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q-bio

1432 papers

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What Knowledge Can Be Extracted from Single-Cell Data? An Empirical Analysis of Donor-Robust Cell-Type Annotation

An empirical analysis of human pancreatic single-cell RNA-sequencing data demonstrates that for abundant, canonical cell types, cell-type annotation models generalize robustly across donors with only modest performance drops when evaluated via leave-one-donor-out compared to random splitting, underscoring the necessity of explicitly stating the population and technical scope when claiming knowledge extracted from single-cell data.

Liu Chen2026-07-24
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When Do Single-Cell Foundation Models Beat PCA? A Simulation-Based Empirical Analysis of Label Scarcity and Perturbation Generalization

This simulation-based study demonstrates that single-cell foundation models significantly outperform classical PCA pipelines in label-scarce annotation tasks (1–5 labeled cells per class) but offer little to no advantage over simple linear baselines when sufficient labels are available or when predicting responses to novel perturbations.

Liu Chen2026-07-24
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Does Candidate-Space Restriction Destabilize Cross-Tissue Gene Regulatory Network Benchmark Rankings? An Empirical Analysis of Analytic Flexibility in Computational Biology

This empirical analysis demonstrates that restricting candidate spaces in gene regulatory network benchmarks significantly destabilizes cross-tissue method rankings, indicating that candidate definition choices can alter comparative conclusions and should be reported alongside results rather than treated as neutral.

Liu Chen2026-07-24
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Bacteria getting wired: The porin-cytochrome complex Om(abc)B kickstarts extracellular electron transfer and nanowire formation

This study reveals that *Geobacter sulfurreducens* utilizes a sequential, two-stage extracellular electron transfer strategy where the porin-cytochrome complex Om(abc)B first enables the energy-intensive synthesis of OmcS nanowires, allowing cells to switch from a wireless to a wired mode that dramatically expands their access to Fe(III) for replication.

Nikhil Malvankar, Joseph Erwin, Kejue Jia, Cong Shen, Vanessa Saldivar, Aldo Salazar Morales, Vasilije Pentalic, Fadel S (…)2026-07-24
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Bacteroides acidifaciens derived pentadecanoic acid alleviates MAFLD by sensitizing senescent macrophages to ferroptosis via JNK-JUN-NCOA4 pathway

This study demonstrates that pentadecanoic acid, a metabolite derived from *Bacteroides acidifaciens*, alleviates MAFLD by sensitizing senescent macrophages to ferroptosis through the activation of the JNK-JUN-NCOA4 signaling pathway, thereby promoting their clearance and reducing hepatic steatosis.

Rui Kong, Huiyu Wang, Nan Wang, Chunli Zhou, Yuqing Zhou2026-07-24
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Integrative genomic and transcriptomic analyses identify functionally relevant causal genes for exercise in a large animal model

This study integrates genomic and transcriptomic data from Thoroughbred horses to identify specific causal genes and variants underlying athletic performance traits, distinguishing between inherited genetic factors and acquired molecular responses to exercise and training.

Mian Feng, Thomas J. Hall, John F. O’Grady, Kseniia Maksimova, Michael Salter-Townshend, John A. Browne, David E. MacHug (…)2026-07-24
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Agar oligosaccharides mitigate lipopolysaccharide-induced apoptosis and inflammatory damage in rumen epithelial cells via the tlr4-myd88-nf-κb signaling pathway

This study demonstrates that agar oligosaccharides (AOS) mitigate lipopolysaccharide-induced apoptosis and inflammatory damage in ovine rumen epithelial cells by inhibiting the TLR4-MyD88-NF-κB signaling pathway, suggesting AOS as a potential green feed additive for alleviating ruminant metabolic diseases.

Aihong Lao, Xiaolin He, Jian Ma, Chunmei Du, Fuquan Yin, Yanli Lu2026-07-24