210 papers
The paper introduces FEMA-Long, a computationally scalable framework that extends linear mixed-effects modeling to flexibly capture unstructured, time-dependent covariances and non-linear covariate effects in high-dimensional longitudinal data, enabling the discovery of dynamic genetic patterns as demonstrated in a large-scale genome-wide association study of infant growth.
By integrating high-throughput RB-TnSeq fitness screens in tomato plants with comparative evolutionary genomics, this study reveals that *Ralstonia solanacearum* pathogens rely on both conserved physiological adaptations and strain-specific antimicrobial warfare mechanisms, including Type VI secretion systems, to thrive within the plant vascular niche.
Population-genomic analysis of 507 global isolates reveals that the wheat stripe rust pathogen's global success is driven by two ancient nuclear lineages that diverged before modern agriculture, forming distinct homozygous and globally dominant heterokaryotic hybrid populations that utilize both clonal expansion with somatic nuclear exchange and sexual recombination to achieve convergent evolutionary adaptation.
This paper introduces the CattleGTEx Phase 1 resource, a comprehensive multi-tissue atlas of regulatory effects across 43 tissues and 82 breeds that resolves the majority of GWAS signals for complex traits, elucidates evolutionary and selection mechanisms in cattle, and offers translational insights for human disease genetics.
This study identifies the dual-function variant rs7214410 on chromosome 17 as a key regulator that modulates both circular RNA expression and gene splicing, thereby refining the genetic susceptibility locus for multiple sclerosis.
Ancient whole-genome sequencing of the purported remains of medieval emperors Otto I and Heinrich II confirms their historically attested great-uncle/grandnephew relationship, thereby authenticating the remains and establishing them as valuable ground-truth resources for refining bio-archaeological dating methods and tracing elite European lineages.
This study demonstrates that parallel adaptive walks in crop breeding metapopulations generate cryptic genetic heterogeneity and epistatic interactions, which are revealed upon crossing elite lines and necessitate accounting for epistasis in germplasm exchange strategies.
This meta-analysis of chromatin accessibility QTLs (caQTLs) across diverse tissues demonstrates that they are more effective than expression QTLs (eQTLs) at identifying regulatory variants at functionally important genes, thereby offering a more sensitive mechanism for interpreting the heritability of complex traits discovered through genome-wide association studies.
This paper introduces Genomic Informational Field Theory (GIFT), a novel method that enables the identification of genetic associations for complex traits with high precision using small sample sizes, as demonstrated by its successful application to uncover insulin-related genetic loci influencing pony height.
This study utilizes single-cell RNA sequencing of over 80,000 CD4+ T cells from Systemic Sclerosis patients and healthy controls to reveal distinct disease-associated transcriptomic signatures, including interferon-driven activation, specific T cell subset expansions, and TCR clonal changes, while providing a publicly accessible interactive platform for the research community.
This study identifies 36 novel and known PRNP genetic variants in 358 wild Montana mule deer, utilizing computational modeling and RT-QuIC assays to elucidate how specific mutations like V12F and S225F influence protein structure and potentially affect susceptibility to Chronic Wasting Disease.
This study investigates the body size, dental pathology, and maternal genetic diversity of ancient horses in the eastern Baltic and western Russia, revealing that wild populations were pony-sized, the earliest domestic horses in Lithuania date to 799–570 cal BCE with confirmed bit wear, and high mitochondrial DNA diversity indicates multiple maternal lineages.
This study reveals that incomplete dominance of the Agouti (ASIP) Ay allele over the a allele in Hungarian Puli dogs, which results in the unique "fakó" coat color, is associated with specific mutations in the interacting MC1R gene.
This paper presents a holistic meta-analysis of *C. elegans* germ granule proteomics data, revealing low reproducibility in individual interaction screens due to the dynamic nature of these condensates and introducing a novel algorithmic approach to robustly identify granule-associated proteins and map their complex organizational dynamics.
The authors present S-SELeCT, a novel system of human-evolved serine integrase fusions that enables efficient, site-specific integration of large (10 kb) genetic cargo into a true endogenous human safe-harbor locus, offering a promising solution for treating genetic diseases caused by mutations in large genes.
This study demonstrates that incorporating EBV uncertainty via MCMC-based optimum contribution selection significantly improves the robustness of breeding decisions in Norway spruce and Loblolly pine by identifying unstable selections that, when constrained, enhance genetic gain stability with minimal loss in overall gain.
This study demonstrates that within the multinucleate networks of the fungal pathogen *Botrytis cinerea*, "cheater" nuclei exploiting public goods can gain a competitive advantage through frequency-dependent selection, a social dynamic that decouples virulence from reproduction and buffers the evolution of antifungal resistance.
By analyzing 81,440 *Escherichia coli* genomes using Direct Coupling Analysis, this study reveals that selection efficiency varies dramatically across lineages—dropping 10,000-fold in pathogenic populations compared to the species as a whole—and demonstrates how population genetics data can validate protein-level mutation scores while highlighting the vast difference in selection intensity between synonymous and non-synonymous mutations.
This paper introduces Blockbuster, a deterministic program that achieves the theoretical limits for inferring recent demographic history from genome-wide Site Frequency Spectra by accurately estimating the timing and intensity of population size changes while offering a method to mitigate the confounding effects of population structure.
This study utilizes CRISPR/Cas9-generated mouse and human embryonic stem cell models to demonstrate that heterozygous PCDH19 mutations cause PCDH19-Cluster Epilepsy through specific gene expression defects in developmental and neuronal pathways, while revealing that neurite morphology correlates directly with the levels of wild-type PCDH19 protein.