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The paper investigates alternative splicing and gene expression differences in three sex conditions of the eastern three-lined skink, identifying sex reversal-specific intron retention in Ttll7.

The paper introduces CoPhasing, a method to phase chromatin contacts with haplotype specificity, revealing structural differences between homologous chromosomes.

This paper introduces an annotation-based gene-peak linkage method that improves gene expression prediction from chromatin accessibility in human kidney multi-omics data.

This study examines the epigenetic effects of prolonged fasting in humans, finding changes in DNA methylation and epigenetic aging clocks linked to metabolic responses.

This study introduces targPred, a method using genomic regulatory blocks to connect non-coding SNPs with target genes, and demonstrates its application to childhood obesity and psychiatric diseases.

The paper uses single-nucleus multiomics to study pituitary cell changes during the mouse estrous cycle, finding stage-dependent gene regulatory circuits and validated ETS2-driven gene expression patterns.

The paper assesses the cellular dependencies of AFib-associated genes across tissue types to identify potential therapeutic targets with minimal off-target effects.

The paper decontaminates 30 sponge genome assemblies using a pipeline that combines k-mer analysis, DIAMOND, and Kraken2, achieving high accuracy and precision in identifying and removing contaminants.

The paper uses long-read sequencing to characterize lentiviral provirus insertions in clonal CAR-T cell lines, revealing structural variations missed by short-read and ddPCR methods.

The paper identifies high mutation rates in histone genes due to AID/APOBEC enzymes and introduces HistMTR to predict pathogenicity, showing histone mutations contribute to diseases.

This paper shows that trustworthy agentic genome interpretation requires executing validated skills as code rather than relying on models to reason or retrieve information, ensuring deterministic and auditable results.

This paper introduces GAFM and HBP methods to improve GWAS fine-mapping by leveraging biological structure, achieving higher accuracy and speed across multiple species and datasets.

GENE-FAM is an automated pipeline for gene family mining applied to MADS-box genes in Cannabis sativa, identifying conserved and divergent subfamilies across species.

The paper develops lrSAGA, a tool to improve genome assembly from long-read MDA sequencing of single cells, achieving higher completeness and fewer misassemblies.

The paper presents a chromosome-level genome assembly for Rana dybowskii using PacBio HiFi and CiFi, achieving high completeness and gene prediction.

The paper introduces Terminal Mapping, a high-throughput method to detect viral integration sites without restriction enzymes or ligation, showing improved recovery of HIV-1 insertion sites compared to inverse PCR.

This paper presents the first functionally annotated genome of the coffee bean weevil, identifying a unique insect-encoded P450 detoxification pathway for caffeine, distinct from bacterial mechanisms.

The paper identifies dynamic regulatory network hubs in human lineage specification using Perturb-Seq and constructs a deep learning model to predict perturbed TFs in patient transcriptomes.

The paper analyzes mutation counts and profiles in single human colon crypts to assess somatic mutation rates and their implications for aging and disease.

This study uses wavelet analysis to show that recombination rates vary significantly between human populations, especially at fine scales, suggesting population-specific maps are needed for accurate genetic analyses.