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Keisuke Ishihara

@ishiharaksk.bsky.social
309 followers 380 following 8 posts

Assistant Professor, University of Pittsburgh. cell biology, biological physics, synthetic morphogenesis of brain and cardiac organoids www.ishiharalab.bio

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Reposted by Keisuke Ishihara
Lennart Hilbert @lennarthilbert.bsky.social · 02/10/2026
Normalization: most important part of any analysis, also the part nobody talks about. This paper, in my view, is all about appropriate normalization. Then check against “all available data”, and get one clean conclusion. Really neat! Joe Paggi @binzmit.bsky.social www.nature.com/articles/s41...
nature.com
Euchromatin forms condensed domains with short active regions on the surface - Nature Genetics
Simulations integrating micro-C and imaging data provide a coherent view of chromatin organization from nucleosomes to clutches to domains, revealing that most regions form compact domains but short r...
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Keisuke Ishihara @ishiharaksk.bsky.social · 24/09/2026
We’re happy to see our pykarambola software paper out in @bioinfoadv.bsky.social ! Minkowski tensor computation is now immediately accessible to Python-based research community. Stay tuned for a story on how we leverage this for 3D bioimage analysis 🔬
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 08/09/2026
Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @natgenet.nature.com reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation🚧 🔗 www.nature.com/articles/s41... (1/2)
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Nozomu Yachie @nzmyachie.bsky.social · 04/09/2026
Maybe it’s time to say goodbye to UMAP and other low-dimensional embeddings (at least in many single-cell analyses). We developed MILK to encode single-cell populations into tree representations at unprecedented scales. www.biorxiv.org/content/10.6... Here’s what MILK is: 🧵
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Paul Francois @pfrancois.bsky.social · 14/07/2026
New paper 🧵 What if the "landscape" that guides cell differentiation isn't fixed, but is sculpted, in real time, by the very cells moving through it? We call this a 'sandscape' : grains of sand that carve dunes as they move, while the dunes' shape simultaneously steers where the grains go next.
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Shayan Shamipour @shamipourshayan.bsky.social · 03/07/2026
🚀Excited to share our latest efforts in bringing highly multiplexed whole-mount imaging to intact multicellular systems! Shield-4i: an integrated platform to study multi-scale information flow in 3D embryos and embryo-like systems. Kudos to @rhornb.bsky.social for this major milestone in the lab!🚀
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James Briscoe @jamesbriscoe.bsky.social · 08/06/2026
Our latest: Minimal essential requirements for neural tube self-organisation How does a single cell give rise to a tissue with the right cell types in the right proportions? We deconstruct and rebuild a self-organising tissue from first principles A thread🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Minimal essential requirements for neural tube self-organisation
The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from p...
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Reposted by Keisuke Ishihara
Tjian + Darzacq Lab, UC Berkeley @tjiandarzacq.bsky.social · 02/06/2026
Out now in Science! Our study challenges long-standing assumptions about transcription factor specificity in eukaryotes. Novel single-molecule measurements of TF behavior in living cells reveal an independence of locus-specific binding from DNA sequence recognition.🧵 www.science.org/doi/10.1126/...
science.org
Unstructured transcription factor interactions enable emergent specificity
How intrinsically disordered regions (IDRs) shape chromatin binding and nuclear organization of transcription factors (TFs) remains unclear. We used proximity-assisted photoactivation (PAPA), a single...
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Reposted by Keisuke Ishihara
James Gagnon @james-gagnon.bsky.social · 28/04/2026
Using light-activated CRISPR in zebrafish, we triggered synchronized DNA breaks and track the repair process. ⚡🐟⚡ 

