404 papers
The paper introduces KLinterSel, a Python-based software tool that employs two complementary statistical tests to rigorously evaluate whether overlaps in candidate genomic regions detected by different selective sweep methods exceed random expectations, thereby distinguishing genuine methodological concordance from artifacts caused by underlying genomic structure.
This study reveals that intrinsically disordered regions in human transcription factors have uniquely evolved to become increasingly disordered over time, distinguishing them from other proteins by their association with developmental regulation, larger regulatory networks, stronger evolutionary constraints, and a higher burden of pathogenic mutations.
Genome-wide analysis of 38 individuals from Gothic-associated sites in Late Antique Bulgaria reveals that despite shared material culture and burial practices, these communities comprised genetically distinct groups with varying proportions of Anatolian and northern European ancestry, indicating that Gothic affiliation functioned as a cultural-political framework encompassing biologically diverse populations who experienced admixture prior to documented Gothic-Roman contacts.
This study demonstrates that leveraging tissue-specific long-read RNA-seq assemblies to refine transcript annotations significantly improves the specificity of regulatory inference and the identification of candidate causal isoforms for breast cancer risk, uncovering critical genetic associations that are missed by standard pan-tissue annotations like GENCODE.
This study demonstrates that while yeast species with distinct thermal niches adapt to rising temperatures through predictable, convergent mutations in conserved regulatory networks like TORC1, PKA, and MAPK, the resulting phenotypic outcomes remain divergent due to species-specific constraints and regulatory rewiring.
The paper introduces Hypercoding, a scalable, low-cost digital detection platform that utilizes error-correcting fluorescent codes to enable rapid, sensitive, and highly multiplexed quantification of diverse biomarkers, including pharmacogenomic variants and copy number variations, with high accuracy and a wide dynamic range.
By analyzing whole-genome sequencing data from African and South American samples, this study reveals the existence of two genetically distinct yet recombining cryptotypes of *Plasmodium malariae* across Africa, characterized by specific adaptive signatures that contribute to the parasite's persistence and transmission.
The paper introduces Point Cloud Local Ancestry Inference (PCLAI), a novel method that replaces discrete ancestry labels with continuous coordinate-based representations to model genetic variation at the haplotypic level, enabling time-stratified insights into how genomic segments have migrated across space and time.
This study establishes the first systematic, transcription-based atlas of the canine regulatory genome by mapping 68,446 promoters and 46,661 active enhancers across 56 tissues and developmental stages in 9 dogs, thereby providing a crucial resource for understanding gene regulation, comparative genomics, and disease mechanisms in dogs and humans.
This study presents a high-quality, chromosome-level genome assembly of the biocontrol strain *Fusarium oxysporum* FO12, generated using Nanopore and Hi-C sequencing, which serves as a valuable resource for advancing agricultural applications of this effective biological control agent.
This study reveals that the CGGBP1 protein preserves cytosine content in vertebrate promoters by restricting cytosine methylation, thereby shaping G-quadruplex formation potential and influencing C-T transition rates across amniote lineages.
By applying metatranscriptomic sequencing to 300 PCR-negative severe acute respiratory infection samples in New Zealand, this study uncovered a diverse array of co-infecting viral, bacterial, and fungal pathogens missed by routine diagnostics, demonstrating the critical value of genomic approaches for improving diagnostic accuracy and public health surveillance.
This study demonstrates that standalone Oxford Nanopore sequencing of native DNA is sufficiently accurate for routine foodborne pathogen surveillance when supported by a new quality control framework, alpaqa, which identifies and mitigates systematic assembly errors caused by specific DNA modifications.
This study presents the first comprehensive analysis of genetic diversity in *Apis mellifera* Cytochrome P450 genes across 1,467 individuals from 18 subspecies, revealing that positive selection has driven adaptive variation in detoxification-related CYP3 clan genes, thereby establishing a foundational pharmacogenomic resource to predict pesticide vulnerabilities and enhance pollinator resilience.
This study presents high-quality, annotated reference genomes for four cypriniform fish species from Southeast Asian acidic peat-swamp blackwaters, providing a comparative framework to investigate the genomic mechanisms underlying adaptation to extreme environments and the evolution of body miniaturization.
This study presents a single-cell atlas of pig-to-monkey kidney xenotransplantation that reveals macrophage chimerism and identifies an epithelial-derived IFN-ε axis as a critical orchestrator of a graft-protective immune niche, offering new insights into xenograft adaptation and potential therapeutic targets.
This study employs a novel computational genomics framework on spatial transcriptomics and liquid biopsy data to reveal distinct clonal dynamics, microenvironmental interactions, and histology-specific mechanisms driving the aggressive nature of rare bladder cancer variants compared to pure urothelial carcinoma.
This study establishes a theoretical and experimental framework for "Sparse-Seq," a low-coverage sequencing method that accurately and economically quantifies global 5mC and 5hmC levels with minimal error, offering a superior alternative to mass spectrometry for large-scale epigenetic cohort studies while preserving genomic context.
This study presents two high-quality, annotated *de novo* transcriptome assemblies from juvenile *Sepia officinalis* at different developmental stages and under various metal and pCO2 exposure conditions, providing valuable genomic resources to support environmental and neurobiological research on this model organism.
This paper identifies and quantifies barcode crosstalk as a critical source of error in multiplexed Oxford Nanopore sequencing, particularly for low-biomass samples, and introduces post-ligation pooling (PLP) as an effective library-preparation modification to prevent rather than merely mitigate these false-positive signals.