Lightnews — Scholar-powered news

Loan Vulliard @lvulliard.bsky.social · 15h

🙏 Thanks to all collaborators at the DKFZ, UKHD and Heidelberg University, and UKE Institute of Pathology, to the patients, and funders.
@saezlab.bsky.social
@dkfz.bsky.social
@dkfz-iic.bsky.social
@tanevski.bsky.social
@struxa.bsky.social
@hlsalliance.bsky.social
@erc.europa.eu
@helmholtz.de
5/5

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Loan Vulliard @lvulliard.bsky.social · 15h

Our analysis reveals distinct recurrent CRC trajectories:
🤝 Tumor-CAF metabolic cooperation with immune shielding
🔥 Glycolytic shift with vascular remodeling and myeloid enrichment
Same disease, different mechanisms, suggesting different treatment responses.
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Loan Vulliard @lvulliard.bsky.social · 15h

🧩 To identify which changes co-occur in patients, we built MuVIcell, an open-source Python package that applies the MuVI factor analysis framework to model all spatial, metabolic, morphological, and compositional features per cell type.
Try it yourself: github.com/HartmannLab/...
3/5

GitHub - HartmannLab/MuVIcell: From cell-type stratified features to multicellular coordinated programs

From cell-type stratified features to multicellular coordinated programs - HartmannLab/MuVIcell

github.com

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Loan Vulliard @lvulliard.bsky.social · 15h

⏳ What shifts with pT stage?
Early lesions show high proliferation and fatty acid oxidation capacity. Later, glycolysis rises, stroma and vasculature reorganize, and lymphocytes give way to myeloid cells. Spatial architecture predicts stage better than composition or metabolic state.
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Loan Vulliard @lvulliard.bsky.social · 15h

🧭 Colorectal cancer doesn’t follow a single path.
Using spatial proteomics on ~500 tumors, we found distinct trajectories from early to late stage, involving the whole tumor microenvironment and its metabolic state.
📄 Preprint: arxiv.org/abs/2510.05083
#SpatialBiology #CRC #ImageBasedProfiling
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Robust multicellular programs dissect the complex tumor microenvironment and track disease progression in colorectal adenocarcinomas

Colorectal cancer (CRC) is highly heterogeneous, with five-year survival rates dropping from $\sim$90% in localized disease to $\sim$15% with distant metastases. Disease progression is shaped not only...

arxiv.org

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Reposted by Loan Vulliard

Saez-Rodriguez Group @saezlab.bsky.social · Aug 25

We present our MetaProViz #Rpackage for #metabolomics analysis & prior knowledge integration to generate mechanistic hypotheses on how metabolic changes affect metabolite classes, pathways & environment interaction

🔗
www.biorxiv.org/content/10.1...

📦
saezlab.github.io/MetaProViz/

🧵 Thread ⬇️

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Reposted by Loan Vulliard

Jess Ewald @ewaldlab.org · Aug 7

Check out this opportunity to join my lab as a postdoc! www.ebi.ac.uk/research/pos...

Every year, faculty from EMBL-EBI and the Wellcome Sanger Institute co-develop projects that allow fellows to be part of ✨both✨ of these amazing research institutes.

EMBL-EBI-Sanger postdoctoral fellowships (ESPOD)

The ESPOD fellowship builds on the collaborative relationship between EMBL-EBI and the Wellcome Sanger Institute, offering projects that combine experimental (wet-lab) and computational (dry-lab) appr...

www.ebi.ac.uk

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Reposted by Loan Vulliard

Martin Garrido-Rodriguez @martingarridorc.bsky.social · Jul 24

This project has been in the making for quite some time. CORNETO not only integrates key concepts and methodologies in biological network inference, but also introduces a novel framework for multi-condition analysis. Congrats to the team, and especially to @pablormier.bsky.social for leading this.

