
Nature @nature.com · 19/03/2025
Experiments suggest that an unusual magnetic material can help harness energy from the planet’s rotation. But not everyone is convinced. go.nature.com/4ixBNxj
go.nature.com
Can Earth’s rotation generate power? Physicists divided over controversial claim
Experiments suggest that an unusual magnetic material can help harness energy from the planet’s rotation. But not everyone is convinced.
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Reposted by Paul Geeleher
danapeer.bsky.social @danapeer.bsky.social · 19/03/2025
So proud of this work, this was a great collaboration and I highly recommend this read and tool. My own tweetorial shortly but @steglelab.bsky.social tutorial is great.
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Reposted by Paul Geeleher
Nature @nature.com · 16/03/2025
An Australian man in his forties has become the first person in the world to leave hospital with an artificial heart made of titanium The device could be a temporary measure for those waiting for a donor organ go.nature.com/427bLLh
go.nature.com
Man survives with titanium heart for 100 days – a world first
Nature - The device, to be tested in more people, could be used as a temporary measure for those waiting for a donor organ.
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Ruth Shouval @shouval.bsky.social · 13/03/2025
This is very much fitting, and exciting, for my first Blusky post 🤩 Thrilled to share our new study on CAFs and NK cells, now online 🌟 in CD_AACR!! t.co/vmq8ZyQ3KV
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Nature Communications @natcomms.nature.com · 12/03/2025
Bone morphogenetic protein signaling reported to be responsible for determining neuroblastoma cell fate and sensitivity to retinoic acid treatment doi.org/10.1038/s414... #CancerResearch
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Reposted by Paul Geeleher
Richard Sever @richardsever.bsky.social · 11/03/2025
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
openrxiv.org
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.
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Chiraag Kapadia @chiraagkapadia.bsky.social · 06/03/2025
Delighted to share my PhD thesis work is now published in @nature.com! This study tracks the journey of blood stem cells in aging mice, examining how the clonal dynmics of blood production change over time. A short 🧵1/n #aging #stemcells #clonalhematopoiesis www.nature.com/articles/s41...
nature.com
Clonal dynamics and somatic evolution of haematopoiesis in mouse - Nature
Isolating and studying haematopoietic stem cells in young and aged mice demonstrates evolutionary processes related to blood production and provides a framework for interpreting future work using labo...
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Nature @nature.com · 07/03/2025
A physicist has published an analysis that pokes holes in the protocol that underpins Microsoft’s claim to have created the first topological qubits. The critique comes amid mounting speculation about the validity of Microsoft’s claim. go.nature.com/4byvwyl
go.nature.com
Microsoft quantum computing 'breakthrough' faces fresh challenge
Analysis pokes holes in protocol that underpins Microsoft’s claim to have created the first topological qubits.
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Reposted by Paul Geeleher
danapeer.bsky.social @danapeer.bsky.social · 07/03/2025
1) I am delighted to share a manuscript long in the making (7 years), elucidating the forces that shape metastatic adaptation PDAC using scRNA-seq across multiple organs from a rapid autopsy combined with a powerful new clonal phylogeny inference algorithm www.biorxiv.org/content/10.1...
biorxiv.org
Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer
Metastasis is the leading cause of cancer deaths; nonetheless, how tumor cells adapt to vastly different organ contexts is largely unknown. To investigate this question, we generated a transcriptomic ...
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Nuria Lopez-Bigas @nlbigas.bsky.social · 05/03/2025
Seven New Cancer Grand Challenges Announced www.cancergrandchallenges.org/new-challenges With awards of up to £20m ($25m). Expressions of Interest are now open. @cancergrand.bsky.social #CancerGrandChallenges
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Paul Geeleher @pgeeleher.bsky.social · 03/03/2025
Can we treat cancer by forcing cancer cells to differentiate? Retinoids are unique cancer drugs that, according to textbooks, make cancer cells mature and lose their malignant behavior. In our new paper, we reveal there’s more to how they really work… 1/n www.nature.com/articles/s41...
nature.com
Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid - Nature Communications
Retinoic acid is known to be effective against bone marrow metastatic neuroblastoma cells, but not primary tumors. Here, authors discover that bone morphogenetic protein signaling is responsible for d...
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St. Jude Children's Research Hospital @stjuderesearch.bsky.social · 28/02/2025
Researchers at St. Jude Children's Research Hospital have uncovered the mechanism behind retinoic acid's selective killing of metastatic neuroblastoma cells. This discovery may pave the way for improved combination therapies. ow.ly/PgBl50V8hZn
ow.ly
St. Jude scientists solve mystery of how the drug retinoic acid works to treat neuroblastoma
Find new research showing how retinoic acid hijacks a developmental pathway in metastasized neuroblastoma in the bone marrow, solving a 50 year-long mystery.
