4 papers · ranked by Valyu relevance
Huihai Wu, Ashleigh Lister, Iain Macaulay, Katie Long + 10 more
Single-cell and spatial transcriptomics are transforming our understanding of cellular heterogeneity and tissue organization, yet their analytical complexity remains a major bottleneck. Here, we present EISCA and EISTA, two standardized, end-to-end pipelines for single-cell RNA- seq and imaging-based spatial…
Xuebin Feng, Emma R. Master
Sequence similarity networks (SSNs) are graphical representations of sequence relationship frequently used for exploring protein sequence space. Conventional SSN workflows typically use BLAST to calculate sequence similarities and rely on external visualization tools to generate the final networks. Consequently, raw…
Braden Charles DeMattei, Stephanie E. Hampton
Understanding species interactions is integral to understanding ecosystem function and predicting how disturbances may affect the services provided to society. Analysis of trophic interactions, however, requires a significant investment of time and resources. Using a simple predator-prey pairing of a semi-sessile…
Olivier Hinse, S. Yasin Tabatabaei Dakhili, Lee Freiburger, Eliot Mar + 5 more
Rheumatoid arthritis (RA) is characterized by a loss of immunological tolerance to synovial self-proteins, yet the initial triggers generating novel neo-antigens remain incompletely defined. Here, we demonstrate that human cathepsin K (hCatK), a key cysteine protease driving joint degradation in RA, catalyzes covalent…