Thanks to @helloeacr.bsky.social for allowing me to attend their annual congress, last June in Budapest. It was a great opportunity to (re-)connect with colleagues, get a broader sense of where cancers therapies are heading, and remember what's exciting about being a scientist! tinyurl.com/2upz6p5u

EACR 2026 Congress Travel Grant recipients share their experiences - The Cancer Researcher

We met in Budapest, Hungary for the most recent EACR Congress, and were delighted to award several Travel Grants to help cancer researchers in need of financial assistance to attend.

magazine.eacr.org

🧵 See 👇 our new preprint on shared and organ-specific gene expression programs of fibrotic diseases 🧬 📄 Paper: doi.org/10.64898/202... 📊 Explore the data: organfibrosis.saezlab.org

Was lovely to see many of you @ I2K! Despite having major FOMO about missing so much stuff this fall (GloBIAS! CytoData! FoundingGIDE! CBIAS!), conferences ARE usually a great way to find @erinweisbart.bsky.social and I. In Episode 19, we talk through great societies/meetings we think you'll enjoy!

Conferences We've Attended Recently - AskErinDearBeth Episode 19

YouTube video by Ask Erin, Dear Beth

youtu.be

Beth Cimini 🔬💻📊@bethcimini.bsky.social · 9mo ago

Episode 18 - @erinweisbart.bsky.social and I hung out IRL at @sbi2.bsky.social, forgot to film TOGETHER, but did ask our friends hard-hitting interview questions. Silliness ensued! Want to hang with us? We're doing a LIVE AMA next week at I2K - Wed Nov 19th, 1PM EST. Sign up at i2kconference.org !

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

@cytodata.bsky.social · last yr.

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.

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...

🧭 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

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

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 ⬇️

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...

ebi.ac.uk

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 · last yr.

🎉 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 👇

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

🔬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

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

🌟 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

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.

🚨 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

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

Alex Kalinin@alxndrkalinin.bsky.social · last yr.

🚨 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

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

Have you ever wondered how protein interactions change across tissues and over time? #networkmedicine #development #aging 👇 Check what we found under the incredible mentorship of #menchelab & @andre-rendeiro.com : www.biorxiv.org/content/10.1...

A multilayer network approach elucidates time- and tissue-specific developmental and aging processes

Understanding the dynamic interplay of proteins across different life stages and tissues is essential for deciphering the molecular mechanisms underpinning development, aging, and disease. Here, we pr...

biorxiv.org

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 · last yr.

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

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

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 · last yr.

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.

🚨 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...

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 · last yr.

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.

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...

nature.com

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 · last yr.

🌟 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...

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...

youtube.com

Big news, you can now follow the CytoData society on BS and get even more image-based profiling in your timeline 🤓

@cytodata.bsky.social · last yr.

👋 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

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!

Nature Biotechnology@natbiotech.nature.com · last yr.

High-dimensional imaging using combinatorial channel multiplexing and deep learning go.nature.com/4hGPfO0

The GBCC2025 Scholarships are here! Thanks to the JXTX Foundation and Galaxy Project, 4 genomics and data science graduate students will receive scholarships to attend GBCC2025 in person. 📅 Apply by April 1, 2025 👉 jxtxfoundation.org/news/2025-2-...

JXTX + GBCC 2025 Scholarships

JXTX + GBCC 2025 Scholarships

jxtxfoundation.org

The first version of NetworkCommons is now published in Bioinformatics. Next, we’ll focus on involving more of the network biology community. academic.oup.com/bioinformati... In parallel, we’ll continue expanding benchmarks and developing new applications. Interested in contributing? Reach out! ⬇️

NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks

AbstractSummary. We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage

academic.oup.com

Saez-Rodriguez Group@saezlab.bsky.social · 2y ago

We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵 Paper: doi.org/10.1101/2024... Docs: networkcommons.readthedocs.io