Saez-Rodriguez Group @saezlab.bsky.social · Jul 22

🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇

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Reposted by Loan Vulliard

cytodata.bsky.social @cytodata.bsky.social · Jul 21

𝗢𝗻𝗲 𝗪𝗲𝗲𝗸 𝗟𝗲𝗳𝘁: Abstract submission for oral presentations 🗣️ and hackathon registration 🧑‍💻 for CytoData 2025 Berlin close July 25!

Submit abstracts or register here: 🔗 cytodata25.eu-openscreen.eu/registration/

#Cytodata2025 #Hackathon #ImageBasedProfiling

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Reposted by Loan Vulliard

Alex Kalinin @alxndrkalinin.bsky.social · Jul 8

🔬API-first feature extraction for image-based profiling workflows

If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.

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Reposted by Loan Vulliard

cytodata.bsky.social @cytodata.bsky.social · Jul 2

Exciting news! We've extended the deadline for oral submissions for Cytodata 2025. You now have until July 25 to submit oral presentations and register for the hackathon. Don't miss this chance! Poster submission closes September 10, and general registration ends October 1

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Reposted by Loan Vulliard

cytodata.bsky.social @cytodata.bsky.social · Jun 20

🌟 𝗥𝗲𝗺𝗶𝗻𝗱𝗲𝗿 🌟
The deadline for abstract submissions for oral presentations at Cytodata 2025 in Berlin is approaching!

👉 𝗦𝘂𝗯𝗺𝗶𝘁 𝘆𝗼𝘂𝗿 𝗮𝗯𝘀𝘁𝗿𝗮𝗰𝘁 𝗯𝘆 𝗝𝘂𝗻𝗲 25!
cytodata25.eu-openscreen.eu/registration/

#BerlinConference #Imageanalysis #Microscopy

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Reposted by Loan Vulliard

cytodata.bsky.social @cytodata.bsky.social · Apr 23

Join us in Berlin for CytoData 2025!
👉 Info & registration: cytodata25.eu-openscreen.eu

🔬 Hackathon: Nov 17–19
📢 Symposium: Nov 20–21

Explore advancements in image-based profiling & high-content screening and Tackle real-world challenges using EU-OPENSCREEN data.

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Reposted by Loan Vulliard

Andre Rendeiro @andre-rendeiro.com · Jun 12

🚨 3 days left to apply!
Join us at CeMM (Vienna) to work on AI + computational pathology projects like LazySlide.
Amazing team, H100 GPUs, real impact.
Apply now: cemm.at/join-cemm/op...

Open Positions

CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences

cemm.at

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Loan Vulliard @lvulliard.bsky.social · Jun 11

If you need to compare profiles across many conditions or perturbations, have a look!

Alex Kalinin @alxndrkalinin.bsky.social · Jun 10

🚨 New paper alert! We developed a versatile information retrieval framework that uses mean average precision (mAP) to robustly quantify sample activity and similarity in large-scale profiling data. Now out ‪@natcomms.nature.com: doi.org/10.1038/s414...

More in the 🧵 below:
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A versatile information retrieval framework for evaluating profile strength and similarity - Nature Communications

Profiling assays measure thousands of features to uncover biological insights but lack reliable methods for quality evaluation. Here, the authors develop a versatile information retrieval framework to...

doi.org

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Reposted by Loan Vulliard

Saez-Rodriguez Group @saezlab.bsky.social · May 23

Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭Our revised comprehensive evaluation of kinase activity inference tools, done in collaboration with the Zhang lab @bcmhouston.bsky.social, is now out @natcomms.nature.com 🔬 tinyurl.com/4twuc6z4

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Loan Vulliard @lvulliard.bsky.social · May 7

If you're interested in finding recurrent spatial patterns in your tissues, now is a good time to check out Kasumi!

