Matouš Elphick
@matous-elphick.bsky.social
PhD Student @ Crick, Imperial and ICR | Spatial and computational approaches to understand cancer evo, TME and ECM.
Bio: https://matouse.github.io
Bio: https://matouse.github.io
Reposted by Matouš Elphick
#paper!
X-rays can resolve #ultrastructure in tissues non-destructively.
www.nature.com/articles/s41...
Shoutout to key collaborators at @crick.ac.uk and @psich.bsky.social Ana Diaz, @adrianawanner.bsky.social and @andreas-t-schaefer.bsky.social, and to the whole team that made this possible.
X-rays can resolve #ultrastructure in tissues non-destructively.
www.nature.com/articles/s41...
Shoutout to key collaborators at @crick.ac.uk and @psich.bsky.social Ana Diaz, @adrianawanner.bsky.social and @andreas-t-schaefer.bsky.social, and to the whole team that made this possible.
Nondestructive X-ray tomography of brain tissue ultrastructure - Nature Methods
Optimizations of X-ray nanotomography including the choice of resin allows high-resolution imaging of mouse brain tissue, approaching the resolution of volume electron microscopy. Since it does not re...
www.nature.com
November 27, 2025 at 11:51 AM
#paper!
X-rays can resolve #ultrastructure in tissues non-destructively.
www.nature.com/articles/s41...
Shoutout to key collaborators at @crick.ac.uk and @psich.bsky.social Ana Diaz, @adrianawanner.bsky.social and @andreas-t-schaefer.bsky.social, and to the whole team that made this possible.
X-rays can resolve #ultrastructure in tissues non-destructively.
www.nature.com/articles/s41...
Shoutout to key collaborators at @crick.ac.uk and @psich.bsky.social Ana Diaz, @adrianawanner.bsky.social and @andreas-t-schaefer.bsky.social, and to the whole team that made this possible.
Reposted by Matouš Elphick
u-Segment3D: a universal framework for 2D to 3D cell segmentation that generalizes across cell types and imaging modalities.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods
u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...
www.nature.com
November 12, 2025 at 2:58 PM
u-Segment3D: a universal framework for 2D to 3D cell segmentation that generalizes across cell types and imaging modalities.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Matouš Elphick
1/17 🧵
🙌Thrilled to share our first hard-core immunology paper out today in Nature Genetics! 👇
➡️We unravel how TGFβ suppresses the innate and adaptive immune system in microsatellite stable colorectal cancer (MSS CRC).
Very proud of the team and efforts behind it.
www.nature.com/articles/s41...
🙌Thrilled to share our first hard-core immunology paper out today in Nature Genetics! 👇
➡️We unravel how TGFβ suppresses the innate and adaptive immune system in microsatellite stable colorectal cancer (MSS CRC).
Very proud of the team and efforts behind it.
www.nature.com/articles/s41...
TGF-β builds a dual immune barrier in colorectal cancer by impairing T cell recruitment and instructing immunosuppressive SPP1+ macrophages - Nature Genetics
Targeting TGFBR1 in transplantable mouse colorectal tumor organoids improves response to anti-PD-L1 therapy. Mechanistically, TGF-β abrogates clonal expansion of T effector and memory phenotypes and i...
www.nature.com
November 7, 2025 at 12:30 PM
1/17 🧵
🙌Thrilled to share our first hard-core immunology paper out today in Nature Genetics! 👇
➡️We unravel how TGFβ suppresses the innate and adaptive immune system in microsatellite stable colorectal cancer (MSS CRC).
Very proud of the team and efforts behind it.
www.nature.com/articles/s41...
🙌Thrilled to share our first hard-core immunology paper out today in Nature Genetics! 👇
➡️We unravel how TGFβ suppresses the innate and adaptive immune system in microsatellite stable colorectal cancer (MSS CRC).
Very proud of the team and efforts behind it.
www.nature.com/articles/s41...
Reposted by Matouš Elphick
How does immunotherapy work, and why do some patients respond while others don’t?
