Malte Kuehl
Computational medicine @ AU
Founder @ KH Biotechnology
Creator of spatiomic, pytximport and https://biocontext.ai
Interested in spatial omics, cancer & ageing
Lab: github.com/complextissue/
Personal: https://maltekuehl.com
Opinions my own.
- Reposted by Malte KuehlWhenever I read discourse on AI energy/water use that focuses on the "median query," I can't help but feel misled. Coding agents like Claude Code send hundreds of longer-than-median queries every session, and I run dozens of sessions a day. On my blog: www.simonpcouch.com/blog/2026-01...
- Reposted by Malte KuehlEpstein-Barr Virus #EBV was linked to #MultipleSclerosis - now a plausible cause has been found, misidentification by longterm memory T-cells that pick on the wrong protein, ANO2, instead of the EBV-antigen. Massive inflection towards the elimination of MS!!! 🧪🧠Cell www.cell.com/cell/fulltex...
- @developers.google.com Benchmark performance is one thing, but reliable systems that devs can rely on are another. Gemini 3 API has been broken for ~14 hours now (responding in JSON, not natural text), with dozens of reports across Gemini forum, GitHub... Yet no solution. Please escalate internally.
- If Google truly wants to increase its API market share, trust needs to be earned.
- Reposted by Malte KuehlProud to close out an incredible year with an update on where scverse is today and where we’re heading. I’d love for you to join me, share your ideas, challenge us, and help shape what comes next. It’s time! 💪
- We will have our final community meeting of 2026 on Tuesday, 2025-12-09 at 11:00 CST/ 9:00 PST! Mikaela Koutrouli (@mkoutrouli.bsky.social) will wrap up a great year of meetings by giving an update on the state of scverse! Zoom registration link for the meeting: lnkd.in/dZpbKKsY
- Reposted by Malte KuehlAI holds huge promise for life science research. But unreliable answers currently limit its impact. @juliosaezrod.bsky.social, Head of Research at EMBL-EBI, discusses how Model Context Protocol (MCP) servers are helping to change this. www.ebi.ac.uk/about/news/p... 🧬💻
- Reposted by Malte KuehlWhat a suitable moment to have a community meeting by @maltekuehl.com and @biocontext.ai! Since we didn’t manage to have him on the conference, join us next Tuesday! 💪❤️
- We will have our next community meeting on Tuesday, 2025-11-25 at 11:00 CST! Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI! More information and Zoom registration link in 🧵
- Reposted by Malte KuehlWe will have our next community meeting on Tuesday, 2025-11-25 at 11:00 CST! Malte Kuehl (@maltekuehl.com) will be presenting on BioContextAI! More information and Zoom registration link in 🧵
- Reposted by Malte Kuehl🤖🧬 New biomedical MCP server added to the registry: Nucleotide Archive MCP server Check it out at biocontext.ai/registry/biocontext…
- Reposted by Malte Kuehl🤖🧬 New biomedical MCP server added to the registry: anndata-mcp Check it out at biocontext.ai/registry/biocontext…
- Reposted by Malte KuehlThe protein concentration in the cytoplasm is so high that the average protein has a water hydration shell with a thickness of only ≈ 10 water molecules separating it from the adjacent protein hydration shell. 1/2
- Reposted by Malte Kuehl📄 BioContextAI is now slightly updated and published @natbiotech.nature.com ➡️ www.nature.com/articles/s41...
- Glad to contribute to this collaborative community platform. A case study shows MCP servers working together - combining BioContextAI Knowledgebase with our omnipath omnipathdb.org MCP (work in progress) to showcase interoperability. Looking forward to see how the ecosystem evolves!
- Reposted by Malte KuehlBioContextAI is a community hub for agentic biomedical systems - @puellesv.bsky.social @biocontext.ai go.nature.com/3JmqKux
- Yet another reason to build with Python
- TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-... 🧵
- Reposted by Malte KuehlWhy does the naked mole rat have the longest lifespan of any rodent, nearly 40 years? A 30-year long mystery unraveled @ScienceMagazine today! Its cGAS enzyme in cells has 4 missense mutations that upends its function, promoting DNA repair and suppressing inflammation www.science.org/doi/10.1126/...