Saez-Rodriguez Group @saezlab.bsky.social · May 7

The latest version of the Kasumi manuscript is now published in Nature Comms www.nature.com/articles/s41... Kasumi identifies patterns in tissue patches, enabling analysis of disease progression and treatment response while providing insights into spatial coordination at cell-type or marker level

Learning tissue representation by identification of persistent local patterns in spatial omics data - Nature Communications

Spatial omics reveal tissue structures and can aid patient stratification. The authors present a method to identify patterns in tissue patches, enabling analysis of disease progression and treatment r...

www.nature.com

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Reposted by Loan Vulliard

Saez-Rodriguez Group @saezlab.bsky.social · Apr 22

We have an opening for a PhD/Postdoc in Spatial Omics for Cardiology in Heidelberg 🫀 #job #academicjob #phd #postdoc #cadiology 👇
jobrxiv.org/job/heidelbe...

PhD/Postdoc in Spatial Omics for Cardiology

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

jobrxiv.org

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Loan Vulliard @lvulliard.bsky.social · Apr 23

Registrations are open for the best scientific event of the year!
Source: my very unbiased and authoritative opinion 😂

Join us in Berlin in November to discuss the best ways to go from images to biological insight and new treatments.

cytodata.bsky.social @cytodata.bsky.social · Apr 23

Join us in Berlin for CytoData 2025!
👉 Info & registration: cytodata25.eu-openscreen.eu

🔬 Hackathon: Nov 17–19
📢 Symposium: Nov 20–21

Explore advancements in image-based profiling & high-content screening and Tackle real-world challenges using EU-OPENSCREEN data.

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Reposted by Loan Vulliard

Jovan Tanevski @tanevski.bsky.social · Apr 22

🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data

We present our new alignment framework TOAST www.biorxiv.org/content/10.1...

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Reposted by Loan Vulliard

Saez-Rodriguez Group @saezlab.bsky.social · Apr 9

Congrats & Good luck to our @slobentanzer.bsky.social as he starts his group @diabresearch-dzd.bsky.social & @comphealthmunich.bsky.social - he is hiring 👇

Computational Health Center @comphealthmunich.bsky.social · Mar 25

We‘re excited to welcome @slobentanzer.bsky.social, new PI at the intersection of @diabresearch-dzd.bsky.social and @comphealthmunich.bsky.social @www.helmholtz-munich.de!

His group focuses on „Accessible Biomedical AI Research“ - and he‘s hiring!

Open positions on slolab.ai and: bit.ly/slolab.

PhD Candidates and Postdocs in Accessible Biomedical AI (f/m/x)

jobs.helmholtz-muenchen.de

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Reposted by Loan Vulliard

Chris Fell @cfell.bsky.social · Apr 9

So excited to share our new paper out today in @nature.com. We repurposed R2 retrotransposons to create STITCHR, a tool that can make virtually any kind of edit in mammalian genomes including the scarless multi-kilobase scale insertions 🧵

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

Reprogramming site-specific retrotransposon activity to new DNA sites - Nature

A study of retrotransposon activity repurposes a retroelement called R2Tocc to create a programmable system called STITCHR that enables diverse genome edits including efficient, scarless large pa...

www.nature.com

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Loan Vulliard @lvulliard.bsky.social · Apr 9

Interested in supporting the advancement of image-based profiling? Want to shape how large cell and tissue image datasets will be analyzed in the future? Please consider hosting CytoData!

cytodata.bsky.social @cytodata.bsky.social · Apr 9

🌟 Call for Proposals: Host CytoData 2026! 🌟

We invite North American institutions to submit proposals for the 2026 symposium, whether in-person or hybrid. Nominate your institution by September 1, 2025. Join us in shaping the future of image-based profiling!
docs.google.com/forms/d/e/1F...

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Reposted by Loan Vulliard

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · Apr 7

Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)

Ask Erin, Dear Beth

On Ask Erin/Dear Beth, bioimage analysis experts Beth Cimini and Erin Weisbart, of the Imaging Platform at the Broad Institute of MIT and Harvard, answer your image analysis questions! Whether it’s ab...

www.youtube.com

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