David Cook
@dpcook.bsky.social
Single-cell and spatial genomics, ovarian cancer, cell plasticity | Scientist, Cancer Research, Ottawa Hospital Research Institute | Assistant Professor, University of Ottawa. https://www.cooklab.ca
Harnessing the Potential of Spatial Statistics for Spatial Omics
Data with pasta. arxiv.org/pdf/2412.01561
Data with pasta. arxiv.org/pdf/2412.01561
arxiv.org
July 16, 2025 at 1:48 PM
Harnessing the Potential of Spatial Statistics for Spatial Omics
Data with pasta. arxiv.org/pdf/2412.01561
Data with pasta. arxiv.org/pdf/2412.01561
Reposted by David Cook
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
June 17, 2025 at 4:40 PM
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by David Cook
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...
www.nature.com/articles/s41...
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...
www.nature.com
June 3, 2025 at 3:35 PM
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...
www.nature.com/articles/s41...
Reposted by David Cook
🧬 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
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
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
May 27, 2025 at 3:42 PM
🧬 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
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
Reposted by David Cook
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...
GitHub - dasuperville/DECIPHER-seq-v2: Data and code to reproduce results from DECIPHER-seq paper. Updated for use with Seurat v5 objects and rLiger v2.
Data and code to reproduce results from DECIPHER-seq paper. Updated for use with Seurat v5 objects and rLiger v2. - dasuperville/DECIPHER-seq-v2
github.com
April 7, 2025 at 5:11 PM
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...
Reposted by David Cook
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...
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
March 26, 2025 at 6:04 PM
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...
@davisjmcc.bsky.social
www.biorxiv.org/content/10.1...
Reposted by David Cook
Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment https://www.biorxiv.org/content/10.1101/2025.02.24.640007v1
February 28, 2025 at 2:58 AM
Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment https://www.biorxiv.org/content/10.1101/2025.02.24.640007v1
Reposted by David Cook
Reposted by David Cook
Happy to share that the preprint to our new scATAC-seq multiplexing method, MULTI-ATAC, is officially online:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
February 20, 2025 at 9:48 PM
Happy to share that the preprint to our new scATAC-seq multiplexing method, MULTI-ATAC, is officially online:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by David Cook
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).
February 12, 2025 at 2:39 PM
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).
Reposted by David Cook
🚀 New investigators, this one’s for you! 🚀
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!
docs.google.com/forms/d/e/1F...
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!
docs.google.com/forms/d/e/1F...
Tell us about yourself and your research group!
Think your research could inspire an exciting logo? If it’s a great fit, you could win a free branding package (valued up to $1,000 CAD)!
📅 Apply by March 4th, 2025
🏆 Winner announced by March 7th, 20...
docs.google.com
February 12, 2025 at 2:11 AM
🚀 New investigators, this one’s for you! 🚀
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!
docs.google.com/forms/d/e/1F...
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!
docs.google.com/forms/d/e/1F...
Reposted by David Cook
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...
www.nature.com/articles/s41...
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...
www.nature.com
January 8, 2025 at 1:30 PM
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...
www.nature.com/articles/s41...
Reposted by David Cook
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...
1/
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.
www.nature.com
December 16, 2024 at 12:02 PM
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...
1/
www.nature.com/articles/s41...
Reposted by David Cook
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
This was an incredible team effort w/ @jennifergarrison.bsky.social #TammyLan @davidsebfischer.bsky.social #AlisonKochersberger #RuthRaichur #SophiaSzady
December 18, 2024 at 2:32 PM
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
This was an incredible team effort w/ @jennifergarrison.bsky.social #TammyLan @davidsebfischer.bsky.social #AlisonKochersberger #RuthRaichur #SophiaSzady
Reposted by David Cook
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...
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...
www.biorxiv.org
December 4, 2024 at 5:33 AM
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...
Reposted by David Cook
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
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
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…
www.sciencedirect.com
December 10, 2024 at 11:48 AM
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
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
Reposted by David Cook
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!
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!
December 9, 2024 at 2:12 PM
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!
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!
Reposted by David Cook
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...
November 27, 2024 at 5:58 PM
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...
Reposted by David Cook
This paper is now online: www.nature.com/articles/s41... and it is fascinating!!
November 27, 2024 at 5:38 PM
This paper is now online: www.nature.com/articles/s41... and it is fascinating!!
Reposted by David Cook
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
~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
November 23, 2024 at 1:27 PM
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
~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
November 23, 2024 at 3:28 PM
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
Beautiful!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
November 20, 2024 at 8:16 PM
Beautiful!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by David Cook
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
biorxiv.org/content/10.1101/2024.11.06.622266v1
November 20, 2024 at 2:29 PM
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
biorxiv.org/content/10.1101/2024.11.06.622266v1
Reposted by David Cook
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
November 20, 2024 at 7:50 AM
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