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The paper uses MPRA to assess context-dependent activity of transcription start sites, finding that promoter, position, and strand effects influence regulatory element function.

The paper introduces BRC-Analytics, a browser-based platform for pathogen genomics, demonstrating its use in analyzing measles virus evolutionary dynamics and revealing asymmetric frame evolution under selective pressures.

The paper analyzes the overlap between transcription factor binding and regulatory targets in yeast, finding that low overlap is due to weakly bound sites.

This paper introduces EPIK, a deep learning framework for detecting higher-order epistasis in GWAS data, showing improved performance on simulated and real datasets and identifying new gene interactions in Parkinson's Disease.

The paper annotates CREs in the barley genome using epigenetic profiling and HiChIP, identifying 77,000 CRE candidates and revealing promoter-promoter interactions.

This paper develops SMART-PTA for single-cell whole-genome and transcriptome sequencing, revealing clonal evolution in aged human esophageal tissue over 70 years.

The paper presents chromosome-scale genome assemblies for two notothenioid fish species, providing insights into their evolutionary history and adaptation to climate change.

The paper introduces a platform that directly sequences 3'UTRs and guide RNAs in fixed cells alongside protein abundance and morphology, enabling CRISPR screening in lung cancer cells.

The paper presents the first complete and annotated genome of Nereocystis luetkeana, a northeastern Pacific bull kelp, providing insights into its genomic diversity and evolutionary features.

BioFrame provides a web-based tool for reproducible and accessible genomics workflows using containerized microservices.

The paper introduces Agro-STARR-seq, an in planta enhancer screening method, and uses AI to design synthetic enhancers, identifying 14,715 active sequences in Arabidopsis.

The paper introduces scJLIM, a cluster-free method for single-cell colocalization testing, improving power to link GWAS loci with gene expression changes in specific cell types.

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

The paper presents the first complete chloroplast genome of Paeonia suffruticosa 'Cun Song Ying', compares it with related species, and identifies potential DNA barcode regions.

The paper identifies a spatial coordination between mRNA initiation and termination sites, proposing a 'Positional Initiation-Termination Axis' that influences isoform diversity.

The paper introduces Telomere-C, a method to map telomeric 3D interactions, revealing ultra-long-range contacts and repetitive element hubs linked to telomere maintenance.

The paper presents the first chromosome-level genome assembly of the golden jackal using PacBio HiFi sequencing, providing a resource for studying its genetics and ecological impact.

The paper investigates mitonuclear discordance in Tropidurus lizards, finding that ancient mitochondrial introgression and demographic processes explain the observed genetic mismatches.

This study investigates how 3D genome organization changes during breast cancer progression using Hi-C and epigenomic data, revealing structural alterations linked to oncogenic gene activation.

This study shows that transient nuclear softening with TSA treatment enhances cell migration and matrix formation in porcine meniscal cells, with full restoration of transcriptional phenotype and function within 7 days.