 Well ... DNA repair is very different in embryos compared to tissue culture cells. Embryos repair DNA breaks incredibly fast - within minutes! www.biorxiv.org/content/10.6...
A cartoon showing how a caged guide RNA poises CRISPR cleavage until release by light. Below, a cartoon of injection of "light-activated CRISPR" into the embryo, followed by activation.
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Institute of Science and Technology Austria (ISTA) @istaresearch.bsky.social · 16/04/2026
Photosynthetic bacteria helped shape Planet Earth. Among them cyanobacteria—microbes that produced the oxygen in Earth’s atmosphere & made complex life possible. They have captivated scientists for decades by offering insights into how life evolved from single cells into multicellular organisms.
Fluorescent Anabaena. Fluorescently labelled CorM filaments inside Anabaena. These represent a newly discovered cytoskeleton in multicellular cyanobacteria. © Loose group
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Reposted by Keisuke Ishihara
Kyogo Kawaguchi @kyogok.bsky.social · 18/04/2026
Hearts have topological defects. By treating the mouse myocardium as a 3D nematic, we found disclination lines threading through it. In situs inversus hearts, twist must match structural chirality for contraction to work, as found by quantifying the nematic chirality. biorxiv.org/content/10.6...
biorxiv.org
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Xavier Trepat @xaviertrepat.bsky.social · 17/04/2026
Our latest work on shape-programmable tissues is out in @science.org. By positioning topological defects in cellular nematics, we encode frustrated 2D force fields that relax into predictable 3D shapes. Collaboration with Marino Arroyo’s lab, led by @pauguillamat.bsky.social at @ibecbarcelona.eu.
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Minas Karamanis @minaskar.bsky.social · 30/03/2026
Hey, I wrote a thing about AI in astrophysics ergosphere.blog/posts/the-ma...
ergosphere.blog
The machines are fine. I'm worried about us.
On AI agents, grunt work, and the part of science that isn't replaceable.
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Keisuke Ishihara @ishiharaksk.bsky.social · 01/04/2026
Check out the powerful chemical biology tool developed by @marchowl.bsky.social to manipulate tissue geometry and progenitor emergence! It was a pleasure to quantitatively interpret the geometric changes observed in these experiments.
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Reposted by Keisuke Ishihara
Arjun Raj @arjunraj.bsky.social · 21/03/2026
One of my very favorite papers from the lab! Shows that individual cells can learn by forming memories. Amazing work by Jess Li!
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Reposted by Keisuke Ishihara
Thibaut Brunet @thibautbrunet.bsky.social · 28/02/2026
Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating). A brief 🧵 (carried over from the old place)
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Brugues Lab @brugueslab.bsky.social · 28/01/2026
Really excited to share our new paper in @nature.com! We uncovered how a physical instability of the cytoplasm coupled with the cell cycle drives cytoplasmic partitioning in early embryos #zebrafish #drosophila. Read more in this🧵 www.nature.com/articles/s41... 🤩 @poldresden.bsky.social @mpi-cbg.de
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Manuel Thery @manuelthery.bsky.social · 10/01/2026
Tubulin controls the number of microtubules!
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Brugues Lab @brugueslab.bsky.social · 07/01/2026
Excited to share Alison's @alisonkickuth.bsky.social paper from the lab out in @nature.com this week! We uncovered how a mechanical ratchet mechanism drives cytokinesis in early #zebrafish embryos. Read more in this thread 🧵 and at www.nature.com/articles/s41... 🤩 @poldresden.bsky.social @mpi-cbg.de
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Physics of Life Dresden @poldresden.bsky.social · 07/01/2026
🎉Exciting findings out today in Nature @nature.com from the PoL group of Jan Brugués @brugueslab.bsky.social! The authors describe a new mechanism driving cell division during early development in #zebrafish, fundamentally altering our view of the process. Read the press release: tud.link/2s3bxj
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Martin Loose @nartimsoole.bsky.social · 26/11/2025
Happy to share a new preprint from the lab: Marko became interested in whether the disordered linker of FtsZ might influence how the protein organizes into the Z-ring. And this led to some surprising findings! Preprint: www.biorxiv.org/content/10.1...
biorxiv.org
Charge segregation in the C-terminal linker of FtsZ enables Z-ring scaling with prokaryotic cell width
Bacterial cytokinesis is orchestrated by the Z-ring, a cytoskeletal structure formed by treadmilling filaments of the tubulin-like GTPase FtsZ. During assembly, filament curvature must match the cell ...
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Kyogo Kawaguchi @kyogok.bsky.social · 20/11/2025
To probe gene-scale chromatin physics, we built 96-mer (20 kb) arrays with defined histone marks. Combining single-molecule tracking, AFM imaging, and developing in vitro Hi-C, we saw how specific modifications dictate chromatin structure and dynamics. www.science.org/doi/10.1126/...
science.org
Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture
Reconstituting 20-kb chromatin shows that tuning acetylation alone reshapes its folding, dynamics, and contact domain formation.
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Reposted by Keisuke Ishihara
Jeremy Berg @jeremymberg.bsky.social · 25/10/2025
Here is the video of the segment with me and @vscooper.micropopbio.org on WTAE (ABC) in Pittsburgh from last night Six Parts 1/6
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Tina Šubic @tincamalinca.bsky.social · 21/10/2025
✨New preprint!✨ We built dLEM - a differentiable Loop Extrusion Model that bridges biophysics and machine learning for 3D genome folding. dLEM makes loop extrusion learnable and interpretable—predicting how genomes fold and how they respond to perturbations. 🧵
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Çağrı Çevrim @cagricevrim.bsky.social · 10/10/2025
I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉 @karalmckinley.bsky.social We built the first transgenic model of menstruation in mice. We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪 www.biorxiv.org/content/10.1... 🧵
biorxiv.org
Induction of menstruation in mice reveals the regulation of menstrual shedding
During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...
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Reposted by Keisuke Ishihara
Miki Ebisuya @ebisuyamiki.bsky.social · 08/10/2025
New preprint from the lab! We discovered a transient fluidization in the basal region of human forebrains by tracking microdroplets in cerebral organoids.This “basal fluidization”, absent in gorilla and mouse, may contribute to greater surface expansion in human forebrains 1/ doi.org/10.1101/2025...
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Markus Deserno @markusdeserno.bsky.social · 26/09/2025
I am super excited to announce that we have a tenure-track faculty position in biophysics open in the Department of Physics at Carnegie Mellon! 🧪 Interfolio link: apply.interfolio.com/174360 PLEASE, share widely across the blue skies! Let me briefly explain what we're looking for: 1/10
Tenure-track Position in Biophysics at Carnegie Mellon University, Department of Physics

