differential expression

This study profiles SCN transcriptomes in soybean roots under single or combined SBA infestations, finding increased SCN gene expression in resistant cultivars under combined treatment.

The paper introduces a uniform method for inferring regulatory networks across cancer subtypes, showing it is adequate for multi-cohort analysis despite not being statistically superior.

This study uses time-resolved single-cell CRISPR screening and a multiome atlas to uncover dynamic gene regulatory networks in human cardiogenesis, identifying stage-specific regulators and CHD-linked gene functions.

The paper constructs a population-scale isoform atlas for lettuce and develops ISONET-GWAS to analyze isoform-based trait associations and regulatory mechanisms.

The paper identifies telotrons, telomeric repeat-containing introns, in multiple eukaryotic genomes and suggests telomerase drives intron creation and remodeling.

The paper compares three plasma proteomic metrics across organ systems to assess their associations with brain structure and neurodegenerative disease, finding distinct relationships and modest predictive value.

This paper introduces PertVI, a deep generative model that disentangles treatment effects from cellular state and batch effects in single-cell perturbation data, revealing state-specific transcriptional responses.

The paper uses in vivo single-cell CRISPR screens to study how tumor suppressor loss and genetic perturbations affect glioma states and immune recruitment in mice.

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.

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

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

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

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

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

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

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.

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

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.

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

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.

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

DisCell identifies and separates spillover from niche responses in spatial transcriptomics data, confirming a previously reported finding about esophageal cancer cells.

This study uses proteomics to identify aging and Aβ-related molecular changes in mouse brains and finds they are conserved in human AD proteomes.

This study shows CD300f is essential for microglial lipid handling and remyelination during demyelination, with deficits in lipid metabolism and motor coordination in its absence.

TailEnrich identifies dysregulated genes in patient subsets by testing expression distribution tails, outperforming DESeq2 and edgeR in simulated data and uncovering novel genes in Alzheimer's disease.

This study identifies FUL2 and STM3 as repressors of secondary growth in tomato stems, showing their role in limiting xylem accumulation during stem development.