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SpliceDecoder prioritizes biologically meaningful splicing events by predicting their impact on transcript productivity, protein sequence, and functional domains.

NetworkSSC improves single-cell clustering by integrating gene network information, outperforming traditional methods on multiple scRNA-seq datasets.

The paper compares transcriptomes of cleptobiotic and non-robber stingless bees to identify molecular adaptations linked to their specialized raiding behavior.

The paper introduces Histo-LCM-Hi-C to study 3D chromatin structure of rare tissue cells, showing distinct chromatin organization in liver Kupffer cells compared to whole liver and in vitro macrophages.

The paper presents the genome sequence of the hemlock woolly adelgid, including chromosome assembly, gene annotation, and mitogenome data.

The study identifies miRNA polymorphisms in goats, finding low variation in seed regions due to purifying selection and higher variation in regulatory regions of isolated populations.

This paper presents a telomere-to-telomere genome assembly of bighorn sheep, revealing immune gene differences that may explain their susceptibility to respiratory pathogens.

This study investigates the role of lncRNAs and thyroid dysfunction in aging HFpEF, identifying novel lncRNA and inflammatory markers in early and late stages.

The paper identifies cis-regulatory elements controlling cellular senescence by performing CRISPR screens in human mesenchymal stromal cells, revealing a primate-specific SINE element that modulates P16INK4a and P15INK4b.

NOMAD provides a rapid, on-site workflow for high-resolution microbiome analysis of raw bovine milk using full-length 16S rRNA sequencing, achieving >90% community richness in 4 hours.

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.

This study demonstrates that a small epigenome-wide association study (EWAS) with high methylmercury exposure variance can identify differentially methylated CpG sites and pathways related to MeHg toxicity.

This study presents a single-cell multi-omic atlas of Alzheimer's disease brain regions, revealing region-specific epigenomic changes and altered cell states.

The paper quantifies NMD efficiency across human tissues and individuals, identifies tissue-specific and inter-individual variability, and links NMD efficiency to genetic factors and clinical outcomes.

This study evaluates genome prediction accuracy in Brassica napus using nested association mapping, finding that rrBLUP and RKHS models and SNaP markers improve prediction accuracy for agronomic traits.

This study uses unsupervised machine learning to identify temporal gene expression components in HeLa cells after cell cycle release, revealing oscillatory and transient patterns linked to cell cycle phases and cancer-related processes.

Tangram2 maps cell-to-cell communication by integrating spatial transcriptomics with single-cell RNA sequencing to identify gene expression changes driven by neighboring cell types.

The paper shows PRC2 controls small RNA dynamics during DNA elimination in Paramecium by selectively degrading non-TE scnRNAs, independent of its histone methyltransferase activity.

The paper generates a high-quality genome assembly and centromere map for T. cruzi using Hi-C and ChIP-seq, revealing structural boundaries and 3D clustering of centromeres.