iPSC-derived neurons predominantly retain fetal-like chromatin architecture, with 96 high-coverage contact maps revealing strong compartmentalization and developmental gene enrichment.
Genome Research
Cold Spring Harbor Laboratory Press · Genomics & Bioinformatics · ISSN 1088-9051, 1549-5469
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Moderated experimental designs can effectively balance batch-effect reduction and cell loss, with cell loss doubling for each additional hashtag used in single-cell experiments.
Massively parallel assays identified 92 regulatory variants linked to adolescent idiopathic scoliosis, including a key variant near ADGRG6 affecting cartilage regulation.
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BiLinT accurately reconstructs cell lineage trees by jointly analyzing gene expression and lineage barcodes, achieving high resolution in single-cell data.
HiDT accurately detects differential topologically associating domains with high precision at low sequencing depths, outperforming existing methods across various datasets.
Optical genome mapping uncovers somatic structural variants in epilepsy brain tissue, revealing clinically relevant deletions in 20% of cases.
STELAR-X infers species trees from 100,000 taxa and 1,000 gene trees in under 35 minutes, marking a new scale for coalescent-based phylogenetic methods.
Long-read sequencing reveals that Caenorhabditis nigoni has 4.0 times more satellite DNA than C. briggsae, significantly contributing to genome size differences.
Ultra-long read sequencing reveals 612 human inversions, tripling known polymorphic IR-mediated inversions and uncovering over 300 additional structural variants.
CARA achieves accurate cross-modal cell type annotation and novel cell type discovery in single-cell ATAC-seq data, outperforming baseline methods across diverse datasets.
STGnet achieves the most accurate spatial cell type deconvolution and functional annotation, outperforming existing methods on simulated and real datasets.
CircExor predicts circRNA localization into extracellular vesicles with an AUROC of 0.743, outperforming existing tools and aiding biomarker discovery.
STAMGC achieves improved spatial domain identification in spatial transcriptomics, outperforming existing methods across multiple datasets with enhanced detail and noise reduction.
Single-cell and spatial transcriptomics reveal significant intra- and intertumor heterogeneity in ovarian high-grade serous carcinoma, with distinct spatial gene expression patterns across subtypes.
Massively parallel assays identified 92 regulatory variants linked to adolescent idiopathic scoliosis, including a key variant near ADGRG6 affecting cartilage regulation.
Moderated experimental designs can effectively balance batch-effect reduction and cell loss, with cell loss doubling for each additional hashtag used in single-cell experiments.
NUMTs in great ape genomes reveal a dynamic evolutionary process, with a 76-kilobase NUMT in chimpanzee being the largest observed among them.
Steroid receptor interactions orchestrate chromatin remodeling and gene activation during ovulation, with PGR and GR promoting transcription while AR is repressed in the ovary.
Meso-scale spatial analysis reveals that tissue signaling and heterogeneity constrain the tumorigenic potential of Hras mutations in skin, with only 6 out of 473 papillomas harboring the mutation.
iPSC-derived neurons predominantly retain fetal-like chromatin architecture, with 96 high-coverage contact maps revealing strong compartmentalization and developmental gene enrichment.
ARIES achieves higher accuracy than existing methods in constructing multiple sequence alignments, especially in low-identity regimes, with near-linear scalability across diverse protein datasets.
UniVI, a mixture-of-experts β-variational autoencoder, achieves integrated, coherent embeddings across multimodal single-cell data, including up to three modalities, with improved label transfer and reconstruction.
virCHap achieves up to 96% recall and over 97% accuracy in viral haplotype reconstruction, outperforming existing tools across multiple viral datasets.
Convergent regulatory evolution in thylacine and wolf is limited, with only one region showing similar activity reduction near the LMO4 gene.
G4Beacon2 achieves accurate genome-wide in vivo cell-specific G-quadruplex prediction with a multilevel ensemble model, outperforming existing tools across multiple cell lines.
DeepAllele predicts allele-specific gene regulation changes with high accuracy, identifying cis-regulatory motifs across more genomic regions than existing models.
Programmed DNA elimination in nematodes involves conserved 3D genome reorganization, with CBRs engaging in pre- and during-PDE interactions across species.
FateScape accurately reconstructs cell division trees and reveals depth-resolved phenotypic patterns with high robustness in single-cell lineage and transcriptomic data.
SwinePan uncovers 185,759 structural variants and integrates multiomics data across 2,598 pigs, enhancing genetic diversity analysis beyond linear references.
Loss of the Ret mcs+9.7 enhancer combined with Ret coding variants causes a 50% reduction in Ret expression, leading to selective depletion of inhibitory motor neurons in the ENS.
KuPID preprocessing enhances isoform discovery accuracy by up to 11.6 points and halves runtime in long-read RNA-seq analysis.
Hundreds of human snRNA variants are transcribed but mostly remain immature, with only 74 actively expressed across diverse biosamples, highlighting complex regulation.
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Moving areas, week to 3 Oct 2026
- Single-cell and spatial transcriptomics10
- Artificial Intelligence in Healthcare and Education8
- CAR-T cell therapy research7
- Neuroinflammation and Neurodegeneration Mechanisms6
- Lung Cancer Treatments and Mutations5
- Diabetes Treatment and Management4
- Pancreatic and Hepatic Oncology Research4
- Photosynthetic Processes and Mechanisms4
- Genomics and Chromatin Dynamics4
- Gut microbiota and health4