Associate Prof doing bioinformatics and computational neuro at @UofT and @CAMHresearch. Tweets about neurons, ephys, and single-cell RNAseq.
Toronto, Ontario
Joined February 2009
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my lab has been lucky to be using brisc over the last few months as early beta testers and I can say that it's truly transformative for you can do with single-cell data.
Thrilled to release the biggest project of my career: brisc, a full-fledged single-cell toolkit that runs multithreaded at 100x the speed of Scanpy and Seurat on tens of millions of cells.
brisc.run
brisc is transformative because it makes traditionally "slow" parts of the single-cell pipeline, like loading data and label transfer, super fast (like minutes on massive datasets). so it's trivial to test out multiple references for label transfer, etc.
I feel like brisc is best suited for situations where you have: 1) A LOT of data (say, like 2M+ cells), 2) have a huge, dense spatial omics dataset (like Atera?), 3) are doing a large snRNAseq meta-analysis (like what we did here: biorxiv.org/content/10.64898…).
My lab does something like a mix of traditional lab meetings (1 presenter for one hour) and continual update lab meetings (everyone briefly presents, 3-5 minutes per person). we do these in separate weekly meetings and it works fairly well.
Shreejoy Tripathy retweeted
John's paper is out. Can the transcriptomic profile of a neuron predict its physiological properties? A tale of ion channels and firing rate adaptation across species.
sciencedirect.com/science/ar…
who knew that countless hours playing starcraft in highschool would pay off handsomely in this era of agentic ai. still need more pylons though.
Shreejoy Tripathy retweeted
Thrilled to see PsychAD published! 🧠
A journey begun in 2019: 60+ investigators, 8 institutions, 1,494 human brains—illuminating brain aging and disease.
Supported by NIA. Made possible by the generosity of donors and families.
psych-ad.org/
nature.com/collections/jfibi…
New preprint from our lab: "Selective depletion of upper-layer somatostatin interneuron subtypes in schizophrenia." The largest case/control single-cell analysis of the schizophrenia brain to date. 🧵
biorxiv.org/content/10.64898…
We release full DE + abundance results for every cortical cell type, all code, and harmonized cell-type annotations for every cell in the 8 public datasets github.com/stripathy/scz_cel….
Really proud of this huge team effort led by the Nicole Endresz at @CAMH_KCNI and our great collaborators, @Etienne_Sibille, @gburgos412 and @LaramieDuncan. Comments welcome!
Really grateful to play a minor part in this exciting study led by @_GA_Craig and Veronica! Huge congrats to the team and excited to see it out!
Oligodendrocyte dysfunction in human age-related cognitive decline dlvr.it/TV977q
Shreejoy Tripathy retweeted
CIHR has been engaging the research community on how to keep the Project Grant program strong, fair, and sustainable as application volume rises.
Read more about key themes that emerged and what comes next: cihr-irsc.gc.ca/e/54795.html…
ALT Project grant update
Shreejoy Tripathy retweeted
Primate brains increased computational power and area specialization during evolution, not by making more neurons per volume of tissue, but by making large and complex 'psychic cells' in the newly evolved prefrontal cortex. nature.com/articles/s41467-0…
Shreejoy Tripathy retweeted
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