Book our free talk by Samra Turajlic, head of the Cancer Dynamics Lab here at the Crick, Director of @cruk-mi.bsky.social and head of the UK-wide MANIFEST programme.
www.eventbrite.co.uk/e/crick-cras...
Book our free talk by Samra Turajlic, head of the Cancer Dynamics Lab here at the Crick, Director of @cruk-mi.bsky.social and head of the UK-wide MANIFEST programme.
www.eventbrite.co.uk/e/crick-cras...
Crick Crash Course: Immunotherapy
Our series of morning lectures sharing science from across the Crick in a simple and accessible way continues.
www.eventbrite.co.uk
November 6, 2025 at 9:15 AM
How does immunotherapy work, and why do some patients respond while others don’t?
Book our free talk by Samra Turajlic, head of the Cancer Dynamics Lab here at the Crick, Director of @cruk-mi.bsky.social and head of the UK-wide MANIFEST programme.
www.eventbrite.co.uk/e/crick-cras...
Book our free talk by Samra Turajlic, head of the Cancer Dynamics Lab here at the Crick, Director of @cruk-mi.bsky.social and head of the UK-wide MANIFEST programme.
www.eventbrite.co.uk/e/crick-cras...
Reposted by Matouš Elphick
Fat storage in the body relies on specialized structures called lipid droplets. In a new Science study, researchers identified the microprotein adipogenin as a regulator of adipocyte lipid droplet size, revealing a key mechanism in lipid homeostasis.
Learn more this week: https://scim.ag/4nFEGO7
Learn more this week: https://scim.ag/4nFEGO7
November 6, 2025 at 7:05 PM
Fat storage in the body relies on specialized structures called lipid droplets. In a new Science study, researchers identified the microprotein adipogenin as a regulator of adipocyte lipid droplet size, revealing a key mechanism in lipid homeostasis.
Learn more this week: https://scim.ag/4nFEGO7
Learn more this week: https://scim.ag/4nFEGO7
Reposted by Matouš Elphick
Scientists point to a long list of findings that emerged out of fundamental research, the type of studies the US government is cutting, and went on to change the world. Nature lists a few of their examples. 🧪
7 basic science discoveries that changed the world
Ozempic, MRI machines and flat screen televisions all emerged out of fundamental research decades earlier — the very types of study being slashed by the US government.
go.nature.com
November 7, 2025 at 2:16 AM
Scientists point to a long list of findings that emerged out of fundamental research, the type of studies the US government is cutting, and went on to change the world. Nature lists a few of their examples. 🧪
Reposted by Matouš Elphick
Happy to share STORIES out now on Nature Methods
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport - Nature Methods
By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data.
www.nature.com
November 4, 2025 at 7:25 AM
Happy to share STORIES out now on Nature Methods
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.
Led by Geert-Jan Huizing and Jules Samaran
www.nature.com/articles/s41...
@pasteur.fr
Reposted by Matouš Elphick
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
Reposted by Matouš Elphick
@lucianomartelotto, not on Bluesky, on a new Spatial RNA imaging method, PRISM. www.nature.com/articles/s41... Now added to #SingleCell #Spatial #Method bit.ly/scmethodstable
High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes - Nature Biotechnology
The 64-plex fluorescence imaging of RNA in tissues is achieved in one imaging cycle
www.nature.com
October 31, 2025 at 10:08 AM
@lucianomartelotto, not on Bluesky, on a new Spatial RNA imaging method, PRISM. www.nature.com/articles/s41... Now added to #SingleCell #Spatial #Method bit.ly/scmethodstable
Reposted by Matouš Elphick
High-resolution imaging mass cytometry enables highly multiplexed imaging of nuclear foci and mitochondrial networks.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
October 30, 2025 at 3:41 PM
High-resolution imaging mass cytometry enables highly multiplexed imaging of nuclear foci and mitochondrial networks.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Matouš Elphick
🧬🩸 Cancer cells “tighten the belt” on their neighbors — Institut Pasteur, CNRS & Université Paris Cité uncover a mechanical killing strategy: tumor cells surround healthy ones and squeeze them to death via a contractile belt.
