407 papers
By integrating GWAS data with a high-resolution map of dexamethasone-induced chromatin dynamics in human trabecular meshwork cells, this study identifies 78 candidate causal genes and elucidates the regulatory mechanisms underlying elevated intraocular pressure and primary open-angle glaucoma pathogenesis.
This study analyzes mutation data from over 20,000 cancer patients to reveal that stop-loss mutations, which generate C-terminal protein extensions, are significantly enriched in oncogenes and tumor suppressor genes and can functionally alter protein processing, as demonstrated by the impaired cleavage of the immunostimulatory peptide thymosin alpha 1 in PTMA.
This study utilizes CAGE technology to map active transcriptional start sites and enhancers during honeybee worker metamorphosis, revealing a lineage-specific regulatory network where the transcription factor tramtrack (ttk) likely controls key developmental genes like Broad complex (Br-c) through enhancers conserved specifically within the Apis genus.
This study demonstrates that while bulk and single-cell RNA/ATAC sequencing profiles of TNFα-treated endothelial cells reveal similar biological pathways, the choice between bulk and single-cell methodologies significantly impacts the predictions of enhancer-to-gene regulatory models, leading to different prioritizations of causal genes for complex traits like coronary artery disease.
By integrating AI-derived facial phenotypes with skin DNA methylation data from 706 individuals, this study introduces EpiVision, a panel of 21 epigenetic predictors that reveals visible skin aging comprises distinct molecular axes with both shared and trait-specific biological drivers, offering a multidimensional framework for understanding and intervening in cutaneous aging.
The paper introduces "Combine," a scalable group lasso framework that integrates local ancestry dosages with genotype data to significantly enhance polygenic risk prediction accuracy and interpretability in admixed populations, outperforming existing multi-ancestry methods while matching optimized individual-level models.
The paper introduces SNACKKSS, a system that automatically curates transcriptomic data and biomedical literature to predict pharmacologic gene regulators, demonstrating that its machine learning-based predictions significantly enhance drug repurposing efforts for Mendelian disorders while highlighting the importance of cross-device model validation.
This study demonstrates the first successful application of portable Oxford Nanopore Technologies to ancient human remains from the Early Jomon period, proving that on-site sequencing can rapidly generate reliable genomic data and ethical, time-resolved analyses while overcoming the logistical and regulatory barriers of traditional laboratory-dependent paleogenomics.
This study reveals that in sex-role reversed northern jacanas, sex differences in brain gene expression are driven by complex genetic and hormonal interactions rather than a simple reversal of typical sex-biased patterns, with male-biased genes predominantly located on the Z-chromosome and specific hormone signaling pathways differentially regulating female competition and male parental care.
This study enhances the FLASH-seq protocol for Oxford Nanopore long-read single-cell RNA sequencing by developing two multiplexing barcoding strategies and a dedicated bioinformatics pipeline, demonstrating successful full-length isoform resolution while highlighting persistent technical challenges such as high chimeric read rates and index swapping.
This study demonstrates that the Ultima UG100 sequencing platform delivers performance comparable to Illumina NovaSeq across multiple genomic assays using FFPE tissues, offering a high-precision, cost-effective alternative for clinical and population-scale research despite minor, non-critical technical differences.
This study presents a novel bioluminescence resonance energy transfer (BRET) assay that enables the real-time measurement of telomere length in living *S. cerevisiae* cells by correlating energy transfer between luciferase-Rif2 and fluorescent Rap1 with telomeric nucleotide counts validated by long-read sequencing.
This study expands the characterization of long G4-rich (LG4) genomic regions beyond humans to 16 diverse species, revealing that these G-quadruplex-forming sequences are widely conserved across taxa and function as evolutionarily preserved enhancers, including a highly conserved LG4 in the MAZ locus that regulates multiple genes in both humans and mice.
This study presents a high-quality, chromosome-level genome assembly for a Chilean *Tigriopus* population (tentatively identified as *Tigriopus* aff. *angulatus*), generated using multi-platform sequencing to provide essential genomic resources for investigating adaptation and diversity within this globally distributed copepod genus.
This study reveals that while biotic-response networks remain conserved in wild *Arabidopsis thaliana* populations across diverse natural environments, the overall transcriptome organization and regulatory relationships differ significantly from those observed in controlled laboratory settings.
This study identifies recurrent, sequencing-center-specific artefactual within-host variants in SARS-CoV-2 deep-sequencing data and proposes a dataset-aware masking framework to eliminate these noise sources, thereby improving the accuracy of downstream evolutionary and transmission inferences.
This study presents the "Codebook" project, a systematic effort that successfully determined the DNA binding motifs for 177 poorly characterized human transcription factors through over 4,000 experiments, thereby expanding the known vocabulary of sequence recognition and revealing tens of thousands of conserved, direct binding sites that predict gene expression across the human genome.
This study utilizes RAD-seq to demonstrate that despite significant demographic heterogeneity among Atlantic Canadian stickleback populations, genomic regions associated with nervous system development and dopamine receptor activity consistently drive parallel marine-freshwater divergence.
By applying combined cell-free DNA and RNA sequencing to plasma samples from HIV-positive individuals, this study reveals that the development of broadly neutralizing antibodies is associated with a distinct early immune activation signature, specific viral genetic features, and enrichment of certain microbial taxa, including GB virus C.
This study reveals that in *Arabidopsis thaliana*, the position of the first intron predicts active chromatin marks near transcription start sites, while the total number of introns correlates with gene-body chromatin features and broad expression, suggesting two distinct mechanisms by which intron architecture shapes chromatin states and gene regulation.