Marco Breinig
@breinigmarco.bsky.social
*The necessity and power of random, under-sampled experiments in biology...
*🍫-🐭, PERTURB-CAST, RUBIX...
*🍫-🐭, PERTURB-CAST, RUBIX...
Reposted by Marco Breinig
The new paper from SPECIFICANCER, published in
@natureportfolio.nature.com reveals that it’s not just the mutation that matters — it’s where in the liver that mutation appears.
Congratulations to the team (co-funded by
@themarkfdn.bsky.social). 👉 Read more: lnkd.in/eTVh9YY6
@natureportfolio.nature.com reveals that it’s not just the mutation that matters — it’s where in the liver that mutation appears.
Congratulations to the team (co-funded by
@themarkfdn.bsky.social). 👉 Read more: lnkd.in/eTVh9YY6
November 20, 2025 at 1:40 PM
The new paper from SPECIFICANCER, published in
@natureportfolio.nature.com reveals that it’s not just the mutation that matters — it’s where in the liver that mutation appears.
Congratulations to the team (co-funded by
@themarkfdn.bsky.social). 👉 Read more: lnkd.in/eTVh9YY6
@natureportfolio.nature.com reveals that it’s not just the mutation that matters — it’s where in the liver that mutation appears.
Congratulations to the team (co-funded by
@themarkfdn.bsky.social). 👉 Read more: lnkd.in/eTVh9YY6
Reposted by Marco Breinig
Published today in @nature.com, @adititm.bsky.social & researchers from the @brianhie.bsky.social lab report that the large-scale genomic model, Evo, is capable of using surrounding genomic context to produce novel, functional genes, enabling an an emergent approach they've termed 'semantic design'.
November 19, 2025 at 6:17 PM
Published today in @nature.com, @adititm.bsky.social & researchers from the @brianhie.bsky.social lab report that the large-scale genomic model, Evo, is capable of using surrounding genomic context to produce novel, functional genes, enabling an an emergent approach they've termed 'semantic design'.
Reposted by Marco Breinig
Pretrained using 335,645 whole-slide images, a foundation model is developed to provide representations for slide- and patient-level tasks. It is capable of performing clinical tasks even in data-scarce scenarios, without further fine-tuning. https://www.nature.com/articles/s41591-025-03982-3
November 18, 2025 at 3:15 PM
Pretrained using 335,645 whole-slide images, a foundation model is developed to provide representations for slide- and patient-level tasks. It is capable of performing clinical tasks even in data-scarce scenarios, without further fine-tuning. https://www.nature.com/articles/s41591-025-03982-3
Reposted by Marco Breinig
Aging represses oncogenic KRAS-driven lung tumorigenesis and alters tumor suppression
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Aging represses oncogenic KRAS-driven lung tumorigenesis and alters tumor suppression - Nature Aging
The mechanisms that impact tumorigenesis during aging are incompletely understood. Here Shuldiner et al. show that in mice, aging represses KRAS-driven lung tumorigenesis and dampens the impact of ina...
www.nature.com
November 16, 2025 at 9:31 PM
Aging represses oncogenic KRAS-driven lung tumorigenesis and alters tumor suppression
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Reposted by Marco Breinig
Paneth-like transition drives resistance to dual targeting of KRAS and EGFR in colorectal cancer www.cell.com/cancer-cell...
November 17, 2025 at 3:15 PM
Paneth-like transition drives resistance to dual targeting of KRAS and EGFR in colorectal cancer www.cell.com/cancer-cell...
Reposted by Marco Breinig
A gene-editing approach enables modification of bacteria within the mouse gut @science.org @harriswang.bsky.social @columbiauniversity.bsky.social @shsternberg.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
November 14, 2025 at 3:36 AM
A gene-editing approach enables modification of bacteria within the mouse gut @science.org @harriswang.bsky.social @columbiauniversity.bsky.social @shsternberg.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Marco Breinig
CONCERT predicts niche-aware perturbation responses in spatial transcriptomics [new]
CONCERT: Predicts niche-aware perturbation responses in spatial transcriptomics using spatial kernels within a generative model.
CONCERT: Predicts niche-aware perturbation responses in spatial transcriptomics using spatial kernels within a generative model.
November 10, 2025 at 6:20 PM
CONCERT predicts niche-aware perturbation responses in spatial transcriptomics [new]
CONCERT: Predicts niche-aware perturbation responses in spatial transcriptomics using spatial kernels within a generative model.
CONCERT: Predicts niche-aware perturbation responses in spatial transcriptomics using spatial kernels within a generative model.