Read more 👉 research.pasteur.fr/en/news/canc...
Read more 👉 research.pasteur.fr/en/news/canc...
Cancer cells tighten the belt around their neighbours forcing them to die - Research
Cancerous cells can expand in our tissues by killing neighbouring healthy cells. Researchers in Institut Pasteur, CNRS and the Université Paris Cité found a new mechanism used by cancerous cells to ki...
research.pasteur.fr
October 22, 2025 at 10:03 AM
🧬🩸 Cancer cells “tighten the belt” on their neighbors — Institut Pasteur, CNRS & Université Paris Cité uncover a mechanical killing strategy: tumor cells surround healthy ones and squeeze them to death via a contractile belt.
Read more 👉 research.pasteur.fr/en/news/canc...
Read more 👉 research.pasteur.fr/en/news/canc...
Reposted by Matouš Elphick
Researchers at the Crick found that virgin female mice can become aggressive towards pups when hungry, but only in certain hormonal states.
It highlights the importance of understanding hormones when observing how different physical states interact in the brain.
www.crick.ac.uk/news/2025-10...
It highlights the importance of understanding hormones when observing how different physical states interact in the brain.
www.crick.ac.uk/news/2025-10...
Hunger influences the behaviour of female mice towards pups
Researchers find that virgin female mice can become aggressive towards pups when hungry, but only in certain hormonal states.
www.crick.ac.uk
October 22, 2025 at 3:14 PM
Researchers at the Crick found that virgin female mice can become aggressive towards pups when hungry, but only in certain hormonal states.
It highlights the importance of understanding hormones when observing how different physical states interact in the brain.
www.crick.ac.uk/news/2025-10...
It highlights the importance of understanding hormones when observing how different physical states interact in the brain.
www.crick.ac.uk/news/2025-10...
Reposted by Matouš Elphick
👏We are pleased to announce Laura Marandino as the 2025 recipient of the ESMO José Baselga Fellowship for Clinician Scientists. This fellowship, supported by AZ, provides the resources & #mentorship for #ClinicianScientists. #ESMO25
October 20, 2025 at 1:07 PM
👏We are pleased to announce Laura Marandino as the 2025 recipient of the ESMO José Baselga Fellowship for Clinician Scientists. This fellowship, supported by AZ, provides the resources & #mentorship for #ClinicianScientists. #ESMO25
Reposted by Matouš Elphick
@science.org High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer | Science www.science.org/doi/10.1126/... @lukekoblan.bsky.social @weissmanlab.bsky.social @zhuanglab.bsky.social @whiteheadinstitute.bsky.social et al.
October 16, 2025 at 7:07 PM
@science.org High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer | Science www.science.org/doi/10.1126/... @lukekoblan.bsky.social @weissmanlab.bsky.social @zhuanglab.bsky.social @whiteheadinstitute.bsky.social et al.
Reposted by Matouš Elphick
Ultra-sensitive DNA sequencing maps mutations that precede cancer @nature.com @imartincorena.bsky.social
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/s41... @bbglab.bsky.social @irbbarcelona.org @nlbigas.bsky.social
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/s41... @bbglab.bsky.social @irbbarcelona.org @nlbigas.bsky.social
Sex and smoking bias in the selection of somatic mutations in human bladder - Nature
Sex bias and association with smoking history identified in the landscape of driver mutations and clonal expansions in normal human bladder tissue may explain the higher bladder cancer risk in men and smokers.
www.nature.com
October 8, 2025 at 5:22 PM
Ultra-sensitive DNA sequencing maps mutations that precede cancer @nature.com @imartincorena.bsky.social
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/s41... @bbglab.bsky.social @irbbarcelona.org @nlbigas.bsky.social
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/s41... @bbglab.bsky.social @irbbarcelona.org @nlbigas.bsky.social
Reposted by Matouš Elphick
Nimbus predicts the likelihood of marker positivity from multiplexed image data in single cells.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Automated classification of cellular expression in multiplexed imaging data with Nimbus - Nature Methods
Nimbus, a deep learning model, uses a large multiplexed imaging dataset to predict the likelihood of marker positivity in single cells.
www.nature.com
October 8, 2025 at 4:37 PM
Nimbus predicts the likelihood of marker positivity from multiplexed image data in single cells.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Matouš Elphick
🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
September 28, 2025 at 5:50 PM
🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
Reposted by Matouš Elphick
new out in Nature www.nature.com/articles/s41...
