Dipanjan Ghosh

Three-dimensional genome reorganization foreshadows zygotic genome activation in Drosophila - Nature Genetics Pico-C, a low-input Micro-C approach, reveals that dynamic three-dimensional genome folding precedes zygotic genome activation in Drosophila.

Excited to share my PhD work!

The question: How is genome organization established? Here, we developed a low-input Micro-C method, Pico-C, and used it to map chromatin architecture across early stages of fly development.

Here’s a quick Blue-torial 🙂 (1/n)

www.nature.com/articles/s41...

On Descriptive Geometry I keep forgetting I am writing for an international audience here! Having referred to Descriptive Geometry (DG) often, I doubt that everybody associates similar mental images with it. Anybody remem…

I am thinking about Descriptive Geometry today - its history, culture, my approach, and my pleasure in practicing an allegedly outdated craft:

New blog post:
elkement.art/2026/03/10/o...

Calling for protocols on The Basics: get a protocol recorded and peer reviewed, and help a colleague learn the tips and tricks by *seeing how it's done*
You don't need to include new results and it does not have to be your original protocol. Just cite well and share the know-how 💕🔥

Get in touch!

Cellquant: a vibecoder's guide to image analysis https://www.biorxiv.org/content/10.64898/2026.03.09.710634v1

First 24 hours of embryonic development in 9 different animal species: (From left to right) Zebrafish, Sea urchin, Black widow spider, Tardigrade, Sea squirt, Comb jelly, Parchment tube worm, Roundworm, Slipper snail. Credit to @tessamontague.bsky.social & Zuzka Vavrušová. #ZebrafishZunday #devbio 🧪

Thread 15: Neural Crest (focusing specifically on neural)

Again, I learned this information and compiled it from my notes on the Neural unit in my biology advisor's 2024 dev bio class.

This thread will largely focus on Path 1 Neural Crest Cells. (1/n)

Please check out our new preprint! Using single cell analysis paired with HCR to visualize transcript localization we have identified cell and tissue-specific expression of various genes encoding tubulins, kifs, and dyneins during neural crest development!

Stages of embryo development

How to draw an owl: Draw some circles. Draw the rest of the fucking owl.

It's slightly upsetting that many online diagrams of a blastocyst turning into an embryo are very 'how to draw an owl'

Break It To Make It: How Fracturing Sculpts Tissues and Organs | Quanta Magazine Growing tissues can crack, break, and dissociate to form structures that can later withstand immense forces.

Sometimes, the only way to build back up is to let everything fall apart. This is certainly true at the cellular level. www.quantamagazine.org/break-it-to-...

Thank you @ehannezo.bsky.social for a great day of Science and friends at @istaresearch.bsky.social. Good to see the the fruitful interface of Physics and #DevBio at work,

Excited to have started my new lab in Human Genetics at Pitt Public Health!

We study wound healing in diabetes & aging using adult zebrafish. Check out this movie showing neutrophil dynamics after injury.

Now recruiting research staff, grad students, and postdocs. DM me if interested.

Let's get this hashtag started! The 2026 Santa Cruz Developmental Biology Meeting is happen this August! We will share updates using #SCDB26.

Can't wait!

scdb2026.sites.ucsc.edu

Recent studies in living animals reveal that the cytoplasm is a thick, jam-like fluid. And yet, miraculously, hoards of molecules find their way to each other in every crowded cell. www.quantamagazine.org/the-biophysi...

We‘re looking for a motivated Master student to join our team!

Do you want to optogenetically control metabolic activity to see how metabolism affects patterning and morphogenesis? 💡🧫🧬🔬

Then please apply!
#optogenetics #metabolism #devbio #hESCs

Please RT. Thank you!🙏

Registration now open for the EMBO Workshop "Quantitative tissue morphogenesis - models, manipulations and mechanisms" in #Alibaug, India, 28 September–1 October 2026.

