Loan Vulliard
@lvulliard.bsky.social
Interested in 🧬💻🔬🎵👩🔬👨🏾💼
President of the CytoData Society
Systems spatial biology to chart molecular heterogeneity. Currently in Heidelberg, Germany – postdoc in the groups of Felix Hartmann and Julio Saez-Rodriguez
http://vulliard.loan
President of the CytoData Society
Systems spatial biology to chart molecular heterogeneity. Currently in Heidelberg, Germany – postdoc in the groups of Felix Hartmann and Julio Saez-Rodriguez
http://vulliard.loan
Reposted by Loan Vulliard
Today is the last chance to register for #CytoData2025. Don’t miss a fantastic program covering the full spectrum of image-based profiling!
cytodata25.eu-openscreen.eu
cytodata25.eu-openscreen.eu
October 31, 2025 at 5:25 PM
Today is the last chance to register for #CytoData2025. Don’t miss a fantastic program covering the full spectrum of image-based profiling!
cytodata25.eu-openscreen.eu
cytodata25.eu-openscreen.eu
Reposted by Loan Vulliard
New work from Iva Buljan @ivabuljan.bsky.social in our lab!
We mapped how human tissue architecture changes with age using ~25k histology slides from 983 donors.
This is the first body-wide atlas of human microanatomy.
📄 Preprint: www.biorxiv.org/content/10.1...
We mapped how human tissue architecture changes with age using ~25k histology slides from 983 donors.
This is the first body-wide atlas of human microanatomy.
📄 Preprint: www.biorxiv.org/content/10.1...
October 15, 2025 at 6:29 AM
New work from Iva Buljan @ivabuljan.bsky.social in our lab!
We mapped how human tissue architecture changes with age using ~25k histology slides from 983 donors.
This is the first body-wide atlas of human microanatomy.
📄 Preprint: www.biorxiv.org/content/10.1...
We mapped how human tissue architecture changes with age using ~25k histology slides from 983 donors.
This is the first body-wide atlas of human microanatomy.
📄 Preprint: www.biorxiv.org/content/10.1...
🧭 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
1/5
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
1/5
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
October 8, 2025 at 5:01 PM
🧭 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
1/5
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
1/5
Reposted by Loan Vulliard
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 ⬇️
🔗
www.biorxiv.org/content/10.1...
📦
saezlab.github.io/MetaProViz/
🧵 Thread ⬇️
August 25, 2025 at 7:07 AM
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 ⬇️
🔗
www.biorxiv.org/content/10.1...
📦
saezlab.github.io/MetaProViz/
🧵 Thread ⬇️
Reposted by Loan Vulliard
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.
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
August 7, 2025 at 9:14 AM
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.
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.
Reposted by Loan Vulliard
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.
🎉 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 👇
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇
July 24, 2025 at 7:51 AM
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.
Reposted by Loan Vulliard
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
Submit abstracts or register here: 🔗 cytodata25.eu-openscreen.eu/registration/
#Cytodata2025 #Hackathon #ImageBasedProfiling
July 21, 2025 at 7:05 AM
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
Submit abstracts or register here: 🔗 cytodata25.eu-openscreen.eu/registration/
#Cytodata2025 #Hackathon #ImageBasedProfiling
Reposted by Loan Vulliard
🔬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.
1/6
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.
1/6
July 8, 2025 at 7:22 PM
🔬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.
1/6
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.
1/6
Reposted by Loan Vulliard
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
July 2, 2025 at 7:38 AM
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
Reposted by Loan Vulliard
🌟 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
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
June 20, 2025 at 10:35 AM
🌟 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
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
Reposted by Loan Vulliard
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.
👉 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.
April 23, 2025 at 7:53 AM
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.
👉 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.
Reposted by Loan Vulliard
🚨 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...
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
June 12, 2025 at 8:27 PM
🚨 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...
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...
If you need to compare profiles across many conditions or perturbations, have a look!
🚨 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:
1/7
More in the 🧵 below:
1/7
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
June 11, 2025 at 7:25 AM
If you need to compare profiles across many conditions or perturbations, have a look!
Reposted by Loan Vulliard
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
May 23, 2025 at 7:38 AM
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
If you're interested in finding recurrent spatial patterns in your tissues, now is a good time to check out Kasumi!
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
May 7, 2025 at 6:39 PM
If you're interested in finding recurrent spatial patterns in your tissues, now is a good time to check out Kasumi!
Reposted by Loan Vulliard
We have an opening for a PhD/Postdoc in Spatial Omics for Cardiology in Heidelberg 🫀 #job #academicjob #phd #postdoc #cadiology 👇
jobrxiv.org/job/heidelbe...
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
April 22, 2025 at 10:28 AM
We have an opening for a PhD/Postdoc in Spatial Omics for Cardiology in Heidelberg 🫀 #job #academicjob #phd #postdoc #cadiology 👇
jobrxiv.org/job/heidelbe...
jobrxiv.org/job/heidelbe...
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.
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.
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.
👉 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.
April 23, 2025 at 8:22 AM
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.
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.
Reposted by Loan Vulliard
🚨 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...
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
April 22, 2025 at 9:37 AM
🚨 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...
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
Reposted by Loan Vulliard
Congrats & Good luck to our @slobentanzer.bsky.social as he starts his group @diabresearch-dzd.bsky.social & @comphealthmunich.bsky.social - he is hiring 👇
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.
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
April 9, 2025 at 7:53 AM
Congrats & Good luck to our @slobentanzer.bsky.social as he starts his group @diabresearch-dzd.bsky.social & @comphealthmunich.bsky.social - he is hiring 👇
Reposted by Loan Vulliard
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...
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
April 9, 2025 at 5:10 PM
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...
www.nature.com/articles/s41...
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!
🌟 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...
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...
April 9, 2025 at 11:23 AM
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!
Reposted by Loan Vulliard
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
April 7, 2025 at 10:11 PM
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)
Big news, you can now follow the CytoData society on BS and get even more image-based profiling in your timeline 🤓
👋 We are CytoData Society (CytoDS)! 🌟 We build and maintain an active community around image-based profiling of biological phenotypes induced by genetic, chemical, or other perturbations of biological systems. Join us to explore, share, and innovate together! #CytoData #Community
March 31, 2025 at 3:27 PM
Big news, you can now follow the CytoData society on BS and get even more image-based profiling in your timeline 🤓
Reposted by Loan Vulliard
Super excited to finally see this published! Our new method to use combinatorial staining and deep learning to push the multiplexing boundaries of spatial proteomics!
High-dimensional imaging using combinatorial channel multiplexing and deep learning go.nature.com/4hGPfO0
High-dimensional imaging using combinatorial channel multiplexing and deep learning - Nature Biotechnology
Protein imaging is multiplexed using combinatorial staining and deep learning decompression.
go.nature.com
March 26, 2025 at 4:12 AM
Super excited to finally see this published! Our new method to use combinatorial staining and deep learning to push the multiplexing boundaries of spatial proteomics!