- Recently, @anthropic.com introduced Claude Skills, including some for the life sciences. But how can you use skills in your own agents that may not support them out of the box? The answer is our new Skill-to-MCP server. More info below ⬇️
- 🤖🧬 New biomedical MCP server added to the registry: Skill-To-MCP Server Check it out at biocontext.ai/registry/biocontext…
- Simply put your skills in a folder, add “uvx skill-to-mcp -s /your/skill_folder” to your MCP configuration and your agent will be able to discover skills and all related files. This pattern is powerful!
- You can organize a ton of your existing code in a few subfolders, add some “SKILL.md” files and make it available to any MCP client that can also execute code. The ease of skills combined with the support and standardization of MCP - with skill-to-mcp now a reality 🎉
- Learn more about biomedical agentic AI at biocontext.ai and join our community to help build out the ecosystem for AI-accelerated science
- Reposted by Malte KuehlPeople outside tech starting to realize how quality software and typing/generating code fast are not correlated
- A truly helpful resource for all things omics! Make sure to check out their MCP server, too: biocontext.ai/registry/sae...
- OmniPath (omnipathdb.org): integrated knowledgebase for multi-omics analysis www.biorxiv.org/content/10.1... 🧬🖥️🧪 Python module github.com/saezlab/pypath R package github.com/saezlab/Omni... #Rstats
- It was a great pleasure to collaborate with this team - a quite different perspective on spatial omics, applying lessons from other scientific fields to biomedicine with robust spatial statistics. Thanks to everybody involved! Tutorial available at: robinsonlabuzh.github.io/pasta/00-hom...
- We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data academic.oup.com/nar/article/...
- If you are working with imaging-based proteomics, make sure to check out spatiomic.org, too, which includes many utility functions to apply lattice-based spatial statistics to your data.
- Reposted by Malte Kuehl💫 The 2025 SIB Innovative Resource Award goes to @scverse.bsky.social 💫 The jury is impressed by the focus of these omics tools on interoperability, usability, and communication. The project’s solid governance and emphasis on open science principles are particularly commendable #SIBawards #bc2basel
- Reposted by Malte Kuehl[Not loaded yet]
- Interesting work by @slobentanzer.bsky.social and team, making BioCypher available through MCP! Check it out on biocontext.ai/registry/bio... or try it in BioContextAI Chat (biocontext.ai/chat, click "cogs" icon to add the remote MCP server).
- 🤖🧬 New biomedical MCP server added to the registry: BioCypher Knowledge Graph MCP Check it out at biocontext.ai/registry/biocypher/…
- Interesting thoughts on using specialized small models for agentic systems. Potential to cut cost and build more sustainable and privacy-preserving local-first solutions? arxiv.org/html/2506.02...
- If you are interested in grounding language models in reality and enabling responsible agentic research applications that leverage existing knowledge and human-in-the-loop validation, check out biomedical MCP servers on biocontext.ai or follow @biocontext.ai to be notified about new servers.
- Reposted by Malte Kuehl🤖🧬 New biomedical MCP server added to the registry: Holy-BIO-MCP's gget server Check it out at biocontext.ai/registry/longevity-…
- Reposted by Malte KuehlNature research paper: Pathology-oriented multiplexing enables integrative disease mapping go.nature.com/3HdZxZG
- Reposted by Malte KuehlGlad to contribute to this collaborative community platform. A case study shows MCP servers working together - combining BioContextAI Knowledgebase with our omnipath omnipathdb.org MCP (work in progress) to showcase interoperability. Looking forward to see how the ecosystem evolves!
- Preprint alert 🚨 Do you use chatbots in your work or even build MCP servers and agentic systems yourself? Or would you like to find a way to use biomedical tools using natural language? Then check out biocontext.ai, now out on bioRxiv: www.biorxiv.org/content/10.1...
- Preprint alert 🚨 Do you use chatbots in your work or even build MCP servers and agentic systems yourself? Or would you like to find a way to use biomedical tools using natural language? Then check out biocontext.ai, now out on bioRxiv: www.biorxiv.org/content/10.1...
- With BioContextAI, we aim to index biomedical MCP servers (think: plugins for chatbots/agents) that expose specialized tools and knowledgebases to help foster a community of reusable components for AI 🤖 No matter, whether you would like to use existing chatbots or build your own biology agent 🧬
- You can find the Registry here: biocontext.ai/registry If you work on biomedical MCP servers, you can contribute it through GitHub or by clicking "Add Your Server". The Registry builds on standard Schema.org ontology and all listed servers have OSI-approved licenses.
