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The paper develops a single-cell multiomics method to analyze replication timing and gene expression simultaneously, showing high correlation with bulk data using few cells.

The paper introduces a framework to jointly decompose Hi-C maps across tissues and development, revealing distinct nuclear architecture patterns and improving gene expression prediction.

The paper introduces LOCATER, a method to test genealogical trees for association with traits, showing improved power over traditional methods in detecting allelic heterogeneity.

This study benchmarks genomic footprinting algorithms for predicting transcription factor binding sites in single-cell data, finding peak-level read coverage as the strongest predictor and proposing an ensemble model to improve concordance with ChIP-seq.

The paper demonstrates how a global pangenomic breeding network can develop and deploy drought and pest-resistant sorghum varieties for smallholder farmers in Niger.

The paper identifies hidden enhancers in mouse embryos that are not detected by conventional chromatin profiling methods, highlighting a significant gap in enhancer discovery.

The paper describes a gene model for the Akt ortholog in Drosophila elegans using a specific genome assembly and annotation protocol.

Varigraph improves variant genotyping accuracy in pangenome graphs for diploid and polyploid genomes, outperforming existing methods in non-human genomes.

This study identifies the genomic footprints of almond domestication, revealing multi-regional origins, gene flow from wild relatives, and population-specific selection on stress and agronomic traits.

This paper introduces an algorithm to reconstruct longitudinal tumor phylogenies from single-cell sequencing data and demonstrates its ability to detect rare clones persisting through treatment.

The paper introduces WMS, a targeted sequencing method for all human miRNA genes, identifying mutations and copy number alterations in cancer samples.

The paper provides a gene model for the ortholog of cnk in Drosophila erecta as part of a dataset studying IIS pathway evolution.

The paper detects mtDNA mutations in oocytes, blood, and saliva across ages and finds mutations increase in blood and saliva but not in oocytes, with age-related differences in mutation frequency distribution.

This paper introduces a pangenome-guided sequence assembly framework that reduces contigs in complex regions using graph traversal optimisation, with potential for quantum computing implementation.

The paper identifies mutations in Fusarium graminearum laboratory strains that reduce virulence on wheat, highlighting the need to monitor lab strains for unintended genetic changes.

The paper identifies cell type-specific regulatory elements in nine mammals and shows their conservation and association with neuropsychiatric and neurodegenerative disease risks.

This study identifies RNA biomarkers in salivary extracellular vesicles for diagnosing Sjogrens subtypes with high sensitivity and specificity.

The paper uses protein language models to uncover evolutionary constraints on synonymous codon choice in yeast by combining sequence analysis with experimental validation.

The paper uses long-read sequencing to generate complete genomes of Mycobacterium tuberculosis complex isolates, revealing increased genomic diversity and improved resolution in transmission analysis.

The paper describes the gene model for the Ilp5 ortholog in Drosophila erecta as part of a dataset for studying insulin pathway evolution.