ShenoyLab
@ShenoyLab
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We develop theoretical concepts and computational models - mechanobiology, matrix mechanics, nano- and energy- materials. Tweets by group members. @CEMB_STC
University of Pennsylvania
Joined June 2020
6/6 🤝 Huge thanks to @ShenoyLab, @Melike_Lak, and @rp_mccord for the collaboration, and @CEMB_STC, the NCI MetNet - @NCIDCB! This work highlights the power of interdisciplinary science.
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5/6 🌟 Beyond domain architecture, we uncover mechanisms of epigenetic regulation, plasticity, and memory—advancing understanding of development, disease states, and targeted therapies.
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4/6 🔬 We applied our model to human mesenchymal stem cells, where it accurately predicts chromatin reorganization in response to substrate stiffness — highlighting its versatility across cell types and mechanical environments.
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3/6 🧫 In A375 melanoma cells, STORM validates our predicted domain sizes, Hi-C maps reveal boundary-driven compartment shifts, and RNA-seq identifies metastasis-related genes near shifting boundaries with altered expression.
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2/6 Our model shows that domain formation is governed by a balance: diffusion of methyl marks drives growth, while acetylation erases these marks and shrinks domains. As domain size adapts to drugs or the environment, boundary-proximal genes shift in and out, toggling expression.
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1/6 We built a sequencing-informed polymer model that integrates STORM, Hi-C, and RNA-seq to reveal how HC domains — especially their boundaries —regulate gene expression during drug treatment, microenvironmental changes, and cell fate transitions. https://t.co/1XLoJ8jXJE
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A new joint theory/experiment paper led by @ZeGongGreg just appeared in Nature Communications! We show how wave-like dynamics of immune cell podosomes arise from the coupling between chemo-mechanical signaling and actin diffusion. @CEMB_STC @PennEngineers
https://t.co/XFKklAYcDd
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Great news: the next meeting of the Invadosome Consortium (9th in this series) will take place in Vancouver, Canada, Oct. 01-04, 2024 Organizers: Karla Williams and Michael Olson Excellent science and beautiful nature, what´s not to like? ⚗️🌲 https://t.co/V9CEK1NTD6
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Incredible speaker lineup uncludes @KoleRoybal, @NF_Steinmetz, @KWhiteheadLab, @NatalieArtzi, @LindaGGriffith1, @ManishButte, @Tang_Lab_UCSF, @ValerieJHorsley , @BellasFATLab, @taabaman, @ShenoyLab, @DoloffLab, @SantiCorreaPhD, @JennyNJiang, @gail_l_rosen, @veiseho and many more!
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Come one, come all, I want to see you here this Fall! Register for #IMES2024! Trainees & early career investigators - submit your abstracts for a chance to win cash prizes and oral presentations! Travel Scholarships are available!🤑 Due: Oct. 1 Link:
drexel.edu
🚨 Last Call: Abstract Submission Deadline Approaching! 🚨 #IMES2024 is the only conference dedicated to convergent research in translational immunology and engineering. 📅 Deadline: Oct. 1, 2024 Submit here: https://t.co/o5gEmsdCdh Learn more: https://t.co/uKh4fLXK5c
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What balances the size of heterochromatic domains in our cells? @ShenoyLab et al explore the interplay of methylated histones, acetylation, and RNA polymerase II-driven supercoiling. Check out the sophisticated model led by Aayush Kant on @NatureComms
https://t.co/nzfxnmgdil
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Last day of the wonderful GRC on Signal Transduction by Engineered Extracellular Matrices #GRCSTEEM organized by Shelly Peyton and @kumarlabucb started with a session on multiscale modelling, with discussion leader Vivek Shenoy and first speaker @davidodde
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Great @CEMB_STC collaborative effort with @Melike_Lak @HeoLab and @MauckLab led by Monika Dhankhar, Zixian Guo and Aayush Kant.
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Our findings reveal how chemo-mechanical environment cues such as changes in cell extracellular matrix stiffness affect not only the availability of epigenetic regulators but also the mechanosensitive binding of heterochromatin to the nuclear lamina.
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By observing the size and shape of LADs via high-resolution STORM imaging by our amazing collaborators @Melike_Lak @HeoLab and @MauckLab, we can quantitatively extract the biophysical parameters - epigenetic reaction rate and chromatin-lamina affinity.
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We theoretically show that the size scale of LADs is dictated by epigenetic reaction rates. On the other hand, LADs could be either discrete bead-like shaped or elongated and spread-out along the nuclear lamina depending on the strength of chromatin-lamina interactions.
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New preprint on integrating biophysical computational modeling with high-resolution imaging to predict how epigenetics and chromatin-lamina interaction energetics regulate the size and shape of lamina-associated domains (LADs)! https://t.co/w5pFobaU3j
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