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- Reposted by Malte KuehlCommunity-based biomedical context to unlock agentic systems biorxiv.org/content/10.1101/202…
- Reposted by Malte Kuehl🎉 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 👇
- Reposted by Malte Kuehl🎉 Such a great work by everyone involved in this major push forward in spatial multiplexing and next-generation pathology. I‘m glad to have been able to contribute to this effort and shed a light on the discovery of sub-cellular to tissue level organization patterns by xAI based on this technology.
- 🚨Scaling multiplexed imaging 📈 We are excited to share Pathology-oriented multiPlexing (PathoPlex). Now out in @nature.com: www.nature.com/articles/s41... 🧵Walk-through thread below ⬇️
- Reposted by Malte KuehlHamburg News: @PuellesVictor and collaborators push tissue analytics to the next frontier. This also marks a remarkable academic path: from postdoc to junior professor in our group to full professor at @UKEHamburg & @AarhusUni @Nature www.nature.com/articles/s41...
- Reposted by Malte KuehlA new imaging technique, PathoPlex, enables simultaneous analysis of over 100 proteins in tissue samples, offering detailed mapping of disease processes and potential for broader clinical applications. doi.org/g9tnd4
- Reposted by Malte KuehlHuge shoutout to @maltekuehl.com &Co for this new publication! Amazing work, exciting science, and well deserved recognition 👏
- 🚨Scaling multiplexed imaging 📈 We are excited to share Pathology-oriented multiPlexing (PathoPlex). Now out in @nature.com: www.nature.com/articles/s41... 🧵Walk-through thread below ⬇️
- Reposted by Malte KuehlPathology-oriented multiplexing enables integrative disease mapping @nature.com www.nature.com/articles/s41...
- 🚨Scaling multiplexed imaging 📈 We are excited to share Pathology-oriented multiPlexing (PathoPlex). Now out in @nature.com: www.nature.com/articles/s41... 🧵Walk-through thread below ⬇️
- Multiplexed imaging techniques have been around for some years and spatial proteomics has been named “Method of the Year 2024” by @natmethods.nature.com Yet, existing methods show multiple limitations, including scalability, image resolution, and data integration.
- PathoPlex represents a flexible framework that leverages off-the-shelf antibodies and covers both multiplex imaging as well as image analysis at a subcellular resolution. Let's go through the parts 🚀
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- Reposted by Malte KuehlI can't imagine a better day of the week to publish this than #FluorescenceFriday: PathoPlex is finally published! 🎉 This presents a revolutionary jump from 4-6 to 100+ markers per sample! 🤯 Read the full story here: www.nature.com/articles/s41...
- #HotFromThePress !! What if instead of analyzing 4-6 pathology markers you could check >100 in the *same* sample? @maltekuehl.com & co @puellesv.bsky.social lab introduce #PathoPlex, method that could even predict disease Full www.nature.com/articles/s41... @focalplane.bsky.social @nature.com 🧪🔬
- Reposted by Malte Kuehl#HotFromThePress !! What if instead of analyzing 4-6 pathology markers you could check >100 in the *same* sample? @maltekuehl.com & co @puellesv.bsky.social lab introduce #PathoPlex, method that could even predict disease Full www.nature.com/articles/s41... @focalplane.bsky.social @nature.com 🧪🔬
- Reposted by Malte KuehlIt's here! ✨ The #ExSRRF protocol paper is out 😍. Full details for merging Expansion Microscopy with our eSRRF analysis. From cells to tissue. A partnership with @puellesv.bsky.social's lab. Lead by Dominik Kylies and @hannah-superres.bsky.social + colleagues. #ExM #eSRRF ➡️ Open link: rdcu.be/euvEw
- Reposted by Malte KuehlNo you cannot determine which drugs are safe and effective with machine learning. You cannot. It will not work. People will die.
- Reposted by Malte KuehlThere is absolutely no reason to think that such models are actually learning biology. So maximizing the perturbation prediction objective does not necessarily result in a "virtual cell". 3/
- Reposted by Malte KuehlUpdate: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”. We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases. arxiv.org/abs/2412.01561
- Reposted by Malte KuehlConfounders are a major bottleneck to understanding biology. Interactions confounded by unobserved regulators (variables) cannot be causality inferred. Gazillion data points from the observed variables cannot compensate for unmeasured confounders. What can help ... 1/2
- Reposted by Malte KuehlUnsurprising finding, but glad to see someone be so comprehensive! Genomics data is SUPER structured and biased and so you need to be extra thoughtful when doing ML. Zero-shot evaluation reveals limitations of single-cell foundation models genomebiology.biomedcentral.com/articles/10....
