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ProtoCloud improves cell type annotation by providing interpretable, uncertainty-aware predictions and better performance on rare cell types across multiple datasets.

The paper identifies locally persistent lineages of STEC O157:H7 that contribute to disease burden and persist for up to 8.6 years in Minnesota.

This study identifies dispersal-specific transcriptional biomarkers in Pseudomonas aeruginosa biofilms by analyzing gene expression across attachment, maturation, and dispersal stages.

The paper identifies genetic variants influencing DNA methylation across tissues and development in mice and humans, revealing two distinct epigenetic programming periods and linking methylation to regulatory elements and disease variants.

CanVAS harmonizes and imputes canine genotype data from multiple sources to create a unified resource for genetic studies.

The paper integrates genome data from Ralstonia solanacearum to identify integration spots linked to adaptive functions and genome plasticity.

This study shows that deleting CK2α in hematopoietic stem cells (HSCs) alters their transcriptome toward an immune-primed state, with tissue-specific effects on inflammatory and immune-related genes.

The paper analyzes single-cell transcriptomes of human islet cells across glycemic states to identify gene expression defects in beta cells associated with type 2 diabetes.

This paper presents a targeted amplicon sequencing panel for cost-effective high-throughput genotyping of Aedes aegypti, showing it can replicate WGS population structure analyses and accurately measure genetic admixture.

The paper demonstrates that the human genome encodes a deterministic computational kernel with four properties, validated through analysis of proteome and chromosome data.

MitoScope is a long-read sequencing workflow for mitochondrial genome analysis that improves sensitivity and precision in variant detection and NUMT profiling.

This study generates the first spatial transcriptomic atlas of the adult Ciona neural complex, revealing molecular zonation and functional roles of key regions like the neural gland.

HM-DyadCap captures and maps hmC/mC CpG dyads in mammalian DNA, revealing their enrichment in gene bodies and depletion at transcription start sites.

The paper identifies the Zld interactome in Drosophila embryos, revealing co-factors essential for ZGA, including dCBP, Fsh, and Smr, and shows RNAPII associates with Zld-bound enhancers.

The paper presents a high-quality reference genome for the critically endangered Philippine Eagle, revealing its evolutionary relationships and population history.

ExTRaCT is a gene search pipeline that identifies APOBEC3 Z-domains in novel bat genomes with high accuracy and efficiency.

This study characterizes somatic mutations in urine-derived iPSCs, showing they reflect age-related genomic changes and can trace developmental lineages non-invasively.

This study uses a chemical method to create controlled chromosomal interactions in yeast to assess Hi-C's quantitative properties, finding it sensitive, unbiased, and linear.

The paper introduces TimeFlies, an snRNA-seq aging clock for Drosophila heads, identifies key lncRNAs as biomarkers, and shows sex-specific aging pathways.

The paper introduces a weighted averaging approach for differential expression analysis in single cell and spatial RNASeq to reduce false positives and negatives without assuming data distributions.