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Nico Kaiser

@n-kaiser.bsky.social

33 followers 184 following 0 posts

PhD student in the field of computational microscopy and spatial omics.

Posts Replies Media

Reposted by Nico Kaiser

Malte Kuehl @maltekuehl.com · 29/07/2025

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...

Diagram showing MCP-enabled research architecture. Part A illustrates the flow between MCP servers (including BioContextAI Knowledgebase MCP and Community-developed MCP servers), Agentic systems connected via Model Context Protocol, and researchers asking research questions. MCP servers connect to knowledgebases and specialized software. Part B details the BioContextAI project components, divided into Registry (Schema.org ontology, Web interface, Open source licensing, MCP-enabled chatbot, Continuous integration) and Community (Documentation, Community forums, MCP server reviews, Shareable collections, Interoperability with tools like BioChatter).

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Reposted by Nico Kaiser

bioRxiv SysBio @biorxiv-sysbio.bsky.social · 25/07/2025

Community-based biomedical context to unlock agentic systems www.biorxiv.org/content/10.1101/202…

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Reposted by Nico Kaiser

Malte Kuehl @maltekuehl.com · 18/07/2025

🚨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 ⬇️

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Reposted by Nico Kaiser

Malte Kuehl @maltekuehl.com · 05/12/2024

Happy to share that pytximport has now been included in the December issue of Bioinformatics and can be read online without downloading the PDF: doi.org/10.1093/bioi...

doi.org

Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python

AbstractSummary. Transcript quantification tools efficiently map bulk RNA sequencing (RNA-seq) reads to reference transcriptomes. However, their output con

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Reposted by Nico Kaiser

Lior Pachter @lpachter.bsky.social · 21/11/2024

You can now run tximport in Python with pytximport thanks to @compmed.bsky.social et al. academic.oup.com/bioinformati...

academic.oup.com

Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python

AbstractSummary. Transcript quantification tools efficiently map bulk RNA sequencing reads to reference transcriptomes. However, their output consists of t

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Reposted by Nico Kaiser

Malte Kuehl @maltekuehl.com · 21/11/2024

Thanks for sharing! Looking forward to see what more options to use data from kallisto & others with scientific python and @scverse.bsky.social ecosystem tools will enable

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