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This paper introduces sensGAN, a deep-learning framework to identify worst-case latent confounders in genomics, improving sensitivity analysis for disease-associated gene associations.

This study analyzes genomic inbreeding and selection signatures in Doberman Pinschers using multiple methods, identifying loci associated with neurodevelopmental pathways.

This study evaluates three cell preservation methods for scRNA-seq across multiple sites, showing concordant cell type results but platform-specific gene expression differences and better granulocyte retention with preservation methods.

This paper introduces SAGE-net, a framework for training sequence-to-function models using personal genomes, showing improved gene expression prediction but limited generalization, while DNA methylation shows better generalization.

This study uses single-cell profiling to analyze immune dysregulation in Long COVID patients, identifying distinct immune signatures associated with symptom severity.

This paper introduces WaveSeekerNet, a calibrated AI model that predicts IAV host origin and identifies key adaptive mutations, revealing host-adaptive distance and the Mammalian Adaptation Zone.

This paper introduces MethylSeqNet, a model that improves sequence-based gene regulation predictions by conditioning on CpG methylation, showing benefits for cell-type-specific regulation and allele-specific phenomena.

The paper uses the ANOSPP amplicon panel to analyze Anopheles mosquitoes and Plasmodium species in Tanzania, revealing 15 Anopheles taxa and five Plasmodium species, including new records of P. caprae and An. funestus-like mosquitoes.

This paper demonstrates that synthetic scRNA-seq data generated by leading methods can be attacked to infer donor membership, showing privacy risks and evaluating noise-based defenses.

ArchVelo models gene regulation and infers cell trajectories using scATAC-seq and scRNA-seq data, improving accuracy and identifying new differentiation trajectories in immune cells.

This paper develops in vivo compressed AAV-Perturb-seq to study gene knockouts in cardiomyocytes, finding mitochondrial transcriptome changes are a common response to genetic perturbation.

The paper identifies associations between macrophage enhancers and cardiovascular disease variants using epigenomic data from immune cells.

The paper assembles the genome of Pavon 76, a Green Revolution wheat cultivar, providing a chromosome-scale reference for CIMMYT-derived wheat and highlighting structural divergence from the standard reference genome.

The paper identifies centromeres as a source of telomeric sequences in Arabidopsis, showing ITR domains arise from centromeres through amplification and adopt a distinct chromatin state.

The paper introduces SeqTag, a single-cell multiomics method, to analyze molecular asynchrony in regulatory layers and model cellular kinetics during aging.

PICTographPlus infers clone-resolved transcriptional programs from bulk RNA-seq by integrating clonal phylogenies and proportions, achieving high accuracy in recovering clone-level expression and localizing pathway changes.

The paper introduces LASSI, a method to measure nucleosome spacing in chromatin interactions, revealing fiber homotypy as a structural pattern influenced by genomic features and cohesin dynamics.

The paper analyzes single-cell multiome data from human HSPCs to show aging-related rewiring of gene regulatory networks, leading to stress hyperactivation, myeloid bias, and identity loss.

The paper reconstructs ancestral linkage groups in 340 dipteran genomes to study chromosome evolution, finding conserved groups in Nematoceran lineages and chromosomal fissions in Brachycera.