James Opzoomer
@jopz.bsky.social
Decoding biology at the single-cell level @RelationRx 🧬 | ML + Genomics for drug discovery | Innovation Lab
Pinned
James Opzoomer
@jopz.bsky.social
· Feb 18
The single-cell war has begun
AI-scale data generation, new tech, latest News and M&A.
sctrends.org
🔥 Single-cell AI scale generation battle heats up: Vevo Tahoe-100M vs CZI Billion Cells Project lead massive data generation efforts. Plus Curio/Takara deal & Parse wins big patent battle against 10x.
Check out all these single-cell industry stories in more detail at sctrends.org/p/the-single...
Check out all these single-cell industry stories in more detail at sctrends.org/p/the-single...
Reposted by James Opzoomer
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 James Opzoomer
Just posted, "The Tiling Tree Method, Part 2: Common Pitfalls and How to Overcome Them" a follow-up to our previous essay on the "tiling tree" method for thinking of all the possible solutions to a problem, by Claire Wang, Nina Khera, and myself. engineeringx.substack.com/p/the-tiling...
The Tiling Tree Method, Part 2: Common Pitfalls and How to Overcome Them
How to really think of every way of solving a problem
engineeringx.substack.com
November 9, 2025 at 6:43 PM
Just posted, "The Tiling Tree Method, Part 2: Common Pitfalls and How to Overcome Them" a follow-up to our previous essay on the "tiling tree" method for thinking of all the possible solutions to a problem, by Claire Wang, Nina Khera, and myself. engineeringx.substack.com/p/the-tiling...
Reposted by James Opzoomer
CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci - Nature Biotechnology
Multiplexed DNA imaging uncovers promoter−enhancer interaction dynamics and effects of epigenetic modifications.
www.nature.com
November 7, 2025 at 12:56 PM
CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by James Opzoomer
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
November 7, 2025 at 10:29 AM
Are you using any of our factor models, such as MOFA? 🛵
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
You might’ve found it challenging to tailor them to your specific use cases - not anymore!
Introducing MOFA-FLEX: a flexible, modular factor analysis framework designed for customizable modeling across diverse multi-omics data scenarios. 1/n
Reposted by James Opzoomer
Squidiff: a diffusion-based model to predict transcriptome response to perturbations.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Squidiff: predicting cellular development and responses to perturbations using a diffusion model - Nature Methods
Squidiff is a diffusion-based model to predict transcriptomic changes in response to perturbations.
www.nature.com
November 7, 2025 at 2:41 PM
Squidiff: a diffusion-based model to predict transcriptome response to perturbations.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by James Opzoomer
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 James Opzoomer
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Enabling options for review: from training and transparency to author-centered AI tools - openRxiv
Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...
openrxiv.org
November 6, 2025 at 2:32 PM
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Reposted by James Opzoomer
BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux
BioContextAI is a community hub for agentic biomedical systems - Nature Biotechnology
Nature Biotechnology - BioContextAI is a community hub for agentic biomedical systems
go.nature.com
November 6, 2025 at 6:28 PM
BioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux
Reposted by James Opzoomer
ESPRESSO: a method that extracts functional information about organelles for deep spatiotemporal phenotyping at the single cell level.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ESPRESSO: spatiotemporal omics based on organelle phenotyping - Nature Methods
ESPRESSO leverages functional information obtained from organelles for deep spatiotemporal phenotyping of single cells.
www.nature.com
November 6, 2025 at 5:40 PM
ESPRESSO: a method that extracts functional information about organelles for deep spatiotemporal phenotyping at the single cell level.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by James Opzoomer
New study of 800K+ genomes from gnomAD reveals most “pathogenic” variants in healthy people aren’t truly disease-tolerant. They are explained by annotation errors, mosaicism, or compensatory variants. 🧬
A big step for precision medicine!
www.nature.com/articles/s41...
A big step for precision medicine!
www.nature.com/articles/s41...
Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database - Nature Communications
Here the authors provide an explanation for 95% of examined predicted loss of function variants found in disease-associated haploinsufficient genes in the Genome Aggregation Database (gnomAD),…
www.nature.com
November 4, 2025 at 3:06 PM
New study of 800K+ genomes from gnomAD reveals most “pathogenic” variants in healthy people aren’t truly disease-tolerant. They are explained by annotation errors, mosaicism, or compensatory variants. 🧬
A big step for precision medicine!
www.nature.com/articles/s41...
A big step for precision medicine!
www.nature.com/articles/s41...