Location: Pittsburgh, PA
Open Date: Sep 19, 2025

Description
The Department of Physics at Carnegie Mellon University invites applications for a tenure-track faculty position in biophysics. The appointment is intended to be at the Assistant Professor level, but exceptional candidates at a higher level may also be considered. We seek outstanding candidates with a strong record in cellular and subcellular biophysics. Topics of particular interest include, but are not limited to, uncovering how key characteristics of living systems arise from the interplay between supramolecular cellular structures, how the emergent cellular circuitry defines goals and enables robust decision making, and how metabolic resources are allocated. This encompasses understanding of how information is learned, stored, transduced, and processed across subcellular structures. Applicants with theoretical, data science, or experimental backgrounds within biological physics are encouraged to apply. The ideal candidate will strengthen and extend research programs of current biophysics faculty in the Department of Physics and collaborate with broader life science activities across many departments at CMU and the wider Pittsburgh area.

More details on Interfolio: https://apply.interfolio.com/174360
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Keisuke Ishihara @ishiharaksk.bsky.social · 19/09/2025
It was great discussing latest research from Pittsburgh-based researchers and our two invited speakers. Stay tuned for next year's Pittsburgh Biological Physics Day!
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Reposted by Keisuke Ishihara
Leo Otsuki @leootsuki.bsky.social · 21/05/2025
Delighted that our work on positional memory is now published. We asked how axolotl cells 'know' which part of the limb to regenerate after injury. www.nature.com/articles/s41... A joy to work with super team Sarah Plattner, Yuka Sugiura, Francisco Falcon and Elly Tanaka. 🧵1/14
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Rita Mateus @ritamateus.bsky.social · 09/04/2025
Super proud of superstar postdocs @nerlielisa.bsky.social and @liujinghui.bsky.social for our lab's most recent preprint! We uncover how wound-induced electrical currents are generated and transmitted in tissues, triggering proliferation, essential for organ #regeneration #bioelectricity #QBio 👇
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Richard Sever @richardsever.bsky.social · 11/03/2025
Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n
openrxiv.org
Homepage - openRxiv
openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.
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Rashmi Priya @rashmi-priya.bsky.social · 10/03/2025
Stoked to present our latest, superbly led by Chris et al & @torres-sanchez.bsky.social We tackled a fundamental problem – how tissues are patterned during development – found that geometry-constrained ECM fractures pattern the myocardium in the vertebrate heart 1/n www.biorxiv.org/content/10.1...
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Keisuke Ishihara @ishiharaksk.bsky.social · 27/02/2025
Awesome work on torque topology and cell division orientation in the fly embryo!
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Reposted by Keisuke Ishihara
Jeremy Berg @jeremymberg.bsky.social · 07/02/2025
ATTENTION If you are someone who had an F31-Diversity (or similar) application submitted this cycle, please DM me here, contact me on signal (jeremymberg.78), or email me at jeremymberg@gmail.com. I will keep all information confidential. 2/n
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Craig Kaplan @triggerloop.bsky.social · 09/02/2025
Very important to see local/state papers covering this. Here is the story from the Pittsburgh Post-Gazette to add to the Alabama story www.post-gazette.com/business/hea...
post-gazette.com
New NIH policy: Pitt faces 25% cut in federal research money
‘We can’t do the science if we can’t keep the lights on.’
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bioZone @thebiozone.bsky.social · 22/12/2024
Science isn’t always linear. More often than not, new discoveries make us re-evaluate what we once thought we knew for certain. The Twitter/X-famous #BlueSoup saga is a great example of this! Learn more here: youtu.be/6g-gNJcGsLY featuring @bielleogy.bsky.social @atinygreencell.bsky.social
