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The paper develops ARES to analyze TF binding data and finds that motif readers, not canonical TFs, determine regulatory outcomes.

ssJSD improves scHiC clustering by integrating spatial interaction patterns and sparsity patterns to better distinguish cell types.

This study defines the single-cell landscape of Class II lupus nephritis and identifies fibroblast transcriptional programs and chronicity index as potential predictors of kidney outcomes.

The paper uses deep learning to analyze Alu elements' impact on genome folding, identifying sequence and genomic context features that influence chromatin interactions and boundary formation.

The paper uses self-supervised deep learning representations of cortical folding to identify more genetic loci associated with cortical shape than classical morphometry in a large cohort.

Saliva methylation from 37 autistic adults vs 188 public controls showed elevated Brain, Blood and Liver SystemsAge subscores, while global clocks (Horvath, GrimAge, DunedinPACE) showed no difference.

The paper identifies genomic scars from alternative end joining and single-strand annealing across multiple cancer types, revealing their association with HR deficiency and local genomic features.

The paper uses RIC-seq and integrates multi-omics data to classify transcription factors into two clusters based on RNA-RNA spatial interactions and their genomic and clinical features.

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

The paper identifies cell-type-specific DNA methylation differences in autism, revealing female-specific X chromosome alterations in microglia.

This study uses multi-omics analysis to investigate the genomic basis of ecological adaptation to dryland environments in Psammochloa villosa.

The paper integrates cell-specific gene expression and chromatin accessibility to identify neurodegenerative disease risk loci specific to microglia.

The paper analyzes mosquito viromes from UK zoos using metagenomics, identifying two novel Orthobunyaviruses, including one potentially arbovirus.

The paper analyzes genomic diversity in Mycobacterium abscessus, finding that dominant clones show increased accessory-gene gains and reduced recombination relative to mutation after establishment.

This study uses electronic genome mapping to analyze how gRNA mismatches affect CRISPR/Cas9 binding specificity across the human genome, revealing key regions for on- and off-target activity.

The paper uses CRISPR-based functional genomics to identify noncoding regulatory elements and variants affecting schizophrenia-associated gene expression.

The paper identifies DNA methylation variability and differential methylation regions associated with aging-related health decline and constructs an epigenetic biomarker that outperforms methylation-only biomarkers in predicting mortality.

Epi-PoreC profiles chromatin conformation, DNA methylation, and chromatin accessibility simultaneously using nanopore sequencing on single DNA molecules.

The paper maps Cas9-induced sister chromatid exchange (SCE) across genomic targets using sci-L3-Strand-seq, showing local SCE enrichment and context-dependent recombination at repetitive loci.

EukPan is a pipeline for eukaryotic pangenome analysis that identifies core and shared accessory orthogroups, revealing differentiation in Aspergillus oryzae beyond core-gene phylogeny.