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Elizabeth McKenna @elizsmckenna.bsky.social · 07/02/2025
The February issue of Cancer Discovery is now online! The cover features "The Evolutionary Forest of Pancreatic Cancer" by Katelyn Mullen, @braphael.bsky.social, Christine Iacobuzio-Donahue, and colleagues. Read the paper and much more here: aacrjournals.org/cancerdiscov...
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Reposted by Paul Geeleher
Nature Biotechnology @natbiotech.nature.com · 04/02/2025
Implantation of engineered adipocytes suppresses tumor progression in cancer models - @nadavahituv.bsky.social go.nature.com/4gqhxvw
go.nature.com
Implantation of engineered adipocytes suppresses tumor progression in cancer models - Nature Biotechnology
Adipose manipulation transplantation can reduce tumor growth and proliferation in vitro and in mouse models.
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Jacob Schreiber @jmschreiber91.bsky.social · 05/02/2025
Insanely good news if this holds up. Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor www.science.org/doi/10.1126/...
science.org
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor
Prion disease is caused by misfolding of the prion protein (PrP) into pathogenic self-propagating conformations, leading to rapid-onset dementia and death. However, elimination of endogenous PrP halts...
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Nature Cancer @natcancer.nature.com · 26/01/2025
Online now! TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states 🖊️by Ilaria Panzeri & John Andrew Pospisilik and colleagues @ilariapanzeri.bsky.social @andrewpospisilik.bsky.social 👇 www.nature.com/articles/s43...
nature.com
TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states - Nature Cancer
Panzeri et al. use a Trim28+/D9 mouse model with intrinsic developmental heterogeneity to show that ‘heavy’ and ‘light’ developmental morphs exhibit different timing, type and severity of cancer, link...
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Anshul Kundaje @anshulkundaje.bsky.social · 26/01/2025
Beautifully elegant work on integrating LoF, GWAS & Perturb-seq data to build causal paths from regulators to genes / programs to phenotype. And it didn't require a foundational virtual cell model (well almost ... gene & protein embeddings r used in GeneBayes)! 😜
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Akshat Nigam @akshatai.bsky.social · 22/01/2025
Excited to share our latest work, published this morning in Nature Biotechnology! 🎉 We developed a hybrid quantum computing-enhanced generative model to design KRAS inhibitors. Check it out here: rdcu.be/d68Fs. Some fascinating insights along the way:
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Jonathan Pritchard @jkpritch.bsky.social · 26/01/2025
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
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Paul Geeleher @pgeeleher.bsky.social · 25/01/2025
Nice review of an interesting/unexpected concept, “Hypoxia as a medicine”. www.science.org/doi/10.1126/...
science.org
Hypoxia as a medicine
Although hypoxia is often pathologic, chronic continuous hypoxia has shown promise in many disease models, inspiring a roadmap for clinical translation.
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Reposted by Paul Geeleher
Nature @nature.com · 20/01/2025
“By moving the technology as close as possible to the biology that we want to study, we can all of a sudden see a whole new view of life" ‘Lab vans’ and other facilities can bring researchers closer to what they study go.nature.com/4gSE3OF
go.nature.com
Science on the go: bringing labs into the field
‘Lab vans’ and other facilities can bring researchers closer to what they study.
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Paul Geeleher @pgeeleher.bsky.social · 20/01/2025
Scientific progress doesn’t happen because every experiment or analysis works perfectly. It’s determined by how you respond when your data defies your expectations—returning the next day, reevaluating your assumptions, refining your approach, and continuing to move forward.
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Paul Geeleher @pgeeleher.bsky.social · 10/01/2025
Unsatisfied with UMAPs and ‘language models’ for single-cell RNA-seq? Looking for a better way to model your data? Check out CSI-GEP—our new approach just published in @CellGenomics 1/6: www.cell.com/cell-genomic...
cell.com
CSI-GEP: A GPU-based unsupervised machine learning approach for recovering gene expression programs in atlas-scale single-cell RNA-seq data
Liu et al. develop CSI-GEP, an algorithm for recovering gene expression programs (GEPs) from single-cell RNA-seq data. GEPs can correspond to cell types or the activity of biological processes. CSI-GEP provides a better model for single-cell RNA-seq data compared to hard clustering. It outperforms existing methods in simulated and real data.
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Anshul Kundaje @anshulkundaje.bsky.social · 25/12/2024
Our ChromBPNet preprint out! www.biorxiv.org/content/10.1... Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
biorxiv.org
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...
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Caleb Lareau @caleblareau.bsky.social · 08/01/2025
Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n www.nature.com/articles/s41...
nature.com
Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics
Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...
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danapeer.bsky.social @danapeer.bsky.social · 09/01/2025
This is an amazing technology, we are already using it ourselves and it is transformative. Kudus to @caleblareau.bsky.social and @ronanchaligne.bsky.social and their teams.
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Oded Rechavi @odedrechavi.bsky.social · 26/11/2024
When you give a lab meeting presentation sitting down
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