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This paper improves genotype imputation for ancient genomes using a region-specific reference panel and benchmark genotypes, showing enhanced accuracy and revealing genetic differentiation linked to cultural differences.

This paper reports the first genome sequence of Valeriana officinalis, identifies candidate genes for valerenic acid biosynthesis and flavonoid metabolism, and provides a foundation for studying specialized metabolism in valerian.

AlphaVaR structures AlphaGenome's per-track variant scores in R and adds multiple-testing-corrected enrichment and shift tests, a tissue-specificity index and transparent ranking; on rs1427407 it recovers BCL11A erythroid-enhancer biology.

The paper maps cellular and molecular changes in the mouse brain during pregnancy and postpartum using spatial single-cell technologies, identifying three gene expression programs and linking depression risk genes to specific brain regions.

CannSelect is a genotyping platform for Cannabis sativa that maps day-neutrality to the Autoflower1 locus with 88.5% capture efficiency.

This study shows that low-heteroplasmy mitochondrial DNA mutations provide reliable clonal information, improving clonal reconstruction in human cells.

This study identifies scenarios where population stratification inflates gene-gene interaction test statistics and proposes a method to control false positives by adding a SNP-population structure interaction term to regression models.

The paper identifies genomic variants associated with endosymbiont shuffling and areal growth in Acropora palmata using genome-wide association and gene expression data.

This study uses single-cell and spatial multi-omics to analyze a malignant peripheral nerve sheath tumor, revealing chromosomal instability drives phenotypic diversity and spatial-temporal evolution.

The paper develops a CRISPR library for TPD-compatible screens to better identify genetic interactions downstream of protein degradation by reducing UPS resistance dominance.

The paper uses PC1-guided transcriptomic stratification to reveal hepatic transcriptional heterogeneity and identifies a myeloid-associated 20-gene signature linked to coronary heart disease.

RegFM improves gene regulation modeling by integrating cis-regulatory elements and trans-acting regulators in human cells, outperforming existing methods in multiple tasks.

This study identifies transcriptional and isoform-level regulation changes in preeclamptic placentas, revealing sex-specific patterns and novel isoform switches linked to dyslipidemia.

The paper introduces a blocking primer to improve detection of tick-borne pathogens in Ixodes scapularis ticks using 16S rRNA metabarcoding, achieving sensitivity comparable to qPCR and detecting additional pathogens.

This study benchmarks artificial cfDNA generated by fragmentation methods against native cfDNA, finding enzymatic methods better replicate native characteristics.

The paper reports the first complete mitochondrial genomes of two West Nile virus vectors in Arizona using long-read sequencing and presents a novel method for obtaining full-length mitogenomes.

The paper examines copy-number variation in the human pepsinogen A gene across Eurasia, linking it to dietary adaptation and selective pressures.

The paper uses cfMeDIP-seq to analyze cell-free placental DNA methylation in maternal plasma, identifying enriched regions associated with preterm birth and IUGR.

The paper uses whole-genome resequencing to analyze gray whale populations, finding that the WNP stock has mixed ancestry from both eastern and western stocks, leading to increased genetic diversity.

The paper uses single-cell RNA sequencing to identify regulatory hubs and cytokine crosstalk in the tumor microenvironment, revealing key signaling pathways involved in tumor progression.