- Happy to see our overview of nanoscale imaging techniques for biology out!
- 🚨🔬💗Whether investigating cell organelles or mapping proteins, together with Victor Puelles's lab we lay a roadmap for selecting optimal #ExM and #SuperResolution #microscopy combinations. Daria Aristova and Dominik Kylies review with amazing co-authors pubs.aip.org/aip/apr/arti...
- Reposted by Malte KuehlRNA abundance is regulated by well-established mechanisms that do not alter chromatin accessibility. I am not sure how to reconcile these mechanisms with the claim in the abstract of this article: 1/n
- Reposted by Malte Kuehlin case you're wondering, "what's the harm in claiming an extinct species has been brought back from the dead" when it most certainly has not, our interior secretary is already using it to justify taking animals off the endangered species list
- Shout out to the home of my monthly column, @newscientist.com, which nailed their headline about the genetically modified GREY wolves www.newscientist.com/article/2475...
- Reposted by Malte KuehlNot to be pedantic here, either, but "AI" is not taking his readers. Google and OpenAI and Perplexity are taking his readers, specifically to drive up their user bases and ad sales, on the back of his (and countless others') work.
- Reposted by Malte Kuehl1/ New preprint! 🍳 @elihei.bsky.social and our team at @embl.org , @dkfz.bsky.social, and @mskcancercenter.bsky.social built #segger - a fast, accurate cell segmentation tool for spatial transcriptomics that assigns transcripts to their cell origins! doi.org/10.1101/2025...
- Reposted by Malte KuehlCell2fate learns which genes have co-regulated transcription rates => spatially mapping velocity modules & improved robustness. Bayesian modelling => easier to add biological realism. Exciting collab with Alexander Aivasidis in Bayraktar & @steglelab.bsky.social www.nature.com/articles/s41...
- Reposted by Malte KuehlWhat explains the divergence between RNA and protein levels ? Protein degradation is a HUGE factor. It accounts for up to 50 % of protein variation across proteins & tissue types. www.biorxiv.org/content/10.1... 🧵
- Reposted by Malte KuehlMean of the training data still absolutely crushing it for perturbation prediction. www.biorxiv.org/content/10.1...
- Reposted by Malte KuehlA long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it. www.science.org/content/blog...
- Reposted by Malte KuehlNew: Trump officials have paused all external communications at health agencies like CDC, FDA, NIH. No health alerts and the famed MMWRs; no updates to key websites or social media posts. And no indication how long the pause will last. With @rachelroubein.bsky.social + Lena Sun.
- Reposted by Malte KuehlWer Wissenschaftsfreiheit ernst meint, stellt sich nun demonstrativ vor die Gender Studies. Allen anderen dient der Begriff nur als inhaltslose Floskel.
- Another important reminder that omics measurements are not immune to many “classic” confounding factors. Modern sequencing technologies need to be complemented with robust cohort selection, study design, identification of possible confounders and confirmation at the protein level.
- For many genes, the RNA and protein levels change in opposite directions with age. Yet, they correlate positively within an age group. ==> A clear example of Simpson's paradox, similar to what we described previously journals.plos.org/ploscompbiol... Furthermore, ...
- Reposted by Malte KuehlWe 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
- Reposted by Malte Kuehl1. I feel like this is such obvious advice that it gets taken for granted & consequently no one says this to young scientists but READ PAPERS, read all the papers. As you move up in your career you will have less & less time to do this. Read everything that appeals to you not just in your field
- Reposted by Malte KuehlHi Bluesky community! 👋 Are you looking forward to 2025 as much as we are? 👀 We just updated our 2025 Annual Poster to include even more events for you to join, so go and have a look! ➡️ s.embl.org/poster-bl #EMBLEvents #molecularbiology #lifesciencetraining
- Had a great time at the European Society for Spatial Biology conference. Many motivated people, inspiring applications of spatial biology across modalities and important discussions about the technical, organizational and political challenges to bring advances to the clinic #ESSB
- Reposted by Malte KuehlThe calm before the storm... #SpaceHack starts tomorrow! Looking forward to 3 intense days of addressing unsolved data analysis problems for #SpatialTranscriptomics. More here: spatialhackathon.github.io
