Debraj Ghose

Memory from variability: Heritable short-term cellular memory emerges from stochastic biochemical reaction networks Cells exhibit a mysterious form of selective heritable short-term memory, influencing outcomes as diverse as cell fate decisions in embryos and environmental responses in cancer cells and bacteria. He...

Thrilled that the lab's first @hhmijanelia.bsky.social project is up on bioRxiv! Story behind the story to follow. www.biorxiv.org/content/10.6...

Sit with this for a moment.

ERC-Plus: jackpot science or missed chance to fix academia? My reflections on ERC-Plus, Europe’s newest ultra-competitive research grant and what it tells us about the academic culture we’re…

I just published: ERC-Plus: jackpot science or missed chance to fix academia?

My reflections on ERC-Plus, Europe’s newest ultra-competitive research grant and what it tells us about the academic culture we’re building.

medium.com/p/erc-plus-j...

Movie S2 20230517 YouTube video by Debraj Shubham Ghose

When stained and unstained human B cell aggregates are placed next to each other, they coalesce, internally mix, and undergo surface tension-like rounding.

www.biorxiv.org/content/10.1...

youtu.be/QAk2ayoVF0M

#FuorescenceFriday

It was a pleasure to co-organize with @allysonsgro.bsky.social Junior Scientist Workshop on Theoretical Biophysics at @hhmijanelia.bsky.social. We had great lectures and tutorials on theoretical approaches used to understand biological phenomena. Can't wait for the 2026 iteration, stay tuned.

Tired of knowing what you are looking for in your tomograms?
Why not try bluesky-less Frosina's new self-supervised algorithm for semantic segmentation and particle picking for #teamtomo (includes a new denoiser without the need for odd/even tomos)

Code is on GitHub if you want to try it out

An exciting PhD opportunity is available in my lab! More info about our group and research can be found here: bdaum2.wixsite.com/daumlab
Application deadline: 8th Jan 2026.
Apply here: www.exeter.ac.uk/study/pg-res...
If you are interested, get in touch!
#ArchaeaSky #CryoEM #TeamTomo

This amazing! Congratulations!!!

Giant KASH proteins and ribosomes establish distinct cytoplasmic biophysical properties in vivo Living tissues maintain unique intracellular biophysical properties under the control of cytoplasmic constraints and crowding.

Thrilled to share that a big piece of my thesis here in the Starr–Luxton is now out in Science Advances! We discovered that the cytoplasm of living animal tissues is extremely crowded and constrained, maintained by ribosomes and the giant KASH protein ANC-1.
www.science.org/doi/10.1126/...

Movie S2 20230517 YouTube video by Debraj Shubham Ghose

Immune tissue behaves as shapeshifting active living matter as it fights intruders. Using liquid-like multicellular B cell droplets, we show that cytokines control the physical state of immune tissue.

www.biorxiv.org/content/10.1...

youtu.be/QAk2ayoVF0M

#biophysics #immunology #activematter

5/5 I am excited to extend these insights to frame immune function as an emergent property of interacting, multicellular active matter.

Many thanks to Tom Ferrante, Don Ingber and his lab, Sloan Foundation's Matter-to-Life program, and the Wyss Institute at Harvard University.

4.1/5

Movie S3 20230517 YouTube video by Debraj Shubham Ghose

4/5 We discovered that the same cytokines driving B cell fate also modulate the material properties of BLOMBs. This suggests that cytokines control the physical state of immune tissue.

youtu.be/ItWdDz2i8io

Movie S2 20230517 YouTube video by Debraj Shubham Ghose

3/5 To identify the biological 'control knobs' of immune tissue, we utilized CD40L-induced B cell aggregates as a model system. We demonstrated that these structures function as liquid droplets, terming them B-Lymphocyte Organized Multicellular Blobs (BLOMBs). youtu.be/QAk2ayoVF0M

2/5 Our computational model predicted that the efficiency of antibody evolution is governed by the tissue's physical state. This motivated our search for chemical signals capable of tuning this material property.

Cytokines control the physical state of immune tissue Unlike most solid-like tissues, immune tissue is protean and reconfigurable—its component cells can patrol vast territories, find rare cellular partners, and dynamically self-organize into functional ...

1/5: New preprint: Cytokines control the physical state of immune tissue. www.biorxiv.org/content/10.1...

Unlike structured organs (heart, liver), immune tissue can shapeshift to form functional structures like germinal centers (GCs), tertiary lymphoid organs, granulomas, etc.

3/5: To search for these control knobs, we studied homotypic aggregates formed by primary human B cells stimulated with GC factor CD40L as a model. We showed they behave like liquid droplets and thus called them B Lymphocytes Organized as Multicellular Blo(m)bs (BLOMBs). youtu.be/QAk2ayoVF0M

How can cells self-organize rapidly into complex patterns during development?

Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM).

Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025...

👇Thread 🧵(1/11)

Beautiful!!

Such an honor to be featured by @focalplane.bsky.social , especially on my favorite day of the week: #FluorescenceFriday! 🔬

Below for reference, a picture of the full hydei testis with the musculature stained (depth-coded) taken together with @saraheclark.bsky.social

#cellbio #devbio #microscopy

Happy #FluorescenceFriday !!! Pt 2: fungal hyphae challenged with various oxidative stressors; nucleic acids - yellow, ROS - magenta feat. bubbles induced by H2O2 from earlier imaging experiments when I had no idea what I was doing :)

Stimulating immune cells in vitro is a common experimental lab model. We profiled 150K blood immune cells treated with 11 different stimuli to compare the effects. The data are freely available for researchers. See the preprint for our findings and to access the data 🧪 doi.org/10.1101/2025...

FINALLY out in #Science Advances! 🎉
3 years of hard work, a fantastic team — and I’m proud to be first and co-corresponding author!

It's about Plexin signaling driving collective cell migration & organ sculpting. Check out the videos 😀

www.science.org/doi/10.1126/...

#DevBio #CellBio #Microscopy

3D printed microscopy we could perhaps try in the lab

onlinelibrary.wiley.com/doi/10.1111/...

#GLSL #Shaders

HIGH-RESOLUTION IN VIVO BRAIN IMAGING OF DROSOPHILA 🪰
New Preprint by Tassara et al.!

www.biorxiv.org/content/10.1...
#FluorescenceMonday #SnoutClub 1/6

A perfectly round liver organoid stained for mitochondria (yellowish/green), e-cadherin in blue and nuclei in pink for #MicroscopyMonday

Pretty!

Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images Author summary Bacteria organize themselves on surfaces in ways that influence the spread of infections, but studying these behaviors is difficult, especially when multiple species are involved or the...

Excited to share our latest paper in PLOS Comp Bio, describing how accurate, multi-species segmentation models for bacteria can be created quickly and easily using image-to-image translation. 🧪⚛️
#biophysics #imageanalysis #microscopy #AI

dx.doi.org/10.1371/jour...

Bonus: ran a quick color variation test — because it's always worth playing with presentation.
Color isn’t just style — it shapes what you see.

#MicroscopyCommunity #ScientificVisualization #Biophysics