400 papers
This study identifies a second thyroglobulin-like gene, HaVipR2, as a novel mediator of Vip3Aa resistance in *Helicoverpa armigera*, demonstrating that a ~16 kb transposable element insertion disrupts this gene to confer high-level resistance and highlighting the critical role of long-read sequencing in detecting such adaptive mutations.
This study demonstrates that experimentally admixing inbred mainland sand lizards with individuals from southern Sweden over 20 years successfully increased genetic diversity, reduced genetic load, and improved fitness, providing empirical evidence for the long-term genomic benefits of genetic rescue.
This study analyzes whole-genome data from wild and captive cheetahs to reveal that deleterious mutations are significantly enriched in sperm-related genes, likely contributing to poor sperm quality, while confirming that captive breeding programs have successfully maintained genetic diversity comparable to wild populations.
By analyzing single-molecule duplex sequencing data from normal kidney and blood samples across 10 countries, researchers discovered that kidney proximal tubule cells accumulate high levels of somatic mutations from both known exogenous carcinogens, such as aristolochic acids, and unidentified systemic mutagens, revealing these cells as highly sensitive sentinels for detecting widespread environmental exposures.
This study reveals that while most *Cadophora luteo-olivacea* strains share a conserved genomic framework and plant-colonizing capacity, they exhibit significant strain-level variation in pathogenicity and host-specific responses, alongside the identification of a highly divergent lineage (CBS 266.93) that warrants taxonomic reassessment.
This study identifies an ancestral introgression of a galectin-like protein from *Cryptosporidium hominis* into the human-restricted *C. parvum anthroponosum* as a likely driver of its adaptation to human hosts through a predicted interaction with the human insulin-degrading enzyme.
This study demonstrates that while graph-based pangenomes and linear references yield similar Mendelian inheritance error rates, pangenome approaches significantly improve the reconstruction of parental haplotype blocks in citrus breeding, offering a superior framework for benchmarking SNP-calling accuracy in non-model systems by mitigating reference bias in diverged genomic regions.
This study reveals that the adult brain plasticity enabling Harpegnathos saltator workers to transition into reproductive gamergates relies on the pre-existing, unusually high 3D chromatin connectivity between socially regulated gene promoters and their enhancers, which facilitates rapid transcriptional reprogramming.
This paper introduces two novel conditional genome-wide association approaches that successfully identified and experimentally validated three previously unknown genes controlling flowering time in *Arabidopsis*, demonstrating the power of knockoff-based frameworks for discovering genes underlying complex traits in agriculture and human health.
This study systematically evaluates genomic features to determine their ability to distinguish functional genes from non-genic regions, concluding that evolutionary conservation and transcriptional activity are the most robust and consistent indicators of both protein-coding and non-coding gene function.
This paper introduces multimodal droplet barcoding, a high-throughput strategy that enables the one-to-one linking of single-cell imaging and gene expression profiling by tracking individual microfluidic droplets across optical and sequencing measurements.
This study reveals that the self-fertilizing nematode *Caenorhabditis tropicalis* exhibits strong geographic genetic structuring and a Pacific origin, utilizing rare, hyper-divergent genomic regions enriched for adaptive genes to maintain global distribution despite low overall genetic diversity.
This study characterizes the extensive natural variation in *Botrytis cinerea*'s resistance to the host defense metabolite linalool and identifies 101 candidate genes, particularly those involved in membrane transport and stress response, that underlie this genetic architecture.
This study reveals that probe set barcoding in the 10x Genomics Flex v1 single-cell RNA sequencing assay introduces substantial, reproducible technical variation that can generate false positive differential expression results when confounded with biological samples, a limitation effectively mitigated by the improved Flex v2 design.
This study introduces STEAM, an evolutionary transfer learning framework that leverages single-cell chromatin accessibility data from mouse development and synteny-supervised training across 241 mammalian genomes to overcome data limitations and enable accurate, genome-wide inference of enhancer landscapes across diverse cell types and species.
By analyzing over 3,500 ancient genomes alongside modern data, this study demonstrates that major historical epidemics in Western Eurasia drove significant, non-random shifts in polygenic traits related to infectious disease susceptibility, particularly involving metabolic pathways that modulate immune responses.
This study introduces Nascent CUT&Tag to reveal that transcription factors like GAGA factor and Pleiohomeotic exhibit distinct, motif-dependent recovery kinetics on newly synthesized DNA following replication, with early GAF binding requiring BAF-mediated chromatin remodeling to support cell cycle progression.
This study utilizes a high-quality chromosome-scale genome assembly and deep sequencing of 12 Chilean Carmenere clones to identify over 9,000 private variants per clone, revealing previously uncharacterized clonal diversity with potential implications for clonal selection and the conservation of genetic resources.
This study analyzes deep whole-genome sequencing data from 440 endometrial tumors to reveal how endogenous mutational mechanisms, retrotransposition activity, and host metabolic factors like BMI distinctively shape the genomic architecture and evolutionary trajectories of molecular subtypes, offering a mutagenesis-centric framework for improved risk stratification and therapeutic strategies.
This paper introduces the personalized variant effect predictor (pVEP) framework, which demonstrates that an individual's genetic background significantly alters AI-predicted clinical variant effects, revealing that many variants are pathogenic in some genetic contexts but benign in others.