Reposted by James Opzoomer
🚀Excited to share our new preprint: “Programming human cell type-specific gene expression via an atlas of AI-designed enhancers”
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
Programming human cell type-specific gene expression via an atlas of AI-designed enhancers
Differentially active enhancers are key drivers of cell type specific gene expression. Active enhancers are found in open chromatin, which can be mapped at genome scale across tissue and cell types. T...
www.biorxiv.org
October 6, 2025 at 4:57 PM
🚀Excited to share our new preprint: “Programming human cell type-specific gene expression via an atlas of AI-designed enhancers”
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
We built the largest repository of AI-designed enhancers, validated across 10 human cell lines + mouse retina.
👉 www.biorxiv.org/content/10.1...
#AI #Genomics #SynBio
Reposted by James Opzoomer
When ChatGPT was asked to rate 40,000 résumés, it ranked the older male candidates as better quality than the younger female applicants.
Age and gender distortion in online media and large language models - Nature
Stereotypes of age-related gender bias are socially distorted, as evidenced by the age gap in the representations of women and men across various media and algorithms, despite no systematic age differ...
www.nature.com
November 2, 2025 at 9:47 PM
When ChatGPT was asked to rate 40,000 résumés, it ranked the older male candidates as better quality than the younger female applicants.
Reposted by James Opzoomer
Looks like the science community has found a home.
academic.oup.com/icb/article-...
academic.oup.com/icb/article-...
Scientists no Longer Find Twitter Professionally Useful, and have Switched to Bluesky
Synopsis. Social media has become widely used by the scientific community for a variety of professional uses, including networking and public outreach. For
academic.oup.com
October 29, 2025 at 2:43 PM
Looks like the science community has found a home.
academic.oup.com/icb/article-...
academic.oup.com/icb/article-...
Reposted by James Opzoomer
Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics.
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
September 15, 2025 at 8:40 AM
Introducing ParTIpy, a python package for Pareto Task Inference that scales to large-scale datasets, including single-cell and spatial transcriptomics.
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
🔗 Manuscript: www.biorxiv.org/content/10.1...
💻 Code: partipy.readthedocs.io
Reposted by James Opzoomer
🚨 New preprints from our lab!
First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”).
👉 www.biorxiv.org/content/10.1...
Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues
High-throughput clonal tracing of primary human samples relies on naturally occurring barcodes, such as somatic mitochondrial DNA (mtDNA) mutations detected via single-cell ATAC-seq (mtscATAC-seq). Fr...
www.biorxiv.org
September 24, 2025 at 12:39 PM
🚨 New preprints from our lab!
First, we introduce Cryo-mtscATAC-seq, led by Maren (@ms-maren.bsky.social ), enabling high-throughput clonal tracing from frozen human samples by isolating nuclei with their mitochondria (“CryoCells”).
👉 www.biorxiv.org/content/10.1...
Reposted by James Opzoomer
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
A fascinating and important read!
Thank you to everyone reading my new memoir - you’ve made it an instant Sunday Times bestseller 🗞️
This Is for Everyone is available now from thisisforeveryone.timbl.com
@thetimes.com
This Is for Everyone is available now from thisisforeveryone.timbl.com
@thetimes.com
September 22, 2025 at 8:53 AM
A fascinating and important read!
Reposted by James Opzoomer
🚨 New preprint
We present an extended version of ScAPE, the method that won one of the prizes 🏆 in the @neuripsconf.bsky.social 2023 Single-Cell Perturbation Prediction challenge.
📄 preprint: doi.org/10.1101/2025...
🧬 code: github.com/scapeML/scape
We present an extended version of ScAPE, the method that won one of the prizes 🏆 in the @neuripsconf.bsky.social 2023 Single-Cell Perturbation Prediction challenge.
📄 preprint: doi.org/10.1101/2025...
🧬 code: github.com/scapeML/scape
September 19, 2025 at 7:45 AM
🚨 New preprint
We present an extended version of ScAPE, the method that won one of the prizes 🏆 in the @neuripsconf.bsky.social 2023 Single-Cell Perturbation Prediction challenge.
📄 preprint: doi.org/10.1101/2025...
🧬 code: github.com/scapeML/scape
We present an extended version of ScAPE, the method that won one of the prizes 🏆 in the @neuripsconf.bsky.social 2023 Single-Cell Perturbation Prediction challenge.
📄 preprint: doi.org/10.1101/2025...
