Joined October 2013
- Tweets 1,976
- Following 1,212
- Followers 1,412
- Likes 8,013
168 Photos and videos
Pinned Tweet
18 Nov 2023
Excited to announce the Cook Lab will be opening at the Ottawa Hospital Research Institute Jan 2024. We'll be focusing on intratumoural heterogeneity and therapy resistance in ovarian cancer
Eager to work more with the ovarian cancer research community!
cooklab.ca
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David Cook retweeted
May 5
Hey Twitter!
~2 yrs ago we dropped a preprint on clonal analysis of mouse development. During revisions the computational side grew so much we split it in two: experimental & computational. Today's thread is about the latter. Let's dig in 🧵 biorxiv.org/content/10.64898…
26 Nov 2024
(1) Hi, X!
Don't miss Igor's thread about our recent preprint, it’s a very cool reading! Here I will try to go a bit deeper into the computational part of the study — our new method clone2vec, how we developed it, what it does, and what it doesn't do. Grab a drink, and let's go!
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David Cook retweeted
Mar 23
Excited to share our paper on engineering spatially targeted immune cells is now out in @NatImmunol. nature.com/articles/s41590-0…
#CRISPR activation screens reveal that engineering metabolite-sensing NK and T cells provides programmable mechanisms to target solid tumors.
Congrats to @komong0702, Mike Tsai, and the team!
Thanks to @ocrahope, @StanfordCancer, @AllenInstitute, @BWFUND, @czbiohub, @genome_gov, Tull Family Foundation, @stanfordcbio, @Stanford Genetics and @StanfordMed for the support.
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Mar 12
Thanks University of Ottawa for highlighting our work to improve outcomes for women with gynecologic disease. March is Endometriosis Awareness Month and it means a lot to see this focus not just on the science, but the patients who drive it.
🏆 Recipient of the Polanyi Prize in Physiology and Medicine for excellence in early-career research, Professor David Cook is advancing research into gynecologic diseases and paving the way for better healthcare for women.
🔗 uottawa.ca/research-innovati…
ALT Professor David Cook in his lab
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David Cook retweeted
26 Dec 2025
I just updated the scDiffEq Python API (v1.1.0) to include animated visualizations of simulations.
You can generate GIFs (or still images) showing:
- Temporal gene expression dynamics
- UMAP projections of simulated trajectories
During my PhD, I found animations like these useful in presentations.
Available now in the latest release: scdiffeq.com/_tutorials/visu…
22 Dec 2025
How does a stem cell "decide" its fate?
Development requires both reliability (consistent cell types) AND flexibility (diverse outcomes from identical progenitors). Cells achieve this by dynamically tuning deterministic drift and stochastic diffusion.
New in @NatMachIntell: scDiffEq models state-dependent drift AND diffusion, improving fate prediction by ~8% over SOTA. scDiffEq also enables genome-wide in silico perturbation screens and reveals temporal gene dynamics.
🧵nature.com/articles/s42256-0…
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David Cook retweeted
15 Nov 2024
Excited to share our recent manuscript out at @Nature . @piraner and @majo__duran from @roybal_lab and @Mohamad_Abedi and @AdamChazin in David Baker's lab engineered synthetic receptors that sense natural and designer soluble cues. nature.com/articles/s41586-0…
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David Cook retweeted
1 Nov 2024
📢Excited to share our work on @biorxivpreprint "Spatiotemporal map of the developing human reproductive tract at single-cell resolution"! Beyond grateful to our amazing team @ceci_icoresi @LuzGarAl @roserventotormo @MarioniLab and collaborators for their contributions. 🧵[1/10]
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David Cook retweeted
29 Oct 2024
A protein expression atlas on tissue samples and cell lines from cancer patients provides insights into tumor heterogeneity and dependencies. nature.com/articles/s43018-0…
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David Cook retweeted
28 Oct 2024
This is great! @NIAIDNews have launched a collection of public domain illustrations (currently 550 individual icons) bioart.niaid.nih.gov/
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1/🧵Excited to re-introduce Memento in (cell.com/cell/fulltext/S0092…), a scalable method for differential analysis of scRNA-seq data. It provides first-in-class performance in statistical power and calibration for comparing differences in mean, variability, and gene correlation.👇
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David Cook retweeted
19 Oct 2024
Interactive design and validation of antibody panels using single-cell RNA-seq atlases biorxiv.org/content/10.1101/…
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David Cook retweeted
17 Oct 2024
snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives👏 nature.com/articles/s42003-0…
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David Cook retweeted
10 Oct 2024
Happy publication day for us! Labor of love with @CoffmanLab #TLS #ovariancancer @UPMCHillmanCC @PittTweet
The activity of tertiary lymphoid structures in high grade serous ovar... sciencedirect.com/science/ar…
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David Cook retweeted
7 Oct 2024
🚀 Excited to share our new publication in @NatureBiotech! We explore scalable strategies for phenotypic screening using innovative methods with to address the challenges when the number of candidates is simply too large. Check out the details tinyurl.com/5f8vjhpp! (1/10)
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David Cook retweeted
4 Oct 2024
STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging | bioRxiv
@DrJasPlummer @hoheyn @pascual_reguant @eliseinsing @cnag_eu @ACEpigenetics @StJudeResearch biorxiv.org/content/10.1101/…
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David Cook retweeted
28 Sep 2024
3D cellular CODA maps of the fallopian tube are used to guide the design of "assembloids" that recapitulate the complex architecture and ciliated-based motion of oocytes.
See more here: science.org/doi/10.1126/scia…
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David Cook retweeted
12 Sep 2024
FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics | Nature Methods nature.com/articles/s41592-0…
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David Cook retweeted
6 Sep 2024
FixNCut: A Practical Guide to Sample Preservation by Reversible Fixation for Single Cell Assays bio-protocol.org/en/bpdetail…
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David Cook retweeted
2 Sep 2024
(1/n) Excited to announce a new article with @rafalab @AviSahuAI describing our approach scDist for finding cell types with transcriptional changes between conditions in single-cell data!
nature.com/articles/s41467-0…
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David Cook retweeted
26 Aug 2024
Using single-cell and spatial transcriptomics data, FlowSig provides a unified signaling modeling framework by connecting intercellular communication mediated by ligand-receptor interactions and intracellular gene expression modules.
nature.com/articles/s41592-0…
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David Cook retweeted
23 Aug 2024
Our new #paper is out in @NatImmunol. Applying #spatial transcriptomics at subcellular resolution to 130 ovarian #cancer tumors, followed by data-driven experimental design and high content #CRISPR screens to map immune evasion in ovarian cancer nature.com/articles/s41590-0… (1/15)
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