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LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery
Most human genes produce multiple RNA isoforms, yet it remains unclear which isoforms are translated into stable, functional proteins. Long-read RNA-sequencing resolves full-length transcript structures and, when paired with mass spectrometry, can provide empirical evidence of isoform translation. Despite this opportunity, comprehensive workflows integrating isoform discovery, open reading frame prediction, peptide identification, and protein inference remain limited, leaving users to handle...
Genetic Diversity and Population Structure of the Black-Footed Cat: Insights into Felis's Deadliest Predator
Background Black-footed cats (Felis nigripes) are one of Africa's least studied felines. The population dynamics and demographic history of this solitary species have not been well-described. Reports of ongoing decline of present-day populations resulted in the IUCN Red List categorizing the species as vulnerable to extinction.
Ultra-low biomass sequencing workflow (LBV-Seq) enables de novo metagenomic reconstruction of DNA and RNA viral genomes
Genome-resolved virome analysis remains inaccessible for many samples, including those with clinical relevance, because viral nucleic acid recovered after enrichment is often too scarce to support de novo genome assembly. As a result, many analyses are limited to sparse read-level detection, which cannot recover divergent viruses, resolve strains, or interpret gene-level variation. Here, we developed Low Biomass Viral Sequencing (LBV-Seq), a workflow that couples low-input viral sample...