Francesco
@francescorubbo.bsky.social
ML for Cell Biology
Particle Physicist by training
Publications: https://scholar.google.com/citations?user=iPfDBYkAAAAJ&hl=en
GitHub profile: https://github.com/francescorubbo
Particle Physicist by training
Publications: https://scholar.google.com/citations?user=iPfDBYkAAAAJ&hl=en
GitHub profile: https://github.com/francescorubbo
Pinned
Francesco
@francescorubbo.bsky.social
· Nov 18
A Combined AI and Cell Biology Approach Surfaces Targets and Mechanistically Distinct Inflammasome Inhibitors
Inflammasomes are protein complexes that mediate innate immune responses whose dysregulation
has been linked to a spectrum of acute and chronic human conditions which dictates
therapeutic development ...
www.cell.com
Check out this work fresh off the (cell) press! We leveraged unbiased representations of cell morphology in high-content imaging for mechanistic understanding of inflammasome inhibitors. A similar approach can be applied to any mechanistic model with convergent pathways.
#ImmunoSky #microscopy
#ImmunoSky #microscopy
Reposted by Francesco
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".
ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
A nicely written opinion piece comparing small molecule vs genetic screening
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
The limitations of small molecule and genetic screening in phenotypic drug discovery
Phenotypic screens carried out with functional genomics or small molecules have led to novel biological insights, revealed previously unknown targets …
www.sciencedirect.com
November 13, 2025 at 2:35 PM
A nicely written opinion piece comparing small molecule vs genetic screening
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Glad to see this work finally published! We used nELISA in combination with CellPainting for our exploration of inflammasome inhibitors.
November 8, 2025 at 12:19 PM
Glad to see this work finally published! We used nELISA in combination with CellPainting for our exploration of inflammasome inhibitors.
Reposted by Francesco
Job alert!
We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?
See also on the forum:
forum.image.sc/t/research-e...
We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?
See also on the forum:
forum.image.sc/t/research-e...
Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA
Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...
forum.image.sc
October 7, 2025 at 12:39 PM
Job alert!
We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?
See also on the forum:
forum.image.sc/t/research-e...
We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?
See also on the forum:
forum.image.sc/t/research-e...
Reposted by Francesco
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
October 10, 2025 at 4:47 PM
15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵
Very cool! Why call it CellTransformer, though, if the underlying inductive bias is organization in tissue? So confusing…
Introducing CellTransformer, a new AI tool developed with UCSF that makes it easier to explore massive neuroscience datasets and identify important subregions of the brain. 🧵
October 7, 2025 at 6:13 PM
Very cool! Why call it CellTransformer, though, if the underlying inductive bias is organization in tissue? So confusing…
Reposted by Francesco
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)
📄 arxiv.org/pdf/2507.01009 (1/N)
September 23, 2025 at 8:32 AM
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)
📄 arxiv.org/pdf/2507.01009 (1/N)
Reposted by Francesco
Morph Map is now published in Nature Methods. Excited to see what the community discovers with this resource mapping ~15,000 human genes!
rdcu.be/ezGre
rdcu.be/ezGre
August 7, 2025 at 1:36 PM
Morph Map is now published in Nature Methods. Excited to see what the community discovers with this resource mapping ~15,000 human genes!
rdcu.be/ezGre
rdcu.be/ezGre
Reposted by Francesco
One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/
June 28, 2025 at 10:38 AM
One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/
Reposted by Francesco
Taking pictures of cells with a microscope, then extracting thousands of features from them is uncannily effective for quantifying cell state, esp. for genes and chemicals (e.g., Cell Painting). But we often average the rich single-cell data to simplify analysis. Can we do better?
