@LabPresse

Data modeling. Co-founder @SaguaroAI. Occasional Bach & Shostakovich musings #fluorescence #ai #bayesian #biophysics #microscopy #optics #ABCsofDataModeling

 Arizona State University, USA
labpresse.com
Joined July 2020
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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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Even fleeting glimpses can reveal molecular kinetics. Our new JCP article (pubs.aip.org/aip/jcp/article…) quantifies how much kinetic information is retained in brief or broken traces.

Many short traces are nearly as informative as one uninterrupted trace in recovering hidden-state...

Hidden Markov models are widely used to infer state-to-state kinetics from noisy traces (i.e., time series), but many experiments do not produce one uninterrupt

pubs.aip.org
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It’s been 23 years since I finished undergrad at @mcgillu @McGillChemistry 😬 Meeting up with Dr. Grazyna Wilczek, who had such a deep impact in my formative years after so long was very special. Thanks to all the educators who continue to inspire. 🙏
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Steve thoughts alone: New 50% US tariffs imposed by the Trump admin affect ~ $20B imported from 🇨🇦, which translates to ~ 5.2% of U.S. goods imported from 🇨🇦 Straight out the academic handbook: not picking one’s battles and ruining one’s reputation over a 2.6% net change.
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Good morning from Arizona (Echinopsis candicans)
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Our recent PNAS and Nature Communications papers were recently featured in ASU News. Check it out!! news.asu.edu/20260701-scienc… A testament to our great team. #ASU #PNAS #NatureCommunications #Biophysics #Bayesian
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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.

Accurate tracking of lytic granules via simultaneous particle tracking, phase retrieval and point...

3D tracking and localization of particles, typically fluorescently labeled biomolecules, provides a direct means of monitoring cellular transport and communication. However, sample-induced wavefront...

biorxiv.org
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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

Center for Single Molecule Biophysics | ASU Biodesign Institute

The Biodesign Center for Single Molecule Biophysics allows researchers to study the physical processes on which life is based using cells and tissue.

biodesign.asu.edu
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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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#SingleMoleculeBiophysics #ComputationalBiology #BayesianInference #ArizonaStateUniversity #BiodesignInstitute
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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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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…

Simulation-based inference captures non-Markovian effects as exemplified in protein production...

Inferring protein production kinetics in dividing cells is complicated by protein inheritance from the mother cell. For instance, fluorescence meas...

pnas.org
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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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