mysteries of science: the #bluesoup saga featuring interviews from Sebastian Cocioba and Elinne Becket. now on YouTube
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David Oriola @davidoriola.bsky.social · 21/12/2024
Really happy to share with you my last work from my time in @embl.org with the @viktri08.bsky.social group. We studied the dynamics of cell fate transition in gastruloids and found that cells communicate with each other to control the timing of symmetry breaking. www.biorxiv.org/content/10.1...
biorxiv.org
Cell-cell communication controls the timing of gastruloid symmetry-breaking
In the embryo, morphogenetic signals instruct regional patterning thereby defining the body axes of the future animal. Remarkably, in the absence of such signals, collections of pluripotent stem cells...
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Tina Šubic @tincamalinca.bsky.social · 20/12/2024
🧵 We @mosaicgroup.bsky.social just published in @aip-publishing.bsky.social JChemPhys (doi.org/10.1063/5.02...): Turns out that grid resolution in stochastic reaction-diffusion models represents molecule size! This completely changes how we understand "reaction loss" in these models:
doi.org
Loss of bimolecular reactions in reaction–diffusion master equations is consistent with diffusion limited reaction kinetics in the mean field limit
We show that the resolution-dependent loss of bimolecular reactions in spatiotemporal Reaction–Diffusion Master Equations (RDMEs) is in agreement with the mean-
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James Briscoe @jamesbriscoe.bsky.social · 19/12/2024
Our latest: how to generate the notochord "Timely TGFβ signalling inhibition induces notochord" A thread: www.nature.com/articles/s41...
nature.com
Timely TGFβ signalling inhibition induces notochord - Nature
Through analysis of developing chick embryos and in vitro differentiation of embryonic stem cells, a study develops a method to generate a model of the human trunk with a notochord.
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Jeremy Berg @jeremymberg.bsky.social · 24/11/2024
A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.
media.tenor.com
homer simpson from the simpsons is holding a cup in front of a picture
ALT: homer simpson from the simpsons is holding a cup in front of a picture
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Florian Jug @florianjug.bsky.social · 27/10/2023
😱📣 BlueSky-ers: WE NEED YOUR HELP!!! 🙏 All of you who ever liked a lecture of mine... All of you who liked one of the courses I teach in... All of you I work(ed) with in one way or another... All of you who see my desperation! 😜 PLEASE re-post! 🙏 careers.humantechnopole.it/o/postdoc-in...
careers.humantechnopole.it
Postdocs in Artificial Intelligence
Human Technopole (HT) is an interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health
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David Ryan Koes @dkoes.compstruct.org · 18/11/2024
We are hiring compbio faculty at all career stages! www.linkedin.com/posts/univer... @pittcsb.bsky.social
linkedin.com
University of Pittsburgh Computational and Systems Biology on LinkedIn: #hiring
We are now #hiring! The Department of Computational and Systems Biology is accepting applications for full-time, tenure stream Assistant and Associate…
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Keisuke Ishihara @ishiharaksk.bsky.social · 19/11/2024
Join our department as faculty! We work on broad topics in biomedical science with a shared passion in quantitative and computational approaches: www.csb.pitt.edu
csb.pitt.edu
Department of Computational Systems Biology | School of Medicine | University of Pittsburgh
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Keisuke Ishihara @ishiharaksk.bsky.social · 19/11/2024
Join our department as faculty! We work on broad topics in biomedical science with a shared passion in quantitative and computational approaches: www.csb.pitt.edu
csb.pitt.edu
Department of Computational Systems Biology | School of Medicine | University of Pittsburgh
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