🧬 Category

q-bio

5862 papers

🧬 biology

The necessity of data-driven optimization of the number of principal components in scRNA-seq analysis - examples on real and simulated data

This study demonstrates that while fixed defaults for the number of principal components often work, data-driven optimization is essential for scRNA-seq analysis due to variable optimal ranges across diverse datasets, and it provides practical recommendations for selecting these methods based on a comprehensive evaluation of real and simulated data.

Manja Grønberg, Alisa Pavel, Line Clemmensen2026-10-23
🧬 biology

The reassembly of plant-pollinator interactions along tropical forest succession

While pollinator abundance and network structure remain resilient and facilitate pollen flow across agricultural landscapes during tropical forest recovery, the full restoration of specialized plant-pollinator interactions and old-growth network complexity is significantly delayed, taking decades to reassemble.

Ugo Diniz, Alexander Keller, Gunnar Brehm, Claus Rasmussen, Katharina Veltman, Santiago Erazo, Santiago Burneo, Marco Ts (…)2026-10-23
🧬 biology

Restoring the p53--Nrf2--SIRT3--TFAM Axis via Therapeutic Epigenetic Shielding Reverses Bioenergetic Collapse and Nucleoid-Phagy Failure in Long COVID

This study proposes a systems biology framework demonstrating that Long COVID's bioenergetic collapse and chronic inflammation stem from CD147-mediated suppression of the p53--Nrf2--SIRT3--TFAM axis, which impairs mitochondrial function and nucleoid-phagy, but can be reversed through therapeutic epigenetic shielding to restore this regulatory cascade.

Boominathan Lakshmanane2026-10-23
🧬 biology

Predicting Macroscopic Axon Topology from Microscopic Kinematics: An Interactive Tracking and Random Walk Pipeline for Substrate-Dependent Cortical Neurospheres

This study introduces an interactive tracking and random walk pipeline that utilizes size-controlled cortical neurospheres to quantify substrate-dependent axonal kinematics, successfully linking microscopic growth dynamics to macroscopic network topology for predicting circuit architecture in vitro.

Chunghwan Kim, Myungbo Kim, Hanlin Cao, Tsung-yeh Hsieh, Yongjie Jessica Zhang, Tzahi Cohen-Karni, Victoria A. Webster-W (…)2026-10-23
🧬 biology

Deep Learning and Computational Modeling for Epitope-Focused Immunogen Design Targeting Monkeypox

This paper presents a deep learning-based computational framework that outperforms traditional machine learning models in predicting T-cell and B-cell epitopes from the monkeypox virus proteome, offering a scalable and adaptable strategy for designing epitope-focused immunogens against emerging viral variants.

Gurudeeban Selvaraj, Satyavani Kaliamurthi, Gilles H Peslherbe, Dongqing Wei2026-10-23
🧬 biology

IL-33 signaling uncouples pulmonary regulatory T-cell specialization from suppressive function during type 2 inflammation

The study reveals that during type 2 inflammation, IL-33 signaling uncouples the specialization from the suppressive function of pulmonary regulatory T cells by upregulating IL-4Rα to drive glycolysis-dependent STAT6 signaling, thereby promoting pathogenic TH2 memory while simultaneously impairing TREG-mediated immune restraint.

Ciriaco Piccirillo, Fernando Alvarez, Lydia Labrie, Tho-Alfakar Al-Aubodah, Roman Isotomine, Katherine Restori, Jörg Fri (…)2026-10-23
🧬 biology

Farming system shapes the microbiota of Bactrocera oleae across Spanish olive regions: consequences for host fitness and pest management

This study demonstrates that farming practices and geographic location jointly shape the bacterial microbiota of the olive fruit fly (*Bactrocera oleae*) in Spain, where organic orchards foster diverse, beneficial microbial communities that enhance host fitness compared to conventional systems, suggesting new avenues for microbiome-based pest management.

Imen Blibech, Francisco José Beitia, Manuel Ruiz Torres, Francisco José Cabrero Sañudo2026-10-23
🧬 biology

Integrated metabolomic and genomic characterization of antifungal Streptomyces halstedii S14 from Melipona mondury larval food

This study integrates spatial metabolomics and genome mining to characterize the antifungal activity of *Streptomyces halstedii* S14 from *Melipona mondury* larval food, revealing a spatially structured chemical interaction involving compounds like caboxamycin and bafilomycin C1 without attributing the phenotype to a single molecule.

Yuri Ribeiro Diogo, Luciana Teresa Dias Cappelini, Keith Dayane Leite Lira, Ana Calheiros de Carvalho, Nubia Gonçalves d (…)2026-10-23
🧬 biology

Replicator--Mutator Dynamics on Networks with Spatial Nonlocality: Theory and Applications

This paper introduces a generalized replicator-mutator model incorporating nonlocal interactions via dd-path Laplacians to demonstrate that long-range influence on networks reduces the mutation intensity needed for diversity and can trigger abrupt transitions from behavioral flocking to uniform distributions, thereby promoting both increased effective diversity and homogeneity of behavioral frequencies.

Porikshit Mondal, Ernesto Estrada2026-10-23
🧬 biology

Gut microbiome differences in youth with perinatally acquired HIV and fatty liver disease: a multicentre study

This multicentre study reveals that while HIV infection significantly alters gut microbiome diversity and composition in youth, the presence of metabolic dysfunction-associated fatty liver disease (MAFLD) is associated with only modest microbial changes, specifically reduced *Parabacteroides* abundance, highlighting the dominant influence of HIV on the gut-liver axis in this population.

Germán Vallejo, Moreno Elena, María Luisa Montes, Antonio Oliveira, Maria Mercadal, Carmen Busca, Luis Escosa, Cristina (…)2026-10-23