SPP1 is required for maintaining mesenchymal cell fate in pancreatic cancer - Nature
Mutual paracrine regulation of the cytokines GREM1 and SPP1 mediate mesenchymal and epithelial cell fate in pancreatic cancer.
www.nature.com
September 26, 2025 at 7:55 AM
new out in Nature www.nature.com/articles/s41...
Reposted by Matouš Elphick
Global matrisome changes in obese lung are linked to fibroblastic stroma and premature aging
Global matrisome changes in obese lung are linked to fibroblastic stroma and premature aging
Rottmann et al. use multi-omics and functional assays to show that obesity remodels the lung matrisome and enhances fibroblast contractility, exhibiting hallmarks of aging. These changes mirror premature aging signatures in the lung, linking overnutrition to impaired pulmonary function.
dlvr.it
September 22, 2025 at 2:38 PM
Global matrisome changes in obese lung are linked to fibroblastic stroma and premature aging
Reposted by Matouš Elphick
Come join us next year at the @embo.org meeting "The Many Faces of #Cancer evolution"! Organised by @ciriellolab.bsky.social @magnanilab.bsky.social @turajliclab.bsky.social & Céline Vaillot! In beautiful Rimini 🇮🇹
More information in the poster below ⬇️ and at
meetings.embo.org/event/26-cancer-evo
More information in the poster below ⬇️ and at
meetings.embo.org/event/26-cancer-evo
September 17, 2025 at 2:28 AM
Come join us next year at the @embo.org meeting "The Many Faces of #Cancer evolution"! Organised by @ciriellolab.bsky.social @magnanilab.bsky.social @turajliclab.bsky.social & Céline Vaillot! In beautiful Rimini 🇮🇹
More information in the poster below ⬇️ and at
meetings.embo.org/event/26-cancer-evo
More information in the poster below ⬇️ and at
meetings.embo.org/event/26-cancer-evo
Reposted by Matouš Elphick
CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 11, 2025 at 2:25 PM
CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Matouš Elphick
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods
CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...
www.nature.com
September 10, 2025 at 9:37 AM
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Matouš Elphick
Systematic Growth Factor Profiling Platform for 3D Tumor Models Reveals Estradiol-Responsive Cellular Mechanisms of Immunotherapy Resistance https://www.biorxiv.org/content/10.1101/2025.09.04.674374v1
September 10, 2025 at 3:49 AM
Systematic Growth Factor Profiling Platform for 3D Tumor Models Reveals Estradiol-Responsive Cellular Mechanisms of Immunotherapy Resistance https://www.biorxiv.org/content/10.1101/2025.09.04.674374v1
Reposted by Matouš Elphick
NEW content online!
Unravelling the genetics and epigenetics of the ageing tumour microenvironment in cancer
Nature Reviews Cancer, Published online: 08 September 2025; doi:10.1038/s41568-025-00868-xIn this Review, Easwaran and Weeraratna outline how ageing leads to epigenetic alterations in the tissue microenvironment, enhancing clonal expansion of mutations and ultimately increasing cancer risk.
www.nature.com
September 8, 2025 at 4:56 PM
NEW content online!
Reposted by Matouš Elphick
Evidence that mitochondria in macrophages are destroyed by microautophagy
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Evidence that mitochondria in macrophages are destroyed by microautophagy - Nature Communications
Mitophagy, the selective degradation of mitochondria, has been thought to occur via macroautophagy. Here, the authors present data indicating that microautophagy also mediates mitophagy in macrophages...
www.nature.com
September 1, 2025 at 4:59 AM
Evidence that mitochondria in macrophages are destroyed by microautophagy
www.nature.com/articles/s41...
www.nature.com/articles/s41...