Deadline: 30 April 2026

https://meetings.embo.org/event/26-tissue-morphogenesis
#EMBOTissueMorphogenesis #EMBOevents 🧪

#ZebrafishZunday: Valentine's Day Edition ❤️ Beating heart of a transgenic zebrafish embryo. Credit to @zebrafish007.bsky.social. 🧪

The genome isn't a blueprint. But what is it?

I originally imagined this as a reported feature on metaphors of the genome, but it ended up being an essay.

And at the end I share the metaphor I personally ended up landing on. If you want to tell me why it is wrong, you'll need to read the story ;)🧪

Annnd we did Secret Santa gift exchange in February (again)😁! It seems like February Secret Santa has become our lab tradition now. Gastrulating into the holiday spirit in February ;).

New preprint! We show how mesoscopic nonequilibrium fluctuations in active gels emerge from the breaking of detailed balance at the molecular scale. Warning: Long technical paper ahead! Enjoy! @mpipks.bsky.social @ub.edu @ubics.bsky.social @icreacommunity.bsky.social

arxiv.org/abs/2601.20483

Advanced grad students + postdocs: apply for the 2026 #kitpqbio summer course, "Physical Principles of Morphogenesis in Plants and Animals," at buff.ly/OXXMKEv. Apply by Feb. 1.
Course directors Adrienne Roeder (Cornell) and Sebastian Streichan (UCSB)

Summer program for workshops at the Aspen Center for Physics

With @tzerhan29.bsky.social, @jasnir.bsky.social and Asja Radja, we are thrilled to organize an Aspen summer workshop (Aug 9-Sept 6) on the "Physics of Collective Function in Active Living Matter". Applications are open at aspenphys.org/event/physic... till Jan 15!!
Please share and apply soon!

Self-organized or instructed?

My @natrevgenet.nature.com Journal Club traces how classic papers revealed two modes of developmental patterning & why the debate between Turing and Wolpert is as timely as ever for organoid engineering today

www.nature.com/articles/s41...

Thread highlights new work from @nikhil-mishra.bsky.social & @heisenbergcplab.bsky.social 🐟

Link to open-access article: www.nature.com/articles/s41...

🔬 New paper in Developmental Biology 🐟
Our researchers have now tested a largely ignored hypothesis—that the geometry of an embryo drives its development. Read more in the 🧵below.

📷 Zebrafish in ISTA’s Aquatic Facility.

🚨 What if evolution is the ”law”… and networks are the machines that do the work?

In this paper (just published) I try to formalize how living systems are non-equilibrium, information-processing, adaptive matter. With a great biological flavor! 🧪🌐🌍🧬🦠

👉 iopscience.iop.org/article/10.1...

🧵 1/

Our review article is now available in Annual Review of Condensed Matter Physics: “Full-Integer Topological Defects in Polar Active Matter.” @luizaangheluta.bsky.social @emmalaang.bsky.social doi.org/10.1146/annu...

Now published in @natcomms.nature.com! 🥳

👉 rdcu.be/eATn3

We developed image analysis tools to capture the nematic orientation field of 3D tissue surfaces. Tested on epithelial aggregates, zebrafish hearts, myoblasts on spheres & micro-vessels, we combined soft matter physics with exp. biology.

Generative epigenetic landscapes map the topology and topography of cell fates | PNAS Epigenetic landscapes were proposed by Waddington as the central concept to describe cell fate dynamics in a locally low-dimensional space. In mode...

Very happy to share our 'Evoscape' paper, now published in PNAS ! www.pnas.org/doi/10.1073/...

A slow motion Christmas sea angel 👼🪽taken by Jamie with some of our dive-collected specimens from the Gulf of California #zooplankton #oceanography 🌊

Mapping genes to phenotype, using dynamical systems, by Pere Alberch (1991)

#Evolution #ComplexSystems 🧪🧬🌐

link.springer.com/article/10.1...