David Cook

Harnessing the Potential of Spatial Statistics for Spatial Omics
Data with pasta. arxiv.org/pdf/2412.01561

STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social
www.cell.com/cell/fulltex...

Acquired resistance in cancer: towards targeted therapeutic strategies - Nature Reviews Cancer Acquired therapeutic resistance is a key contributor to cancer treatment failure, requiring new approaches to address its complex mechanisms. In this Roadmap, Soragni, Knudsen and colleagues discuss t...

Acquired resistance limits the efficacy of cancer treatments & accounts for therapy failure in most patients. Our Roadmap explores how innovative technologies bridge the gap between fundamental research on resistance and clinical translation into actionable strategies
www.nature.com/articles/s41...

🧬 We're hiring - join our lab in Toronto, Canada! 🇨🇦

Exciting postdoc joint with @hartjackson.bsky.social developing machine learning methods for the next generation of spatial histopathology technologies joint with industry partners in the Bay Area.

👉 apply.interfolio.com/168307

Running NMF on your scRNAseq data? Check out my updates to Lyndsay Murrow's DECIPHER-seq package, now compatible with Seurat v5 objects and rliger v2! github.com/dasuperville...

Excited to share Ruqian has developed a package for this transcript based niche analysis. Check out the preprint and the package! This is a flexible approach and we're working on extending this for other spatial analyses!

@davisjmcc.bsky.social

www.biorxiv.org/content/10.1...

Awesome work! Apologies if I’m missing it in there—any sense whether segger could improve on 10x’s multimodal segmentation or is it fairly similar? I feel like it’s significantly better than their nuc expansion, but obviously challenging for some tissue compositions

Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment https://www.biorxiv.org/content/10.1101/2025.02.24.640007v1

Single-molecule live-cell RNA imaging with CRISPR–Csm Nature Biotechnology - Single-molecule live-cell fluorescence in situ hybridization uses an RNA-targeting CRISPR–Csm complex to image and track endogenous RNAs.

So cool!
rdcu.be/eboxL

Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC Large-scale scATAC-seq experiments are challenging because of their costs, lengthy protocols, and confounding batch effects. Several sample multiplexing technologies aim to address these challenges, b...

Happy to share that the preprint to our new scATAC-seq multiplexing method, MULTI-ATAC, is officially online:
www.biorxiv.org/content/10.1...

So much happening in the segmentation space for bioimage analysis. These two papers that were published online today really stood out to me as noteworthy (a thread).

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Are you a new investigator (<5 years) with a research group? Think your work would make an amazing logo? We’re giving away a FREE branding package (valued up to $1,000 CAD) to one lucky research group!

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Very cool work! Love seeing more SCCOHT research

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...

CRISPR-StAR enables high-resolution genetic screening in complex in vivo models - Nature Biotechnology Pooled genetic CRISPR screening is improved in complex models through leveraging internal controls.

Today we published a new paradigm to do CRISPR screens in complex model systems such as in vivo but also e.g. in organoids. The publication came out in Nature Biotechnology.
1/
www.nature.com/articles/s41...

Excited to share our lab's first preprint: we used spatial transcriptomics to dissect how aging disrupts the cycling ovary! 🧵

This was an incredible team effort w/ @jennifergarrison.bsky.social #TammyLan @davidsebfischer.bsky.social #AlisonKochersberger #RuthRaichur #SophiaSzady

Single-cell spatial atlas of high-grade serous ovarian cancer unveils MHC class II as a key driver of spatial tumor ecosystems and clinical outcomes The tumor microenvironment (TME) is a complex network of interactions between malignant and host cells, yet its orchestration in advanced high-grade serous ovarian carcinoma (HGSC) remains poorly unde...

New preprint alert ‼️ @farkkilab.bsky.social We generated a single-cell spatial atlas of 280 metastatic #ovariancancer and found tumor MHCII as a key driver of tumor ecosystems and clinical outcomes. www.biorxiv.org/content/10.1...

Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer Anti-tumor immunity is crucial for high-grade serous ovarian cancer (HGSC) prognosis, yet its adaptation upon standard chemotherapy remains poorly und…

1/n New paper alert 🚨 We're thrilled to share our just published paper in #CancerCell
Do you ever wonder how the #TME in #HGSC changes during chemotherapy? Check it here: www.sciencedirect.com/science/arti... and let’s dive into the highlights together #spatialbiology #ovariancancer #cancerresarch

Very pleased to announce that our package for Multiscale Spatial Analysis - MuSpAn - has landed!

The preprint is on biorxiv now, but you can find a lot more details at www.muspan.co.uk, including documentation, worked tutorials (an ever-expanding list), install guides, and how to get the code!

1/23 Big news for the #ObenaufLab! So excited to finally share our new study providing another puzzle piece, why immunotherapy fails in many tumors, now out in @Nature 🧵👇 www.nature.com/articles/s41...

This paper is now online: www.nature.com/articles/s41... and it is fascinating!!

Both #Cancer #Research starter packs are now completely full!

~300 researchers, oncologists, students, postdocs, patient advocates, and organizations supporting cancer research 🧪🔬⚕️

I hope you'll find these useful to build our community here

Pack 1: go.bsky.app/FEoaJMc
Pack 2: go.bsky.app/6EcjWNA

Is anyone else having issues with all hyperlinks on Nature sites being non-functional in Safari for both macOS and iOS?? Can’t click anything. Have been experiencing it for the last couple months

Ex vivo imaging reveals the spatiotemporal control of ovulation - Nature Cell Biology Thomas, Marx et al. devise a live imaging approach to spatiotemporally dissect mouse ovulation ex vivo.

Beautiful!
www.nature.com/articles/s41...

1/ 🧬 Single-cell genomics reveals biological variations beyond cell types. Unveiling these in separate latent dim’s is known as disentanglement. Led by @AmirAliMoinfar, we develop DRVI to learn nonlinear, disentangled & interpretable latent spaces.
biorxiv.org/content/10.1101/2024.11.06.622266v1

Need to design your next Xenium/CosMx/Merfish experiment? Spapros, now out @naturemethods, allows for probe set selection for target spatial tx. Led by @KuemmerleLouis, it optimizes both cell type ID & within-cell type variation. nature.com/articles/s41592-024-02496-z github.com/theislab/spapros