Reposted by Marco Breinig
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - @jshendure.bsky.social @troymcdiarmid.bsky.social @uwgenome.bsky.social go.nature.com/49eTPCu
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - Nature Biotechnology
Prime editing in mammalian cells benefits from a comprehensive list of genetic parts.
go.nature.com
November 11, 2025 at 4:36 PM
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - @jshendure.bsky.social @troymcdiarmid.bsky.social @uwgenome.bsky.social go.nature.com/49eTPCu
Reposted by Marco Breinig
🔬 Toward histopathology 2.0: spatial transcriptomes inferred from routine diagnostic H&E images + a chat interface for cell-resolution histopathology through English language. (1/6)
July 18, 2025 at 10:40 PM
🔬 Toward histopathology 2.0: spatial transcriptomes inferred from routine diagnostic H&E images + a chat interface for cell-resolution histopathology through English language. (1/6)
Reposted by Marco Breinig
Multimodal learning enables chat-based exploration of single-cell data - @bocklab.bsky.social @cemm.oeaw.ac.at @meduniwien.ac.at go.nature.com/3WPGJnW
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
go.nature.com
November 11, 2025 at 4:58 PM
Multimodal learning enables chat-based exploration of single-cell data - @bocklab.bsky.social @cemm.oeaw.ac.at @meduniwien.ac.at go.nature.com/3WPGJnW
Reposted by Marco Breinig
Synthetic biology could enable new types of programmable therapeutics. Our new preprint introduces synthetic protein circuits that selectively trigger cell death in Ras-mutant cancer cells, with interesting advantages compared to existing approaches.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
June 3, 2025 at 12:11 AM
Synthetic biology could enable new types of programmable therapeutics. Our new preprint introduces synthetic protein circuits that selectively trigger cell death in Ras-mutant cancer cells, with interesting advantages compared to existing approaches.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Marco Breinig
Our latest collaboration with @rongfan8.bsky.social, spatial triomics to investigate myelin and cortical brain development, and demyelination, spearheaded by Leslie Kirby in our lab @ki.se and Di Zhang in Rong's lab! Check it out @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Spatial dynamics of brain development and neuroinflammation - Nature
A tri-omic atlas of the mouse brain from postnatal day 0 to P21 reveals that layer-specific projection neurons have a role in coordinating axonogenesis and myelination.
www.nature.com
November 5, 2025 at 4:03 PM
Our latest collaboration with @rongfan8.bsky.social, spatial triomics to investigate myelin and cortical brain development, and demyelination, spearheaded by Leslie Kirby in our lab @ki.se and Di Zhang in Rong's lab! Check it out @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Marco Breinig
We’re releasing CytoSyn, our new diffusion model for synthetic histopathology image generation. REPA-E architecture. H0-mini conditioning.
Model: huggingface.co/Owkin-Biopti...
Supporting article: www.owkin.com/blogs-case-s...
Model: huggingface.co/Owkin-Biopti...
Supporting article: www.owkin.com/blogs-case-s...
November 5, 2025 at 10:30 AM
We’re releasing CytoSyn, our new diffusion model for synthetic histopathology image generation. REPA-E architecture. H0-mini conditioning.
Model: huggingface.co/Owkin-Biopti...
Supporting article: www.owkin.com/blogs-case-s...
Model: huggingface.co/Owkin-Biopti...
Supporting article: www.owkin.com/blogs-case-s...
Reposted by Marco Breinig
A computational method designs receptors called T-SenSERs, which have predictable signalling responses to tumour microenvironment soluble factors and can be co-expressed with conventional CARs in T cells to enhance their therapeutic activity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
November 4, 2025 at 1:04 AM
A computational method designs receptors called T-SenSERs, which have predictable signalling responses to tumour microenvironment soluble factors and can be co-expressed with conventional CARs in T cells to enhance their therapeutic activity.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Marco Breinig
MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart https://www.biorxiv.org/content/10.1101/2025.11.02.686137v1
November 4, 2025 at 1:34 PM
MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart https://www.biorxiv.org/content/10.1101/2025.11.02.686137v1
Reposted by Marco Breinig
We dived into cancer cell interactions with COMPOTES. Using MOSAIC data, we uncovered 45 programs across major cancers, shedding light on immune dynamics and therapeutic paths.
Pre-print at: doi.org/10.1101/2025...
Pre-print at: doi.org/10.1101/2025...
