Postdoctoral researcher at @JohnsHopkinsSPH ; Neuroscientist ; Computational Biology. Person who stutters; Opinions are my own
Joined September 2009
- Tweets 5,600
- Following 1,530
- Followers 1,229
- Likes 18,548
260 Photos and videos
Pinned Tweet
17 Sep 2025
Very excited to share my second postdoc paper with you all, now out in @ScienceAdvances! We used targeted snRNA-seq to profile four major subnuclei of the primate across three species (including humans). 1/14 science.org/doi/10.1126/scia…
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Michael Totty retweeted
Jun 10
Arguably the most boring step in genomics is the first one: normalization. Settled science. Scale log. Move on.
Except that here's been a huge blind spot in the field. And it matters for AIxBio. A 🧵about what I think may be one of the most important papers I've written. 1/
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Michael Totty retweeted
May 14
NEW: A serious staffing shortage — of the Trump admin's own making — is delaying the agency's ability to send billions to universities around the US, leaving labs reeling.
“I thought we were at rock bottom”, a senior NIH official said. “We are below rock bottom now.”
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May 11
19 on my K99 resubmission! Massive thanks to my mentors and letter writers for all their support. Hard to tell if it will actually translate to funding in this climate, but I'll take the win regardless!
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May 11
Fwiw, my initial submission was scored competitively (26) last August and it finally bumped to "Pending" 40 days ago. Still no word, but maybe I'll get an NOA one of these days! I know others are in the same boat.
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Michael Totty retweeted
Apr 14
Online now: Dual-engram architecture within a single striatal cell type distinctly controls alcohol relapse and extinction dlvr.it/TS2Fkt
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Michael Totty retweeted
Apr 12
If you use dim. reduction, you may be interested in two recent preprints we've posted on contrastive PCA:
The Rayleigh Quotient and Contrastive Principal Component Analysis I & II
w/ @MariaCarilli & Kayla Jackson. They cover a lot of ground from theory to practice. 1/🧵
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Michael Totty retweeted
Apr 3
❗️❗️❗️NEWS︱Nature Neuroscience
👏👏👏Prof. Tianle Xu’s Team Uncovers Core Molecular Mechanisms Underlying the Formation and Extinction of Fear Memories.
👇MORE
nature.com/articles/s41593-0…
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SpaLP
Spatial Local Pooling
Index matrix (linear!)🤠
Cluster Visium HD 1.2M cells, 18k transcripts, 2 sections in 43 s🤯
vs adjacency matrix #GraphNeuralNetwork method BANKSY NicheCompass HERGAST
300-fold⏫computational efficiency
Cross-platform integration - STARmap PLUS MERFISH CosMx Xenium Visium HD Stereo-seq
3D spatial atlas MERFISH 8.4M cells, 239 sections on a single GPU in 4 min
A local pooling-based spatial omics foundation model😎
@BingjDai bioRxiv 2026
biorxiv.org/content/10.64898…
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Michael Totty retweeted
EVoC is a library designed specifically for fast clustering of high dimensional embedding vectors. It can produce high quality clusters extremely efficiently, and requires little to no hyperparameter tuning.
Better clustering than UMAP HDBSCAN; faster clustering than KMeans.
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Michael Totty retweeted
Mar 25
cell types are hierarchical, but single-cell models ignore this
we introduced hierarchical cross-entropy: a simple loss to align models with biological ontologies to improve cell type annotation
nature.com/articles/s43588-0… @NatComputSci
great work @sebacultrera @davide_dascenzo!
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Mar 22
I’ve never seen a fanbase so out of touch with a sport. It’s like this really was the second basketball game they’ve ever watched before.
Mar 22
I don’t know why I’m so triggered by this Nebraska fanbase. It’s like the small town high school that is just angry for 2 hours at the officials and they actually have no idea why.
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Michael Totty retweeted
Mar 22
I don’t know why I’m so triggered by this Nebraska fanbase. It’s like the small town high school that is just angry for 2 hours at the officials and they actually have no idea why.
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Michael Totty retweeted
Mar 19
New leaked Epstein documents show the FBI removed the hard drive from the prison's camera system and wiped all footage from the night Jeffrey Epstein was murdered..
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Michael Totty retweeted
Stress undermine behavioral therapies for PTSD; beta-blockers may alleviate this problem. We hope that this work in animals will inform clinical interventions in humans. Thanks to @NIH for supporting the work and my lab group @BeckmanIllinois for this outstanding effort!
One of the most-viewed PNAS articles in the last week is “Locus coeruleus–amygdala circuit disrupts prefrontal control to impair fear extinction.” Explore the article here: ow.ly/zQbQ50Ywubf
For more trending articles, visit ow.ly/EqH150Ywub9.
ALT Stimulation of BLA-projecting LC neurons promotes the IED. (A) Surgery schematic. (B) Behavioral schedule—6 wk after surgeries, animals received injections of VEH or CNO, and underwent the same immediate extinction procedure as described above in panel B. (C) The animals that received injections of hM3Dq-carrying viruses and CNO injections had higher freezing levels during conditioning, immediate extinction and retrieval when compared to the other groups.
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Michael Totty retweeted
Mar 18
Please stop insulting the centuries of effort put in by biologists & computational biologists who built those prior knowledge networks & literature that u piggy back on by calling ur nearest neighbor look up engine a virtual cell. 26/
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Michael Totty retweeted
Mar 16
By tracking nearly every movement of a tiny fish’s life from adolescence to death, a new Science study reveals a hidden behavioral blueprint of aging—one that can predict a fish’s age or how long an individual will live.
Learn more: scim.ag/4dm1GA9
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Michael Totty retweeted
Mar 16
Vanderbilt vs. the actual 4 seeds—hard to figure
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Michael Totty retweeted
Mar 16
Vanderbilt & Michigan State: both No. 4s in bracket preview on Feb. 21
MSU: one Q1A win since then | 2 wins over tourney teams. Rose to a 3
Vandy: three Q1A wins | 4 wins over tourney teams. Fell to a 5
Brand bias at its worst.
cbssports.com/college-basket…
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Michael Totty retweeted
Mar 10
Spatial perturb-seq: single-cell functional genomics within intact tissue architecture
Scale up your in situ CRISPR screens
Out in @NatureComms
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