So excited to build this with @mweber.bsky.social and @hattaca.bsky.social ! Together we’re combining geometric AI, multi-species genomics, and human cardiac organoids to ask why some animals regenerate their hearts and we can’t. Grateful to #Googleorg for the support. #AIforScience

Computational & Systems Biology Dept. at Pitt @csbpitt.bsky.social · 2w ago

We're thrilled to share that the lab of Assistant Professor Keisuke Ishihara has been selected as one of 17 recipients of the Google.org Impact Challenge: AI for Science! Learn more about the Impact Challenge and the Ishihara lab's work: tinyurl.com/IshiharaImpact #Googleorg #AIforScience

Bloop 🫧 bloop 🫧 bloop 🫧 Fluid-filled lumens are everywhere in our body How do they get soooo big? We find that osmotic pressure vastly dominates mechanical forces in controlling lumen swelling in mouse embryos biorxiv.org/content/10.6... @louise-dagher.bsky.social @matteo-bassanini.bsky.social

🚀 Rxiv-Maker is now peer-reviewed and open access! Write your manuscript in Markdown and get a typeset PDF or an editable Word file, with figures, citations and cross-references numbered for you. Led by Bruno Saraiva, with @guijacquemet.bsky.social's lab 🔬 doi.org/10.1242/jcs.265183

Are you a biologist working with microscopy images? A computer scientist wanting to work with microscopy data? Their boss??? None of these, but curious how AI has transformed microscopy image analysis? 🔬🤖 This one's for you: 📄 doi.org/10.1146/annu... More in the thread! 🧵

From Pixels to Discovery: Microscopy Image Analysis in the Age of Artificial Intelligence

Modern microscopy generates data volumes that far exceed human analytical capacity. Over the past decade, artificial intelligence (AI) has transformed microscopy image analysis into an engine for quan...

doi.org

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...

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...

nature.com

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 🔬

Bioinformatics Advances@bioinfoadv.bsky.social · last mo.

📐 New in Bioinformatics Advances: "pykarambola: Minkowski tensor morphometry of 3D structures"  Read it here: https://doi.org/10.1093/bioadv/vbag273 Authors include: @ishiharaksk.bsky.social

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)

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: 🧵

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.

🚀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!🚀

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...

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...

biorxiv.org

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/...

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...

science.org

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...

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.

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...

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.

Hey, I wrote a thing about AI in astrophysics ergosphere.blog/posts/the-ma...

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.

Miki Ebisuya@ebisuyamiki.bsky.social · 7mo ago

New preprint from the lab! How do tissue shapes influence cell fate decisions? By manipulating brain organoid geometry, we show that lumen rounding directs apical progenitor division mode and promotes the emergence of basal progenitors. www.biorxiv.org/content/10.6... 1/

One of my very favorite papers from the lab! Shows that individual cells can learn by forming memories. Amazing work by Jess Li!

Waggoner Lab@labwaggoner.bsky.social · 7mo ago

AP-1 mediates cellular adaptation and memory formation @natcomms.nature.com @pennmedicine.bsky.social @arjunraj.bsky.social @penngenetics.bsky.social www.nature.com/articles/s41...

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)

Nature Portfolio@natureportfolio.nature.com · 8mo ago

A study in Nature shows that the single-celled form of a tiny, aquatic organism can turn into a multicellular version by three different routes. The discovery adds insight to the possible origins of multicellular life, suggesting a previously unrecognized degree of flexibility. 🧪

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

Tubulin controls the number of microtubules!

bioRxiv Cell Biology@biorxiv-cellbio.bsky.social · 10mo ago

Tubulin autoregulation controls the biosynthesis of γ-tubulin to ensure mitotic fidelity https://www.biorxiv.org/content/10.64898/2026.01.09.698560v1

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

🎉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

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...

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 ...

biorxiv.org

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.

science.org

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

✨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. 🧵

bioRxiv Genomics@biorxiv-genomic.bsky.social · last yr.

Mechanistic Genome Folding at Scale through the Differentiable Loop Extrusion Model https://www.biorxiv.org/content/10.1101/2025.10.17.682904v1

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... 🧵

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...

biorxiv.org