Steffen Plunder
@SteffenPlunder
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Research in developmental biology with math and (Julia) programming (https://t.co/mWb9twr2XD). @uni_kl → @univienna → post-doc @Ashbi_KyotoU
ASHBi, Kyoto University
Joined January 2017
Want to try the models?*. Just click here; it runs even on your phone For extra fun, drag & drop the cells during the simulation! 😜 . The critical question to consider in the sims: .Which factors impact the direction of extrusion most?.
semtor.github.io
Interactive EMT simulator (sEMTor)
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RT @max28staff: 12月4日(水)にMACS共催で発生ー細胞生物学分野の国際シンポジウムが開催されます。.タイトル：Dynamics in Cell Communications.場所：北部キャンパス セミナーハウス.ウェブサイト：.
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RT @Seirin_Lab: My three postdocs, runners @jinghc2 @SteffenPlunder + manager @YingXie378208 , made it!!! 😄A Full marathon consisting of tw….
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RT @HiroFujiwara: Join us for the BDR/Multimodal ECM Seminar . "Shaping growing tissues by basement membrane mechanics".🗣️Dr. Stefan Harman….
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RT @RioTsusumi: 先週理研BDRで開かれていたEMBO/CoB Workshopでoral presentation prizeを貰いました。運営してくれた方への感謝を込めて、30000円(！)頂きました。一緒にデータやプレゼンを作ってくれた方々への感謝を込めて還….
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Since Zotero 7 recently got out, here is a great blog post by Ilya Kashnitsky on how to keep your papers/references sorted:.
fosstodon.org
Attached: 1 image Zotero tutorial is updated 🌟 https://ikashnitsky.phd/2024/zotero7/ Recently @zotero had a major update to version 7, which altered some of the long-standing routines. Hence I'm...
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New preprint with Claudia Wytrzens, Sara Merino-Aceituno and Havva Yoldaş: We coarse-grain a system with elliptic particles, which yields a complicated PDE. A cool feature is that alignment emerges from contact interactions, not explicit alignment terms.
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At the last JuliaCon, my second talk was purely for fun: ."A live coding music performance with Julia" | JuliaCon 2024: I'm still working on making the code presentable, but the code used is already online on my GitHub.
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New publication from Herny Jäger, Elise Grosjean on modeling of meniscus regeneration in a bio-engineering setting: It combines mechanics (elasticity equations) and models for intercellular signaling to model ECM production.
onlinelibrary.wiley.com
We study the dynamics of a seeding experiment where a fibrous scaffold material is colonized by two types of cell populations. The specific application that we have in mind is related to the idea of...
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RT @BBenazeraf: Very important work on the influence of tissue mechanics on embryonic axis formation !.
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I prefer twitter for science news. But hey, the right music is essential for pushing research!. Linkin Park is back.
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RT @JuliaLanguage: Julia and @ChapelLanguage continue their streak in the Fast + Small corner of the CLBG, illustrating once again that ver….
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Open Source.We used #JuliaLang for fast development without compromising runtime!. Reproduce correlation plots for heterogeneous EMT sims in the cloud-computing @CodeOceanHQ capsule (no installation needed):.
codeocean.com
Julia implementation for a computational model for epithelial-to-mesenchymal transition-like events in a pseudostratified epithelium. See also https://semtor.github.io/
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The computational challenge:.Heterogeneity is always tricky; there are too many possibilities 🤯 We went from 100 to over 150.000 sims to get proper correlation stats!. Possible, thanks to PBD! Not our invention, but totally underutilized in #biomath.→
arxiv.org
NVIDIA researchers have pioneered an explicit method, position-based dynamics (PBD), for simulating systems with contact forces, gaining widespread use in computer graphics and animation. While...
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TLTR.For cells to extrude basally at EMT, there is a seemingly optional sequence of events (A)?! But, in our simulations and stats, that sequence is far less correlated to basal extrusion than other factors like basal positional and early protrusive activities (B)! . [Fig. 10]
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It's also a back-to-back submission with @MigeotteLab: . Eric's idea to adapt our math model to #mouseembryo just worked, as we strictly followed the **minimal assumptions-only** rule from the beginning! 🤫 .
nature.com
Nature Communications - During mouse gastrulation the primitive streak is an area of cell division and epithelial-to-mesenchymal transition, though how mitoses and cell delamination are linked is...
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New publication in @NatureComms where we look at heterogeneous #EMT in #mouseembryo #neuralcrest. Combining computer models and in vivo experiments! My fav kind of #biomath! . Big thanks to @EricTheveneau, Sara Merino-Aceituno, and the team!.
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