q-bio papers | Gist.Science

Reading Mechanism off Biological Foundation Models: An Empirical Analysis of Genomic Neighborhood Structure in scGPT Gene Embeddings

This empirical study demonstrates that the scGPT biological foundation model exhibits a small but reproducible association between its static gene embedding geometry and linear genomic neighborhood, revealing that genes located close together on the same chromosome are more similar in the model's representation than distant genes, even though this spatial information was not explicitly provided during training.

Liu Chen2026-07-27

📄 other

The effect of dietary fiber based on fermentability and viscosity on the gut microbiome composition in chronic kidney disease: a systematic review of experimental and clinical trials

This systematic review of 22 experimental and clinical trials concludes that isolated dietary fiber interventions yield variable and largely inconsistent effects on gut microbiota composition in chronic kidney disease patients, with no clear pattern emerging based solely on fiber fermentability or viscosity.

Seyedeh Nooshan Mirmohammadali, Claudia Carrillo, Jason B. Reed, Brandon M. Kistler, Hannah E. Wilson, Bruce Hamaker, Sh (…)2026-07-27

📄 other

Regional sequence and embedding divergence among five grass OsNAC25-like proteins

This study analyzes five grass OsNAC25-like proteins to demonstrate that while sequence identity and structure-prediction confidence consistently show higher conservation in the N-terminal DNA-binding domain compared to the C-terminal region, protein-language-model embeddings are significantly influenced by specific candidate identity, highlighting the finger-millet sequence as a priority for further phylogenetic investigation.

Neil Sumanth2026-07-27

📄 other

A Curvature Guided Composite Kernel Framework for Differential Gene Selection in Cancer Transcriptomics

This paper proposes a curvature-guided composite kernel framework that leverages quantum mechanics principles to project RNA-seq data into a Hilbert space, utilizing a gravitational search mechanism to identify differentially expressed genes by minimizing representational loss on the latent manifold.

Manan Gupta, Arka Prava Sarkar2026-07-27

📄 other

Natural Language Processing Psychometrics

This paper introduces "NLP Psychometrics," a framework that leverages Large Language Model personas and interpretable AI techniques to link psychological prediction scores to specific linguistic features, demonstrating that while synthetic data can effectively expose biases and predict mental health outcomes like depression and life satisfaction, it cannot replace human validation.

Edoardo Sebastiano De Duro, Emma Franchino, Massimo Stella2026-07-27

📄 other

Comparative Transcriptomics Reveals a Conserved Antibacterial Immune Program with Pathogen-Specific Remodeling of Macrophage Cellular Functions

This study utilizes comparative transcriptomics of four distinct bacterial infections to reveal that macrophage antibacterial immunity is organized around a conserved inflammatory core, which is overlaid by pathogen-specific remodeling of cellular functions such as metabolism and cell-cycle regulation.

Umama Shahid, Sonia Dangi2026-07-27

📄 other

Compartment Mismatch Produces Near-Perfect Apparent Discrimination in Blood-Referenced DNA-Methylation Classifiers: A Public-Cohort Reanalysis of Hematologic-Malignancy Series

This study demonstrates that blood-based DNA-methylation classifiers often achieve near-perfect apparent discrimination in hematologic malignancy cohorts not due to disease detection, but because of unaccounted mismatches between the cellular compartments of the healthy reference and the diseased samples, rendering such uncorrected validations uninterpretable.

Frederic Scheer2026-07-27

📄 other

Biases, blind spots and signals in public One Health genome data for carbapenemase-producing Enterobacterales

An analysis of nearly 140,000 public genomic records reveals that while carbapenemase-producing Enterobacterales data exhibits distinct source-specific patterns, the overwhelming dominance of clinical samples highlights a significant surveillance blind spot in environmental, animal, and food sectors, indicating that repository composition rather than true prevalence drives current visibility.

Georgios Miliotis2026-07-27

📄 other

Real-time Visualization of Spliceosome Assembly Reveals Basic Principles of 3’ Splice Site Selection

By developing a kinetic model based on single-molecule imaging, this study reveals that the spliceosome achieves high-fidelity 3' splice site selection through a partial kinetic proofreading mechanism involving DDX42, where commitment occurs after U2AF binding rather than during initial interaction.

Dan Larson, Benjamin Donovan, Bixuan Wang, Gloria Garcia, Stephen Mount2026-07-27

📄 other

Evolving genetic landscapes of Plasmodium falciparum Kelch-13 polymorphisms in Nigeria: A systematic review and meta-analysis

This systematic review and meta-analysis reveals that *Plasmodium falciparum* Kelch-13 polymorphisms in Nigeria are highly diverse and independently emerging rather than dominated by a single mutation, underscoring the urgent need for sustained genomic surveillance to prevent the spread of artemisinin resistance.

Aaron Onyebuchi Nwana, Emmanuel Afolabi Bakare, Isaac Segun Oyedeji, Happiness Oluwatosin Ismail2026-07-27

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