👋 Welcome to BioF3's Paper Digest! Today's edition features 0 GitHub projects and 4 research papers from bioRxiv, arXiv, and PubMed.
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1. Topology of Multi-species Localization
📄 arXiv Paper | Date:
2026-03-03| Category:q-bio.QM
Authors: Abhinav Natarajan, Thomas Chaplin, Joshua A. Bull et al.
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Spatial relationships in multi-species data can indicate and affect system outcomes and behaviors, ranging from disease progression in cancer to coral reef resilience in ecology; therefore, quantifying these relationships is an important problem across scientific disciplines. Persistent homology (PH...
2. Sparse autoencoders reveal organized biological knowledge but minimal regulatory logic in single-cell foundation models: a comparative atlas of Geneformer and scGPT
📄 arXiv Paper | Date:
2026-03-03| Category:q-bio.GN, q-bio.CB
Authors: Ihor Kendiukhov
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Background: Single-cell foundation models such as Geneformer and scGPT encode rich biological information, but whether this includes causal regulatory logic rather than statistical co-expression remains unclear. Sparse autoencoders (SAEs) can resolve superposition in neural networks by decomposing d...
3. A tumor-derived lactate/ENO1 lactylation feedback loop facilitates osimertinib resistance of lung adenocarcinoma.
📄 PubMed Article | Date:
2025 Dec 26| Category:Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy
Authors: Gan L, Sui Q, Xu MD et al.
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A tumor-derived lactate/ENO1 lactylation feedback loop facilitates osimertinib resistance of lung adenocarcinoma....
4. Multi-omics approaches for identifying the PANoptosis signature and prognostic model via a multimachine-learning computational framework for intrahepatic cholangiocarcinoma.
📄 PubMed Article | Date:
2025 Apr 15| Category:Hepatology (Baltimore, Md.)
Authors: Yu Y, You Y, Duan Y et al.
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Multi-omics approaches for identifying the PANoptosis signature and prognostic model via a multimachine-learning computational framework for intrahepatic cholangiocarcinoma....
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