gene regulatory network inference

Age-associated repression of HNF4α is a driver and potential therapeutic target in liver metabolic dysfunction

This study identifies age-associated repression of HNF4α as a driver of liver metabolic dysfunction and shows that restoring HNF4α can reverse some age-related liver defects.

Tfcp2l1 recruits Thrap3 to sustain ESC self-renewal via Jmjd1c exon-5 splicing and DNA repair choice

This study identifies Tfcp2l1 and Thrap3 as regulators of ESC self-renewal through exon-5 splicing of Jmjd1c and DNA repair pathway choice.

Quantitative trait loci mapping identifies genetic loci modifying MafAS64F-mediated dysglycemia

This study maps quantitative trait loci modifying glycemia in MafAS64F-driven dysglycemia using genetically diverse mice.

Uncertainty-Aware Personalised Gene Expression Prediction Improves Cell-Type-Specific Association Testing

ATTICUS improves gene expression prediction and association testing by incorporating uncertainty awareness and personalized training, enhancing accuracy and cell-type specificity in disease studies.

Rapid generation of marsupial induced pluripotent stem cells suitable for use in next-generation conservation

This study generates transgene-free iPSCs from the fat-tailed dunnart, demonstrating their pluripotency and potential for use in conservation biotechnology.

Host control and regulation of human anellovirus persistence

This study identifies host factors and cellular contexts governing anellovirus persistence through genomic, transcriptomic, and functional analyses.

Transcriptome profiling reveals gene regulatory network governing seed size in Brassica napus

The paper identifies gene regulatory networks governing seed size in Brassica napus through transcriptomic analysis of developmental stages and seed organs.

Pseudo-observations of longevity improve detection of resilience-associated genes in the Radiation Late Effects Cohort of rhesus macaques.

The paper uses pseudo-observations of longevity to identify resilience-associated genes in rhesus macaques exposed to radiation and aging challenges.

Integrative Transcriptomic Analysis Reveals Differential Exon Usage and Virulence Gene Family Dynamics in Plasmodium falciparum during Severe Malaria

ERV-derived dsRNAs induce stress granules that drive neural crest fate to initiate melanoma

Network inference at single-cell resolution reveals morphoregulatory divergence and multilayered buffering in limb evolution

The paper compares gene regulatory networks in mouse and pig limb development to reveal conserved and divergent regulatory programs and mechanisms of developmental robustness.

A largely shared genetic architecture underlies Saccharomyces cerevisiae persistence across different mouse host genotypes

This study shows that Saccharomyces cerevisiae persistence in mice is polygenic with strong additive effects and minimal host-genotype interactions.

Contrasting within-donor gene covariation identifies disease-associated cells and genes in case-control single-cell studies

Programmable interphyla communication for Staphylococcus aureus by transferability of homoserine lactone sensors between Bacillales bacteria

This study demonstrates the transferability of homoserine lactone sensors between Bacillales bacteria, enabling programmable interphyla communication between Gram-negative and Gram-positive species.

Hypoxic Stress Induces LARP1-Driven Stress Granules That Protect mRNAs from Decay to Sustain Mitotic Cell Cycle Progression

This study shows hypoxia induces LARP1-driven stress granules that protect mRNAs from decay, sustaining mitotic progression in cancer cells.

GeneEmbedLLM: Harnessing Large Language Models for Gene Functional Embedding and Association Prediction

This paper introduces GeneEmbedLLM, a framework using large language models to generate gene embeddings from multi-source textual annotations, achieving competitive performance in various downstream tasks.

HomoeoGWAS enables experiment-wide homoeolog-group interaction mapping in allopolyploid crops

HomoeoGWAS identifies homoeolog-group interactions in allopolyploid crops by analyzing genotype encodings and controlling family-wise error across multiple species.

scPolyA enables efficient, interactive and agent-guided alternative polyadenylation analysis in single-cell and spatial transcriptomes

scPolyA provides a framework for analyzing alternative polyadenylation in single-cell and spatial transcriptomes, revealing APA patterns in cancer tissues.

Transcriptomic and Metabolomic Analysis of the Caudate and Putamen in ADHD

This study identifies region-specific molecular dysregulation in ADHD brains, including dopamine and metabolite changes, immune responses, and gene modules linked to synaptic pathways.

Ogg1 regulates context-dependent glial states in Alzheimer's disease

This study shows Ogg1 has opposing effects on glial states in Alzheimer's disease, improving memory and reducing amyloid burden in a mouse model while impairing memory under physiological conditions.

PCB-Exposed Gut Microbiota Recapitulate Neurobehavioral Deficits and Reprogram Hippocampal Transcriptomic Signatures

This study shows that transferring PCB-exposed gut microbiota to offspring reproduces neurobehavioral deficits and induces sex-biased molecular changes in the brain.

ApoE isoforms establish distinct antioxidant trajectories across the aging brain

This study shows ApoE isoforms influence antioxidant pathways differently across aging, with ApoE4 showing stronger transcriptional responses but less effective protein production, linking to neurodegenerative risk.

Cell cycling throttles epithelial--mesenchymal transition

This study shows that G1 phase cells exhibit stronger EMT gene expression and RNA velocity than cycling cells, suggesting cell cycle phase influences EMT and should not be regressed out.

Human medial frontal neurons represent integrated semantic content and sensory evidence to inform decision-making

The paper identifies how medial frontal cortex integrates semantic content and sensory evidence for decision-making using human neurosurgical data and a vision-language model.

Tardigrades survive reversible dormancy during spaceflight: In-orbit revival, post-flight recovery, and transcriptomic responses

This study shows that tardigrades can survive and revive after spaceflight, with transcriptomic changes indicating stress responses and reduced energy metabolism.

Identification and characterization of new P. aeruginosa phages using a surface receptor platform

The paper introduces a SURFAR platform to identify and characterize new P. aeruginosa phages by targeting specific receptors, isolating two novel phages with distinct host ranges.

Fatty Acid Synthase Binds Cellular mRNAs and its Depletion Reduces Translational Efficiency

This study identifies FASN's RNA binding sites and shows its depletion reduces translational efficiency of associated mRNAs.

The MarR-family regulator TilR links biosynthesis of enterotoxin tilimycin with physiologic adaptation in Klebsiella oxytoca

This study identifies TilR, a MarR-family regulator in Klebsiella oxytoca, as a repressor of tilimycin biosynthesis and links it to metabolic and virulence-related gene expression.

Multi-omics integration reveals candidate genes and molecular mechanisms associated with resistance to sugarcane smut

The paper integrates association mapping and transcriptomics to identify candidate genes and molecular mechanisms associated with sugarcane resistance to smut.

Massive inter-animal horizontal gene transfer contributes to stress tolerance in the fungus gnat Bradysia coprophila

This study identifies extensive horizontal gene transfer in the fungus gnat Bradysia coprophila, showing these genes contribute to stress tolerance and ecological adaptation.