Data modeling. Co-founder @SaguaroAI. Occasional Bach & Shostakovich musings #fluorescence #ai #bayesian #biophysics #microscopy #optics #ABCsofDataModeling
Joined July 2020
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21 Dec 2025
It’s been 30 yrs since Zwanzig’s “non-eq stat mech”
As written, it has solidified the notion that theory develops models, and MD (perhaps) should be left to parametrize.
Maybe it’s time to re-pitch the work using functional integrals & tie this formulation to likelihoods :)
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Jun 9
New preprint out!
biorxiv.org/content/10.1101/…
Here, we developed the first framework for simultaneous particle tracking, phase retrieval and PSF reconstruction directly from the input data.
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Applied to lytic granules in T cells, our framework uncovered direct transport toward the immunological synapses followed by a slowdown near plasma membrane, revealing key dynamics of lytic granules during cell polarization.
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🚀 Major Announcement
I am honored to announce my new role as Director of the Center for Single Molecule Biophysics at the @ASUBiodesign @ASU .
biodesign.asu.edu/single-mol…
#ArtificialIntelligence #BiomedicalResearch #Biophysics #PrecisionMedicine @ASUResearch
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in human health.
I am excited to work with colleagues across ASU and our clinical partners to build this next chapter of interdisciplinary biomedical research.
Hiring soon at all levels.
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May 19
New preprint
“𝗦𝘁𝗼𝗰𝗵𝗮𝘀𝘁𝗶𝗰 𝗰𝗼𝗹𝗼𝗻𝗶𝘇𝗮𝘁𝗶𝗼𝗻 𝗮𝗻𝗱 𝗵𝗼𝘀𝘁-𝘁𝗼-𝗵𝗼𝘀𝘁 𝘁𝗿𝗮𝗻𝘀𝗺𝗶𝘀𝘀𝗶𝗼𝗻 𝘀𝗵𝗮𝗽𝗲 𝗴𝘂𝘁 𝗯𝗮𝗰𝘁𝗲𝗿𝗶𝗮𝗹 𝘃𝗮𝗿𝗶𝗮𝗯𝗶𝗹𝗶𝘁𝘆.”
biorxiv.org/content/10.64898…
Using C. elegans as host, we find that bacterial predators (bdellovibrio)
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act through suppression of host to host transmission of gut-expelled prey (E. Coli) bacteria in the environment rather than acting within the host!
This further exaggerates the stochastic effect of rare gut colonization on steady state host gut populations.
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May 13
How do we quantify molecules inside a cell?
Often, we make them fluorescent.
Thus, In single-cell experiments, it is natural to interpret a bright cell as a cell that is highly active.
In our new PNAS, we show how this can be misleading.
pnas.org/doi/10.1073/pnas.25…
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In our recent PNAS paper, we showed that explicitly accounting for this memory across cell divisions can qualitatively change the inferred biology. In a yeast stress-response system in yeast we observe that cells were only active ~5% of the time
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In summary:
High fluorescence doesn't always means active cells.
Sometimes, it is memory.
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Our PNAS is out 📢📢
doi.org/10.1073/pnas.2517309…
Biological snapshots can be misleading: fluorescence in a cell may reflect protein inherited from previous generations, not only current expression.
We fix account for this using simulation-based inference to recover hidden memory.
19 Jun 2025
No likelihood? No problem
The class of stochastic models we can simulate is A LOT larger than the ones we can write likelihoods.
What if we could learn the likelihood directly from simulation? See the 🧵👇
arxiv.org/abs/2506.09374
#SimulationBasedInference #Neuralnetworks #AI
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