differential expression

This study shows that maternal separation alters cerebellar circuitry and synaptic plasticity, leading to behavioral and neurobiological deficits 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.

This study identifies SAMP1 as a protector of alveolar type 2 cells against DNA damage-induced senescence and shows its role in limiting pulmonary fibrosis in a mouse model.

The paper explores whether quantum entanglement, measured via von Neumann Entropy, influences TP53 mutation patterns, finding elevated entropy at known mutational hotspots but cautioning about limited validation.

memVar links human membrane protein variants to molecular contexts and disease, revealing enrichment of pathogenic variants in transmembrane regions and interaction sites.

The paper identifies promoter hypomethylation as a driver of transcriptomic plasticity and aberrant gene expression in colorectal cancer, linking it to distinct cell states and metastatic behavior.

The paper evaluates how small reference sample sizes affect substructure estimation and proposes bias corrections for improved accuracy.

This study identifies genetic polymorphisms in NKG2C, CD16a, and HLA-E that influence NKG2C expression and ADCC capacity in HCMV-infected individuals.

The paper identifies CD200R1 as a marker for an immature NK-cell precursor in tonsils, distinguishing between oligopotent and more restricted developmental stages.

The paper shows that neural RNA splicing models rely on reading frame information that the splicing machinery cannot access, leading to errors in predicting poison exons.

NPlasmid-seq detects sub-percent contamination and sequence heterogeneity in plasmid preparations using Cas9-encoded terminal signatures, revealing structural variants missed by consensus-based methods.

The paper identifies methylation changes associated with dysplasia and cancer progression in Barrett's esophagus using whole-genome methylation profiles.

This study shows that Polycomb-marked promoter methylation gains in aging and cancer occur independently of replication and are driven by age-related epigenetic drift rather than oncogenic signaling.

This paper detects neuronal DNA in cfDNA using non-CpG methylation patterns, finding elevated levels in neurological conditions and brain-dead donors.

This study uses deep learning to predict cis-regulatory effects of human-specific mutations across 305 tissues, revealing their role in gene expression evolution.

The paper maps m6A modifications in lncRNAs at single-base resolution, revealing distinct patterns linked to transposable elements, RNA structure, and splicing.

The paper identifies biallelic DDX41 variants in LCA/EOSRD patients and shows they disrupt retinal homeostasis through loss-of-function mechanisms in mouse models.

This study identifies c-MYC as a non-canonical origin licensing accelerator, showing it increases licensing speed through TRRAP/GCN5 and histone H1 eviction, particularly in heterochromatin.

This study shows that paternal sperm histone H3K27me3 marks influence offspring development and viability by affecting organ and tissue formation.

This study examines how different dietary fibre regimes affect the gut microbiome, SCFA profiles, and immune responses in zebrafish, showing context-specific effects influenced by sex and dietary context.

This study shows that mTOR signalling, not clock gene rhythms, drives daily physiological variations in mammals and plants.

The paper develops deep learning models to predict transcription initiation patterns from DNA sequences across human tissues and cancers.

Transient low-dose inhibition of DNA polymerase α enhances human cell reprogramming by promoting chromatin plasticity while maintaining genomic stability.

This study evaluates the performance of three large language models on basic bioinformatics tasks compared to human performance, finding LLMs match human accuracy in some areas but struggle with complex tasks like sequence alignment.

This study predicts biological age and clinical biomarkers from cheek mucosa DNA methylation data, showing high accuracy for age and multiple biomarkers compared to blood-derived data.

The paper detects malignant hematopoietic stem cells (HSCs) in myelodysplastic neoplasms (MDS) using low-input sequencing and shows they predict relapse after transplantation.

This study characterizes cis-regulatory elements and predicts enhancers in Heliconiini butterflies using ATAC-seq and histone modification data, revealing temporal divergence and developing a CNN for enhancer prediction.