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Reposted by Malte Kuehl

Gergely Orosz @gergely.pragmaticengineer.com · Jun 27

People outside tech starting to realize how quality software and typing/generating code fast are not correlated

Malte Kuehl @maltekuehl.com · 28d

A truly helpful resource for all things omics! Make sure to check out their MCP server, too: biocontext.ai/registry/sae...

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Reposted by Malte Kuehl

Malte Kuehl @maltekuehl.com · Sep 11

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...

Martin Emons @martinemons.bsky.social · Sep 11

We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data

academic.oup.com/nar/article/...

Harnessing the potential of spatial statistics for spatial omics data with pasta

Abstract. Spatial omics allow for the molecular characterization of cells in their spatial context. Notably, the two main technological streams, imaging-ba

academic.oup.com

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Malte Kuehl @maltekuehl.com · Sep 11

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.

Malte Kuehl @maltekuehl.com · Sep 11

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...

Martin Emons @martinemons.bsky.social · Sep 11

We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data

academic.oup.com/nar/article/...

Harnessing the potential of spatial statistics for spatial omics data with pasta

Abstract. Spatial omics allow for the molecular characterization of cells in their spatial context. Notably, the two main technological streams, imaging-ba

academic.oup.com

1 1 6

Reposted by Malte Kuehl

SIB Swiss Institute of Bioinformatics @sib.swiss · Sep 9

💫 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

Ilan Gold accepting the award for scverse

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Reposted by Malte Kuehl

Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · Sep 9

Love the social media efforts and community building of @scverse !
https://scverse.org/join/
https://scverse.org/events/
#bc2basel

Join scverse

You can also reach us by e-mail for certain matters: [email protected]: core team [email protected]: for matters regarding the next conference [email protected]: steering council (e.g. for questions about sponsorships)

scverse.org

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Malte Kuehl @maltekuehl.com · Aug 28

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).

BioContextAI @biocontext.ai · Aug 28

🤖🧬 New biomedical MCP server added to the registry:
BioCypher Knowledge Graph MCP
Check it out at https://biocontext.ai/registry/biocypher/biocypher-mcp

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Malte Kuehl @maltekuehl.com · Aug 25

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.

BioContextAI

Biomedical context via the Model Context Protocol for agentic systems

biocontext.ai

Malte Kuehl @maltekuehl.com · Aug 25

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...

Small Language Models are the Future of Agentic AI

arxiv.org

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Malte Kuehl @maltekuehl.com · Aug 20

Great work by @jonsch.one and comleagues from @saezlab.bsky.social!

Reposted by Malte Kuehl

BioContextAI @biocontext.ai · Aug 13

🤖🧬 New biomedical MCP server added to the registry:
Holy-BIO-MCP's gget server
Check it out at https://biocontext.ai/registry/longevity-genie/gget-mcp

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Reposted by Malte Kuehl

Nature @nature.com · Aug 1

Nature research paper: Pathology-oriented multiplexing enables integrative disease mapping

go.nature.com/3HdZxZG

Pathology-oriented multiplexing enables integrative disease mapping - Nature

Pathology-oriented multiplexing (PathoPlex) represents a framework for widespread access to multiplexed imaging and computational image analysis of clinical specimens at a relatively high throughput and subcellular resolution.

go.nature.com

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Saez-Rodriguez Group @saezlab.bsky.social · Jul 31

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!