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This paper presents the first chromosome-scale, haplotype-resolved nuclear genome assembly for Chiloglottis trapeziformis, revealing structural variation and repeat-rich features.

GenVarLoader accelerates deep learning applications in personalized genomics by improving data loading speed and compression.

The paper shows genomic structural variants rescue the brown treesnake population from inbreeding after a severe bottleneck.

The paper constructs chromosome-scale genomes for three Cupressaceae species to study chromosomal evolution and speciation, finding chromosomal rearrangements and segmental duplications contributed to species divergence.

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

This study examines age-related changes in the human hippocampus using multi-omics data, revealing cell-type loss and epigenetic reprogramming linked to cognitive decline.

The paper analyzes ancient DNA from Gothic-associated communities in Late Antique Bulgaria, finding genetic heterogeneity and admixture between northern and southern ancestry components.

The paper integrates epigenomic features to identify chromatin-state classes and shows Polycomb-associated chromatin drives cell-type-specific differences.

This study constructs a pan-cancer single-cell multi-omic atlas to uncover gene regulatory principles in cancer cell states and environmental features across diverse cancer types.

HiC2Self denoises Hi-C contact maps using self-supervised learning, reconstructing 3D chromatin structures from low-coverage data across bulk and single-cell samples.

This study shows that genetic background and environmental factors determine the trajectory of cancer evolution in mice, with distinct mutational paths despite similar final tumor states.

The paper uses single-cell RNA sequencing to show that Th1-like CD4 T-cells with CTLA-4 expression control latent C. neoformans infection, and CTLA-4 suppression of Th2 activation is beneficial.

The paper presents a microbial genomes database for the Great Barrier Reef, highlighting underrepresented prokaryotic and viral genomes and their utility in predicting reef management impacts.

VN1K provides a comprehensive multi-omics and phenomics resource for the Vietnamese population, identifying novel variants and functional associations with disease traits and drug responses.

This study identifies lactation-stage specific QTL for milk urea concentration in dairy cattle breeds, highlighting pleiotropic effects and candidate genes.

This paper introduces spRandom-seq, a spatial RNA sequencing method for FFPE tissues, which captures both host and microbial RNAs with higher efficiency than oligo(dT)-based methods.

This study identifies ferroptosis-related biomarkers in early-onset Alzheimer's disease using machine learning and develops a diagnostic model with high AUC-ROC values.

The paper introduces easySHARE-seq, a method for simultaneous single-cell ATAC-seq and RNA-seq, showing improved transcript recovery and scalability in murine liver nuclei.

This study shows histone hyperacetylation disrupts TAD intra-interactions but preserves CTCF-CTCF loops, revealing distinct cohesin populations with different sensitivity to acetylation.