Keisuke Ishihara
@ishiharaksk.bsky.social
Assistant Professor, University of Pittsburgh. cell biology, biological physics, synthetic morphogenesis of brain and cardiac organoids
Reposted by Keisuke Ishihara
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...
Preprint: www.biorxiv.org/content/10.1...
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 ...
www.biorxiv.org
November 26, 2025 at 9:29 PM
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...
Preprint: www.biorxiv.org/content/10.1...
Reposted by Keisuke Ishihara
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/...
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.
www.science.org
November 20, 2025 at 7:46 AM
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/...
Reposted by Keisuke Ishihara
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
Six Parts
1/6
October 25, 2025 at 12:16 PM
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
Six Parts
1/6
Reposted by Keisuke Ishihara
✨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.
🧵
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.
🧵
Mechanistic Genome Folding at Scale through the Differentiable Loop Extrusion Model https://www.biorxiv.org/content/10.1101/2025.10.17.682904v1
October 21, 2025 at 1:51 PM
✨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.
🧵
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.
🧵
Reposted by Keisuke Ishihara
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...
🧵
@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...
🧵
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...
www.biorxiv.org
October 10, 2025 at 12:50 PM
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...
🧵
@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...
🧵
Reposted by Keisuke Ishihara
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...
1/
doi.org/10.1101/2025...
October 8, 2025 at 1:05 PM
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...
1/
doi.org/10.1101/2025...
Reposted by Keisuke Ishihara
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
Interfolio link: apply.interfolio.com/174360
PLEASE, share widely across the blue skies!
Let me briefly explain what we're looking for:
1/10
September 26, 2025 at 3:35 PM
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
Interfolio link: apply.interfolio.com/174360
PLEASE, share widely across the blue skies!
Let me briefly explain what we're looking for:
1/10
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!
The second annual Pittsburgh Biological Physics Day showcased vibrant research in the Pittsburgh area that merged principles of physics and biology.
Read more about the event: tinyurl.com/BioPhysics2025
Read more about the event: tinyurl.com/BioPhysics2025
Second annual Pittsburgh Biological Physics Day showcases research - Department of Computational and Systems Biology
The second annual Pittsburgh Biological Physics Day was held on Sept. 16 at the Mellon Insitute. This event showcased vibrant research in the Pittsburgh area that merged principles of physics and biol...
tinyurl.com
September 19, 2025 at 9:08 PM
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!
Reposted by Keisuke Ishihara
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
www.nature.com/articles/s41...
A joy to work with super team Sarah Plattner, Yuka Sugiura, Francisco Falcon and Elly Tanaka.
🧵1/14
May 21, 2025 at 3:05 PM
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
www.nature.com/articles/s41...
A joy to work with super team Sarah Plattner, Yuka Sugiura, Francisco Falcon and Elly Tanaka.
🧵1/14
Reposted by Keisuke Ishihara
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 👇
How can organs regenerate fast? Bioelectricity helps -- by coupling sub-second electrical injury signals to regenerative proliferation.
First preprint from my potsdoc :D with @liujinghui.bsky.social @ritamateus.bsky.social @mpi-cbg.de and collaborators @mpipks.bsky.social @csbdresden.bsky.social
First preprint from my potsdoc :D with @liujinghui.bsky.social @ritamateus.bsky.social @mpi-cbg.de and collaborators @mpipks.bsky.social @csbdresden.bsky.social
April 9, 2025 at 2:19 PM
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 👇
Reposted by Keisuke Ishihara
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
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.
openrxiv.org
March 11, 2025 at 1:20 PM
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
Reposted by Keisuke Ishihara
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...
March 10, 2025 at 2:43 AM
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...
Awesome work on torque topology and cell division orientation in the fly embryo!
1/n Wanted to share this latest piece of work that came online today on how Scale-independent and Topological interactions govern the spindle orientation and in turn the decision to become embryonic/yolk nuclei.
Freely available to read here:
rdcu.be/ebb0l
Freely available to read here:
rdcu.be/ebb0l
Topological interactions drive the first fate decision in the Drosophila embryo
Nature Physics - Early positioning of the embryo nuclei is not well understood. Now, experiments show that the orientation of the mitotic spindle is controlled by topological interactions, which...
rdcu.be
February 27, 2025 at 10:30 AM
Awesome work on torque topology and cell division orientation in the fly embryo!
Reposted by Keisuke Ishihara
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
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
February 7, 2025 at 4:06 PM
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
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
Reposted by Keisuke Ishihara
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...
February 9, 2025 at 3:10 AM
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...
Reposted by Keisuke Ishihara
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
featuring @bielleogy.bsky.social @atinygreencell.bsky.social
December 22, 2024 at 7:36 PM
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
featuring @bielleogy.bsky.social @atinygreencell.bsky.social
Reposted by Keisuke Ishihara
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...
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...
www.biorxiv.org
December 21, 2024 at 8:17 AM
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...
Reposted by Keisuke Ishihara
🧵 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:
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-
doi.org
December 20, 2024 at 1:00 PM
🧵 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:
Reposted by Keisuke Ishihara
Our latest: how to generate the notochord
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
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.
www.nature.com
December 19, 2024 at 8:52 AM
Our latest: how to generate the notochord
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
"Timely TGFβ signalling inhibition induces notochord"
A thread:
www.nature.com/articles/s41...
Reposted by Keisuke Ishihara
A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.
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
media.tenor.com
November 24, 2024 at 11:31 AM
A bluetorial about some challenges for our two-career family and some flaws in the culture of biomedical research.
Reposted by Keisuke Ishihara
😱📣 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...
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...
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
careers.humantechnopole.it
October 27, 2023 at 3:05 PM
😱📣 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...
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...
Reposted by Keisuke Ishihara
We are hiring compbio faculty at all career stages! www.linkedin.com/posts/univer...
@pittcsb.bsky.social
@pittcsb.bsky.social
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…
www.linkedin.com
November 18, 2024 at 4:28 PM
We are hiring compbio faculty at all career stages! www.linkedin.com/posts/univer...
@pittcsb.bsky.social
@pittcsb.bsky.social
Reposted by Keisuke Ishihara
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
November 19, 2024 at 12:49 PM
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
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
November 19, 2024 at 12:49 PM
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