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!

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

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

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.

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.

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...

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

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...

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

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

🚨 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 👇

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...

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!

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 🤓

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!

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-...

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! ⬇️

Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

Applying LLMs to biomedical research today can go one of two ways: we either use a closed-source web app, or we get coding ourselves. Many researchers lack training for the latter, so their only choice is the former. We want to change that. www.nature.com/articles/s41...

For Maths fans, 2025 is a square. 45² = 45 x 45 = 2025 Also, 9² x 5² = 2025 40² + 20² + 5² = 2025 My favourite? 1³+2³+3³+4³+5³+6³+7³+8³+9³ = 2025 #Mathematics #teaching #education

We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇 Paper: doi.org/10.1101/2024.12.20.629764 Code: github.com/saezlab/greta

I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! www.nature.com/articles/s41...

I was deeply disappointed by the lack of nature/science/climate/enviro on many major end-of-year book lists—so I decided to make my own! Introducing: ✨🎁📚 The 2024 Holiday Gift Guide to Nature & Science Books ✨🎁📚 Please share: Let's make this go viral in time for Black Friday / holiday shopping!

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

One full year to get ready: join us next year in Berlin-Buch if you're into spatial biology, morphology and/or high-content perturbation screens! 🔬💻 #CytoData #Microscopy #ImageBasedProfiling

Hi 🦋 This is the saezlab (saezlab.org) bluesky account. We integrate #omics data with mechanistic molecular knowledge into statistical and machine learning #ML methods, and we share our tools as free #opensource packages (github.com/saezlab/) #systemsbiology #biology #compbio

What if we could look at a human tissue image🔬and quantify its biological age?🧬 And how could we get the same insights without collecting the tissue sample? In our new @biorxivpreprint, we create "tissue clocks" ⏳to do just that! www.biorxiv.org/content/10.1... 📝 #aging #tissue thread below⬇️

What are the key disrupted multicellular processes in heart failure? In our new work we combine 23 years of molecular data with recent single-cell atlases to draw a cross-study patient map doi.org/10.1101/2024...