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The paper investigates how variation in X chromosome inactivation escape across genes and tissues influences sex-biased gene expression in humans.

The paper uses genetic and proteomics analysis on archaeological remains to trace genetic connectivity and inbreeding in Irish goats over 3,000 years.

ADAPRE infers causal gene regulatory networks from Perturb-seq data by using adaptive instrumental variable modeling, improving accuracy over existing methods.

The paper annotates 200 insect genomes using BRAKER3 and VARUS to enable consistent comparative genomics analyses across species.

This paper creates a gut transcriptomics atlas using MERFISH to show how microbiota influences cell types, spatial organization, and molecular responses in the murine gut.

The paper presents a transcriptome time-course of Plasmodium knowlesi A1-H.1 during its intraerythrocytic developmental cycle, identifies stage-specific biomarkers, and develops a webtool for comparative analysis with Plasmodium vivax.

The paper evaluates the Horizon model, a CNV classification tool aligned with ACMG guidelines, showing high accuracy in pathogenicity prediction across multiple datasets.

The paper uses whole-genome data from South American pumas to show how historical climate changes shaped genetic diversity and conservation risks, suggesting strategies to restore connectivity and reduce inbreeding.

The paper introduces PanExonNet, a deep learning framework that predicts splicing patterns by integrating sequence and splicing factor expression, showing improved context specificity and generalization to new cell types.

This study analyzes drought response in a tomato MAGIC population, identifying genomic regions and transgressive lines that enhance drought resilience.

The paper analyzes the genomes of Golden Horde elites to confirm Genghis Khan's Y-chromosome haplogroup and trace their genetic ancestry.

This study investigates fruit shape regulation in peach and apple by analyzing OFP expression patterns and hormone interactions, revealing conserved regulatory circuits.

This study traces the evolutionary history and dispersal of the rice bacterial blight pathogen Xoo, linking its emergence to rice domestication and trade routes.

This study identifies genetic mechanisms of pyrethroid resistance in La Reunion Island tiger mosquitoes, showing it results from local adaptation through detoxification gene over-expression and a large inverted superlocus.

CLM-X is a multimodal single-cell foundation model that outperforms existing methods in cross-modal translation and perturbation prediction across scRNA-seq and scATAC-seq datasets.

The paper introduces HERVarium, a database annotating human endogenous retroviral LTRs and their regulatory features, revealing structural and functional patterns across the genome.

The paper identifies miR-199-5p as a regulator of ifi27l2a expression, linking it to VNN resistance in European seabass through differential expression and functional analysis.

The paper introduces Mahi, a graph neural network framework that integrates molecular context and functional connectivity to predict gene essentiality and perturbation responses across tissues.

The paper analyzes two-hit inactivation frequencies in tumor suppressor genes across 9,000 tumors, identifying factors like mutation impact, zygosity, and chromosomal context that influence these frequencies.

The paper compares the transcriptome of Plasmodium vivax parasites from patients with severe malaria manifestations, identifying differentially expressed pir genes associated with hepatic dysfunction and cerebral malaria.