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

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...

🚨 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...

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)

A fascinating and important read!

🚨 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

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.

“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...

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

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...

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...

In vivo mapping of mutagenesis sensitivity of human enhancers - Nature Human enhancers contain a high density of sequence features that are required for their normal in vivo function.

In vivo mapping of mutagenesis sensitivity of human enhancers

www.nature.com/articles/s41...

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...

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)

We're thrilled to introduce PromoterAI — a tool for accurately identifying promoter variants that impact gene expression. 🧵 (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...

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...

An aging bone marrow exacerbates lung fibrosis by fueling profibrotic macrophage persistence Hematopoietic aging drives lung fibrosis and profibrotic macrophage influx, stalling their maturation via reduced Treg-derived IL-10.

#MedSky🧪 #IDsky #immunosky #publichealth Age-associated changes to the bone marrow impact immune regulation in the lungs, which promotes inflammation and #fibrosis after lung injury.
@knapplab.bsky.social via @sciimmunology.bsky.social

www.science.org/doi/10.1126/...

Butterflies on a blue sky

THREAD

The numbers are in. @bsky.app research sharing volumes vs X Formerly Twitter

In March 2024, on most days, Bluesky hosts more posts linked to research published in 2025 than X.

By quite a lot.

Release the Kraken...

#AcademicSky #HigherEd #Altmetrics
1/11

Looks like a great tool, excited to test this out! (Also a great package name)

Mike spotted this before the rest of us. 🫡

Publications from 2025 are shared more on Bluesky than on X/Twitter.

🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀

Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich.

🔗 Read the preprint: osf.io/preprints/bi...

🧵 (1/15)

Altered immune landscape of cervical lymph nodes reveals Epstein-Barr virus signature in multiple sclerosis Deep cervical lymph nodes of patients with MS have an altered B cell compartment that, in part, transcriptionally resembles an EBV infection.

Our work on deep cervical lymph nodes of patients with multiple sclerosis now out

Brilliant co-first authors Joona Sarkkinen and Dawit Yohannes, vital collaborators Eliisa Kekäläinen, Maria Perdomo - huge thanks to you and the whole team!
www.science.org/doi/10.1126/...

The single-cell war has begun AI-scale data generation, new tech, latest News and M&A.

🔥 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...

Enhancing single-cell transcriptomics using interposed anchor oligonucleotide sequences - Communications Biology Droplet-based sequencing is key to single-cell transcriptomics but faces challenges from bead synthesis errors. A new bead design with anchor sequences improves UMI identification, read recovery, and ...

Bit late, but first paper of 2025. 🧬Enhancing #singlecell #transcriptomics: Our recent study introduces an interposed anchor strategy to improve gene expression profiles in droplet-based single-cell sequencing analyses. www.nature.com/articles/s42...

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...

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/...

Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis - Nature Genetics Xenium spatial transcriptomic profiling of pulmonary fibrosis characterizes cell composition dynamics and histopathological features associated with the disease.

🔬 Epic #PulmonaryFibrosis study mapping 1.6M cells across 35 lungs! Fascinating to see how spatial transcriptomics reveals disease progression starting with alveolar epithelial changes before affecting macrophages! 🫁🧬

www.nature.com/articles/s41...

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 🧵

Freddie Whiting in our group wrote this thoughtful commentary on @karunamdphd.bsky.social's recent paper that explored cell state changes and plasticity in colorectal cancer evolution. He concludes we need to better understand epigenetic control of plasticity. authors.elsevier.com/c/1kTSf5Sx5g...

Massively parallel characterization of transcriptional regulatory elements - Nature Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.

Massively parallel reporter assays (MPRAs) testing >680,000 sequences combined with machine learning to improve regulatory element & variant effect prediction. Amazing work by @vagar.bsky.social, Fumitaka Inoue, @jshendure.bsky.social and many others as part of ENCODE.
www.nature.com/articles/s41...

icCITE-seq (intracellular cellular indexing of transcriptomes and epitopes), a scalable method that simultaneously measures surface and intracellular protein levels alongside gene expression across thousands of cells
doi.org/10.1101/2025...

Does my mutation have the same impact as yours? Population genetics 🤠 🥸 🤓 🤡 meets single cell CRISPRi ⚡ ! www.biorxiv.org/content/10.1... Led by Claudia Feng, Oliver Stegle, Britta Velten, @sangerinstitute.bsky.social .

🎇🎄Some holiday reading: Overdue TWEETORIAL on the latest preprint from our lab 🎇🎄

In this work, superstar postdoc @xinhexue.bsky.social combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.

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...

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...

Here is a more in-depth explanation of the science that will take place in UK Biobank using Next-Gen Proteomics technology Olink (now part of Thermo) and Ultima Genomics.