6 papers · ranked by Valyu relevance
Lena Trnovec, Miha Štajdohar, Gad Shaulsky, Blaž Zupan
dictyExpress 3.0 is a React/TypeScript reimplementation of the Dictyostelium discoideum transcriptomics web server, first introduced in 2009, that unifies bulk and single-cell exploration. A long-standing gene-expression resource for the Dictyostelium community, dictyExpress is also accessible through dictyBase, the…
Florian Köhler, Anna Delgado-Tejedor, Maik Zehnsdorf, Marisol Salgado Albarran + 5 more
Short-read sequencing-based single-cell transcriptomics represents the current gold standard for studying cellular transcriptomes but remains limited in its ability to resolve full-length transcript isoforms and splicing patterns. Long-read single-cell and single-nucleus RNA sequencing (LR sc/snRNA-seq) enables the…
Pedro C Carvalho, Tori Millsteed, Robert J Henry
Spatial transcriptomics (ST) has emerged as a transformative approach for visualizing tissue landscapes, yet it faces significant challenges regarding data standardization, sparsity, and the analysis of complex genomes, particularly polyploid plants. To address these limitations, we introduce Poly Pipeline, a robust…
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…
Francisco Tomás Ribeiro, Ali Hallaj, Roger Mora, Anita Lüthi + 2 more
Membrane potential fluctuations, driven by ion channel activity, are important regulators of processes such as action potential propagation in neurons and muscle cell contraction. These variations also occur in non-excitable cells, influencing various cellular processes, including, but not limited to, direct…
Jahnavi Bhaskaran, Elizabeth Ing-Simmons, Irina Balaguer Balsells, Sara Di Persio + 11 more
Gametogenesis, the production of oocytes and sperm, ensures the faithful transmission of genetic material to the next generation. In males, spermatogenesis occurs within the testis, where germ cells progress through a highly ordered developmental programme in close association with supporting somatic cells. Defects in…