Debraj Ghose
@debrajghose.bsky.social
I study how lymphocytes self-organize into multicellular structures. Also interested in how cells sense and respond to chemical gradients. Currently at UCSF. Previously at Harvard and Duke.
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...
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...
biorxiv.org
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...
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…
medium.com
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
bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 9mo agoCryoSiam: self-supervised representation learning for automated analysis of cryo-electron tomograms https://www.biorxiv.org/content/10.1101/2025.11.11.687379v1
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
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/...
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.
science.org
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.
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 ...
biorxiv.org
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)
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
FocalPlane @focalplane.bsky.social · last yr.Our featured 🔬image this #FluorescenceFriday is of a portion of testis from Drosophila hydei, acquired by @maikbischoff.bsky.social. Learn more about the image and Maik’s research ⤵️ focalplane.biologists.com/2025/07/18/f...
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/...
onlinelibrary.wiley.com
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
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...
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...
dx.doi.org
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
#Microtubule-driven cell shape changes and #actomyosin flow synergize to position the #centrosome, say Alexandre Schaeffer, Manuel Théry (@manuelthery.bsky.social ) and colleagues: rupress.org/jcb/article/... @lblanchoin.bsky.social @gelinmatthieu.bsky.social #Biophysics #Cytoskeleton
My #FlyWeek contribution: The Variety of Testis Shapes in Pomace Fly Species Aren't they beatiful?🌈🪰🔬 An old-school sci-poster meets modern confocal imaging! #Drosophila testis diversity fascinated even Curt Stern (yes, the human genetics textbook guy!) back in the 1930s. #microscopy #insects
indeed, i begin my grad lecture on RNAi/miRNAs by discussing petunias. and mentioning while none of our students will do a plant phd (no faculty), they can learn A LOT by occasionally reading plant literature (think epigenetics, small RNAs, developmental biology, etc etc). also, consider the worm!
c0nc0rdance@c0nc0rdance.bsky.social · last yr.The quest to make darker petunias led to a 2006 Nobel & a fundamental tool of modern molecular biology. In 1986, Richard Jorgensen was trying to make a darker purple petunia to get some VC funding. So he inserted additional copies of the pigment gene into petunias. Instead, they turned WHITE.
What governs where DNA replication begins in human cells? Here, we show that origins of replication in human DNA are epigenetically specified and that crucially, this epigenetic mark is required for both DNA replication and cell proliferation! @narjournal.bsky.social academic.oup.com/nar/article/...
If you're curious about how cells make decisions in complex environments, and how mathematical models can capture such behaviour, our preprint is now live! Check it out here: www.biorxiv.org/content/10.1...
Investigating Local Negative Feedback of Rac Activity by Mathematical Models and Cell Motility Simulations
For polarization and directed migration, cells use a combination of local positive feedback and long-range inhibition. We have previously used mathematical models to show the ability of this core…
biorxiv.org
We found that cells use emergent collective memory—arising from simple chemical reactions—to outperform physical limits of detecting chemical gradients. Curious how? 1/n 8 min talk: www.youtube.com/watch?v=A7XH... bioRxiv: www.biorxiv.org/content/10.1... #biophysics #cellbiology
Local collective memory from ratiometric signaling outperforms cellular gradient sensing limits
YouTube video by Debraj Shubham Ghose
youtube.com
U2OS labeled with OMP25-GFP, an outer membrane marker for mitochondria. Left shows a zoom-in on the dimmer cell. Imaged by OPM (oblique plane microscope). #Microscopy
For #FluorescenceFriday, tau (blue) and long loops of neurofilament proteins are shown in a primary hippocampal neuron 🔬 #Neuroscience #Microscopy
It's #FluorescenceFriday! Here goes one image showing pathological Tau🟢 spreading in the monkey hippocampus. Neurons in 🟢 are dying, and healthy neurons in 🟣. Pathology spreads in a prion-like manner in this novel monkey model of Alzheimer we developed. How do we know that?
Could inhaling Xenon be used someday to prevent or treat Alzheimer's disease? An intriguing experimental model study shows its effect on modulating brain microglia and reducing inflammation www.science.org/doi/10.1126/...
Inhaled xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy
Xenon inhalation modulates microglial responses in mice and is a potential therapeutic agent for treating Alzheimer’s disease.
science.org
