scHiC-Diff improves recovery of chromatin interaction patterns in single-cell Hi-C data by modeling contact matrices with a diffusion transformer.
Genome Research
Cold Spring Harbor Laboratory Press · Genomics & Bioinformatics · ISSN 1088-9051, 1549-5469
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Aging and neurodegenerative mouse models show both shared and distinct early chromatin changes, with aged neurons maintaining TADs while pathological models show disorganization.
Identity-by-descent-based clustering reveals environmental and health disparities at biobank scale, with 17 subcommunities showing differential exposure and disease prevalence.
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virCHap achieves 96% recall in viral haplotype reconstruction, surpassing existing tools by 13.6% on simulated large-genome VZV data.
Nanopore sequencing with SomaGauss-SV detects high-frequency somatic structural variations in 71.79% of LSCC patients, revealing recurrent genomic alterations.
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Protein large language model-based gene homology mapping increases homology gene pairs by approximately 8% while maintaining one-to-one mappings in cross-species single-cell transcriptome integration.
Onco-fetal (OF) cells are detected across multiple cancers, exhibit stem-like properties, and their high abundance predicts worse prognosis and increased drug resistance.
Ascaris CBRs engage in 3D interactions before and during PDE, suggesting physical contacts may contribute to chromosome fragmentation in nematodes.
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Arcane improves gene expression quantification in droplet-based scRNA-seq by efficiently correcting errors in barcodes and UMIs, achieving faster performance than existing methods.
Disruption of epigenetic machinery in murine neuronal progenitors causes convergent transcriptional changes despite differing effects on DNA methylation, with MYC as a shared regulatory node.
HiDT accurately detects differential topologically associating domains from low sequencing depth data, outperforming existing methods at both TAD and subTAD levels.
Meso-scale spatial analysis reveals that tissue signaling programs constrain the expansion of papilloma clones in cancerized skin, with field-level signaling rewiring before tumor formation.
Caenorhabditis nigoni has 4.0 times more satellite DNA than Caenorhabditis briggsae, with 12.8 Mb versus 3.2 Mb, revealing significant divergence in repetitive DNA.
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Optical genome mapping detects somatic structural variants in epilepsy-affected brain tissue, revealing a 13.2kb DEPDC5 deletion at approximately 20% VAF in one patient.
NUMTs in great ape genomes accurately reflect species relationships and are enriched in nonfunctional regions, with a notable 76-kb heterozygous NUMT identified in chimpanzees.
CARA accurately transfers cell-type knowledge from scRNA-seq to scATAC-seq, outperforming baseline methods and robustly detecting novel cell types across diverse datasets.
Steroid receptor interactions in the mouse ovary regulate chromatin remodeling, with PGR and GR binding to novel sites to activate ovulation-related genes.
iPSC-derived neurons predominantly retain fetal-like chromatin architecture, showing stronger compartmentalization and developmental gene enrichment at TAD borders compared to mature neurons.
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Topics moving, week to 22 Oct 2026
- Single-cell and spatial transcriptomics6
- Neuroinflammation and Neurodegeneration Mechanisms5
- Cancer Immunotherapy and Biomarkers5
- Gut microbiota and health5
- Cancer Genomics and Diagnostics4
- Bacteriophages and microbial interactions4
- CAR-T cell therapy research3
- Lung Cancer Treatments and Mutations3
- Liver Disease Diagnosis and Treatment3
- Dementia and Cognitive Impairment Research3