🧬 code: github.com/scapeML/scape
Reposted by James Opzoomer
“The free, open access communications paradigm we have did not arrive like magic. It was the product of a fair amount of political wrangling” - that's why we must continue our fight for the web.
🙏 @washingtonpost.com for reviewing 'This Is for Everyone'
www.washingtonpost.com/books/2025/0...
🙏 @washingtonpost.com for reviewing 'This Is for Everyone'
www.washingtonpost.com/books/2025/0...
Review | The inventor of the web says we can recapture its magic. Is he right?
In “This Is for Everyone,” Tim Berners-Lee writes about the early days of the internet and how we might restore its more democratic roots.
www.washingtonpost.com
September 17, 2025 at 1:01 PM
“The free, open access communications paradigm we have did not arrive like magic. It was the product of a fair amount of political wrangling” - that's why we must continue our fight for the web.
🙏 @washingtonpost.com for reviewing 'This Is for Everyone'
www.washingtonpost.com/books/2025/0...
🙏 @washingtonpost.com for reviewing 'This Is for Everyone'
www.washingtonpost.com/books/2025/0...
Reposted by James Opzoomer
Thank you to @observeruk.bsky.social for this thoughtful review.
“Berners-Lee is clear-eyed about the benefits and the dangers. This Is for Everyone contains some very sharp thinking about what we need to do now.”
We must fight for the web we want.
observer.co.uk/culture/book...
“Berners-Lee is clear-eyed about the benefits and the dangers. This Is for Everyone contains some very sharp thinking about what we need to do now.”
We must fight for the web we want.
observer.co.uk/culture/book...
Nick Clegg and Tim Berners-Lee: the battle for the soul o...
The ex-deputy PM toes the line of his former Meta paymasters, while the web's inventor shares his vision of a utopian digital future
observer.co.uk
September 7, 2025 at 2:55 PM
Thank you to @observeruk.bsky.social for this thoughtful review.
“Berners-Lee is clear-eyed about the benefits and the dangers. This Is for Everyone contains some very sharp thinking about what we need to do now.”
We must fight for the web we want.
observer.co.uk/culture/book...
“Berners-Lee is clear-eyed about the benefits and the dangers. This Is for Everyone contains some very sharp thinking about what we need to do now.”
We must fight for the web we want.
observer.co.uk/culture/book...
Reposted by James Opzoomer
Just published: The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born
authors.elsevier.com/sd/article/S...
A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born
authors.elsevier.com/sd/article/S...
ScienceDirect.com | Science, health and medical journals, full text articles and books.
authors.elsevier.com
July 17, 2025 at 10:07 AM
Just published: The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube
A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born
authors.elsevier.com/sd/article/S...
A global temporal chromatin program, operating across the CNS, directs binding of specific spatial TFs & hence when/where neurons & glia are born
authors.elsevier.com/sd/article/S...
Reposted by James Opzoomer
Reposted by James Opzoomer
How does cryptic genetic variation influence the long-term fate of gene duplicates (paralogs)?
Our new study addresses this question by dissecting the evolutionary potential of redundant myosin paralogs in yeast nature.com/articles/s41... (1/12)
Our new study addresses this question by dissecting the evolutionary potential of redundant myosin paralogs in yeast nature.com/articles/s41... (1/12)
Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network - Nature Communications
Over time, paralogous genes accumulate changes in their sequences that do not affect their function, which is called cryptic variation. Using paralogous myosins, this study shows how cryptic variation...
nature.com
June 1, 2025 at 11:27 PM
How does cryptic genetic variation influence the long-term fate of gene duplicates (paralogs)?
Our new study addresses this question by dissecting the evolutionary potential of redundant myosin paralogs in yeast nature.com/articles/s41... (1/12)
Our new study addresses this question by dissecting the evolutionary potential of redundant myosin paralogs in yeast nature.com/articles/s41... (1/12)
Reposted by James Opzoomer
We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)
May 29, 2025 at 6:29 PM
We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (1/)
Reposted by James Opzoomer
Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data"
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data
Building a mechanistic understanding of cell fate decisions remains a fundamental goal of developmental biology, with implications for stem cell therapies, regenerative medicine and understanding dise...
www.biorxiv.org
May 29, 2025 at 12:08 PM
Our latest "Dynamic Landscape Analysis of Cell Fate Decisions: Predictive Models of Neural Development From Single-Cell Data"
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...
A rigorous mathematical foundation for Waddington's landscape to study cell fate decision making
Applied to ventral neural tube development
www.biorxiv.org/content/10.1...