October 28, 2025 at 2:39 PM
We dived into cancer cell interactions with COMPOTES. Using MOSAIC data, we uncovered 45 programs across major cancers, shedding light on immune dynamics and therapeutic paths.
Pre-print at: doi.org/10.1101/2025...
Pre-print at: doi.org/10.1101/2025...
Reposted by Marco Breinig
Our new multimodal ML models achieve high accuracy in predicting iCCA outcomes (c-index 0.70). This collaborative study with @mskcancercenter.bsky.social enhances understanding of the disease and may guide treatment selection.
Check out the paper: www.sciencedirect.com/science/arti...
Check out the paper: www.sciencedirect.com/science/arti...
October 30, 2025 at 3:49 PM
Our new multimodal ML models achieve high accuracy in predicting iCCA outcomes (c-index 0.70). This collaborative study with @mskcancercenter.bsky.social enhances understanding of the disease and may guide treatment selection.
Check out the paper: www.sciencedirect.com/science/arti...
Check out the paper: www.sciencedirect.com/science/arti...
Reposted by Marco Breinig
High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes - @pku1898.bsky.social go.nature.com/47yENVJ
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
go.nature.com
October 30, 2025 at 4:02 PM
High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes - @pku1898.bsky.social go.nature.com/47yENVJ
Reposted by Marco Breinig
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 Marco Breinig
🧵1/17
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
A plastic EMP1⁺ to LGR5⁺ cell state conversion as a bypass to KRAS-G12D pharmacological inhibition in metastatic colorectal cancer
Abstract. Inhibitors of the oncogene KRAS hold promise for treating metastatic CRC (mCRC). Here we show that a selective, covalent small molecule inhibitor of the active (ON) conformation of RAS-G12D,...
aacrjournals.org
October 23, 2025 at 6:07 PM
🧵1/17
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
📣Thrilled to share our latest study just out in Cancer Discovery!
➡️
aacrjournals.org/cancerdiscov...
Reposted by Marco Breinig
Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes @science.org @shaleklab.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
October 23, 2025 at 6:51 PM
Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes @science.org @shaleklab.bsky.social
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Marco Breinig
Discovery and engineering of retrons for precise genome editing - @texasscience.bsky.social go.nature.com/4nkr7DE
Discovery and engineering of retrons for precise genome editing - Nature Biotechnology
A metagenomic screen identifies retron reverse transcriptases for precise genome-editing applications.
go.nature.com
October 23, 2025 at 2:59 PM
Discovery and engineering of retrons for precise genome editing - @texasscience.bsky.social go.nature.com/4nkr7DE
Reposted by Marco Breinig
Excited that the paper presenting our mouse brain in vivo CRISPR screening platform is out today in @natneuro.nature.com!
Great team effort, led by Biswa Ramani and @ivlrose.bsky.social in the Kampmann lab.
www.nature.com/articles/s41...
Great team effort, led by Biswa Ramani and @ivlrose.bsky.social in the Kampmann lab.
www.nature.com/articles/s41...
CRISPR screening by AAV episome-sequencing (CrAAVe-seq): a scalable cell-type-specific in vivo platform uncovers neuronal essential genes - Nature Neuroscience
The authors developed an adeno-associated virus-based high-throughput in vivo CRISPR screening platform for endogenous mouse brain cell types. Using this platform, they define genes and pathways essen...
www.nature.com
August 22, 2025 at 10:15 PM
Excited that the paper presenting our mouse brain in vivo CRISPR screening platform is out today in @natneuro.nature.com!
Great team effort, led by Biswa Ramani and @ivlrose.bsky.social in the Kampmann lab.
www.nature.com/articles/s41...
Great team effort, led by Biswa Ramani and @ivlrose.bsky.social in the Kampmann lab.
www.nature.com/articles/s41...
Reposted by Marco Breinig
We’re happy to share our new preprint form
@N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat
lab! 🎉
🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation.
🔗 biorxiv.org/content/10.1...
@N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat
lab! 🎉
🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation.
🔗 biorxiv.org/content/10.1...
Spatiotemporal dynamics of tumor microenvironment remodeling
During tumorigenesis, interactions between tumor and stromal cells progressively remodel the tumor microenvironment (TME) towards pro-tumoral functions. Understanding early TME remodeling dynamics is ...
biorxiv.org
July 22, 2025 at 9:48 AM
We’re happy to share our new preprint form
@N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat
lab! 🎉
🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation.
🔗 biorxiv.org/content/10.1...
@N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat
lab! 🎉
🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation.
🔗 biorxiv.org/content/10.1...