#bioML 🧪
1/n
#bioML 🧪
1/n
![(a) Human U2OS cells treated with dimethyl sulfoxide (DMSO) and stained using the Cell Painting assay, which employs six dyes in five channels to label eight cellular compartments. The top row (from left to right) shows mitochondrial staining; actin, Golgi, and plasma membrane staining; and nucleolar and cytoplasmic RNA staining. The bottom row (from left to right) displays endoplasmic reticulum staining, DNA staining, and a montage of all five channels (from Cimini et al. [21]). (b) Thousands of features are extracted from each segmented cell in microscopy images of wells. A learned function f(x) (CytoSummaryNet) aggregates this data into a single feature vector: the sample’s profile. (c) An in-depth look at the model architecture used in this study. The model consists of three elements: a function φ(x), which maps the input data from ℝD to ℝL space, a summation, which collapses the cell dimension, and ρ(z), which maps the collapsed representation from ℝN to ℝL space. (d) During training, replicate compound profiles are forced to attract each other (green arrows) and simultaneously repel every other compound (red arrows) in the learned feature space. Here, all forces are drawn for a single profile of compound B.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:raswr6mjt7sbppdo6kcce4mz/bafkreicppuq2utmxkx5kpaggndigq7qcat6ppdqqajxhphpyi53ydlbbeq@jpeg)
December 19, 2024 at 11:31 PM
Taking pictures of cells with a microscope, then extracting thousands of features from them is uncannily effective for quantifying cell state, esp. for genes and chemicals (e.g., Cell Painting). But we often average the rich single-cell data to simplify analysis. Can we do better?
#bioML 🧪
1/n
#bioML 🧪
1/n
Reposted by Francesco
Excited to present our spotlight paper at #NeurIPS!
MOTIVE is a new dataset + benchmark for predicting drug-target interactions, using Cell Painting data
Location: Fri 13 Dec 4:30 p.m. PST @ East Exhibit Hall A-C #4208
Poster: neurips.cc/virtual/2024...
Paper: arxiv.org/abs/2406.08649
MOTIVE is a new dataset + benchmark for predicting drug-target interactions, using Cell Painting data
Location: Fri 13 Dec 4:30 p.m. PST @ East Exhibit Hall A-C #4208
Poster: neurips.cc/virtual/2024...
Paper: arxiv.org/abs/2406.08649
December 13, 2024 at 12:39 PM
Excited to present our spotlight paper at #NeurIPS!
MOTIVE is a new dataset + benchmark for predicting drug-target interactions, using Cell Painting data
Location: Fri 13 Dec 4:30 p.m. PST @ East Exhibit Hall A-C #4208
Poster: neurips.cc/virtual/2024...
Paper: arxiv.org/abs/2406.08649
MOTIVE is a new dataset + benchmark for predicting drug-target interactions, using Cell Painting data
Location: Fri 13 Dec 4:30 p.m. PST @ East Exhibit Hall A-C #4208
Poster: neurips.cc/virtual/2024...
Paper: arxiv.org/abs/2406.08649
Check out this work fresh off the (cell) press! We leveraged unbiased representations of cell morphology in high-content imaging for mechanistic understanding of inflammasome inhibitors. A similar approach can be applied to any mechanistic model with convergent pathways.
#ImmunoSky #microscopy
#ImmunoSky #microscopy
A Combined AI and Cell Biology Approach Surfaces Targets and Mechanistically Distinct Inflammasome Inhibitors
Inflammasomes are protein complexes that mediate innate immune responses whose dysregulation
has been linked to a spectrum of acute and chronic human conditions which dictates
therapeutic development ...
www.cell.com
November 18, 2024 at 9:25 PM
Check out this work fresh off the (cell) press! We leveraged unbiased representations of cell morphology in high-content imaging for mechanistic understanding of inflammasome inhibitors. A similar approach can be applied to any mechanistic model with convergent pathways.
#ImmunoSky #microscopy
#ImmunoSky #microscopy
Reposted by Francesco
I don't think I saw this on social media at all: a bunch of very clever people (including our team) has put together a federated bioimage repository based on OME-Zarr with 500TB of data in 4 months! ome.github.io/ome2024-ngff...
November 10, 2024 at 6:38 PM
I don't think I saw this on social media at all: a bunch of very clever people (including our team) has put together a federated bioimage repository based on OME-Zarr with 500TB of data in 4 months! ome.github.io/ome2024-ngff...