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The paper models horizontal gene transfer as a stochastic process over a bacterial genus network and uses match length distributions to infer transfer patterns and network topology.

The paper analyzes whole genome sequences of Black Soldier Fly populations to reveal cryptic genetic diversity and the impacts of domestication on genetic variation.

This study uses single-cell RNA sequencing to show that T. cruzi trypomastigote cells express trans-sialidase-like superfamily genes with high heterogeneity and no recurrent combinations.

The paper uses MPRAs to assess context-dependent regulatory activity in type 2 diabetes-linked noncoding regions across different promoters and cell types.

The paper assembles complete mitochondrial genomes for three searobin species and performs a phylogenetic analysis to clarify their relationships within the Prionotinae subfamily.

The paper presents the genome of Echinomermella matsi, a sea urchin parasite, and places it within the nematode order Plectida, highlighting its evolutionary significance for studying aquatic parasitism.

The paper integrates single-cell and spatial multiomic data to show widespread reactivation of developmental programs in diseased human hearts, with insights into transcriptional factors and localized fetal reactivation.

This study develops a model to predict optimal growth temperature in prokaryotes using genomic data, finding that incorporating gene presence/absence improves accuracy for psychrophiles.

CREsted is a software package for modeling and designing cell type-specific enhancers using deep learning, validated across tissues and species.

The paper uses long-read RNA-seq to create a comprehensive placental transcriptome reference, revealing high transcriptional complexity and identifying novel isoforms associated with metabolic and endocrine functions in gestational diabetes.

This study shows that DNMT1 loss causes hypomethylation in late replicating domains but also leads to hypermethylation in some domains due to DNMT3A activity, altering chromatin states.

The paper catalogs structural and sequence variation in the pennycress pangenome, revealing contrasting evolutionary modes across genomic regions and highlighting the utility of pangenomic resources for crop development.

This study investigates whether preconception exposure to metabolic disruptors in mice leads to metabolic and psychiatric alterations in offspring.

The paper identifies exonic enhancers as dual-function regulatory elements that influence gene expression and are associated with disease and evolution.

This study benchmarks imputation accuracy for low-coverage whole-genome sequencing data with and without a reference panel, showing that large datasets can achieve sufficient accuracy without one.

The paper sequenced Mediterranean fin whale genomes to assess genetic structure and conservation status, finding moderate diversity but low connectivity with North Atlantic populations.

MIC-Drop-seq combines CRISPR and scRNA-seq to phenotype mutant zebrafish embryos, revealing known and novel gene functions in development.

The paper develops a blood-based diagnostic biomarker for Alzheimer's disease using microglial single-cell transcriptomics and validates it in plasma omics data.

The paper maps how mutations alter the input-output function of an allosteric hormone receptor using a high-throughput approach, revealing genetic mechanisms that tune signaling parameters.

The paper develops haplotype-resolved genome assemblies for Norwegian Red cattle to improve variant detection and genomic predictions.