10 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…
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…
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…
Yuesong Wu, Haohao Su, Yuehua Cui
Cell-cell communication (CCC) is essential for maintaining tissue organization and driving biological progression, yet its inference from transcriptomic data has long been limited by the absence of spatial context. Advances in spatial transcriptomics (ST) now enable mechanistically grounded analyses of CCC by…
Polina Bombina, Kevin R. Coombes
Comparative studies of trajectory inference (TI) methods evaluate complete computational pipelines, making it impossible to isolate how much distortion is introduced specifically by the dimensionality reduction (DR) step. To our knowledge, no study has directly and systematically evaluated how well DR methods alone…
Tyler R. Ross, Gregory W. Thiemann, Martyn E. Obbard, Kevin R. Middel + 1 more
Accounting for spatial structure within populations is critical for defining appropriate scales of management, particularly in the Arctic, where habitats of ice-dependent species such as the polar bear (Ursus maritimus) are being transformed at an accelerated rate. We examined broad-scale patterns of space use and…
Lieke Michielsen, Andrey D. Prjibelski, Careen Foord, Yelizaveta Spiegelman + 10 more
Spatial long-read technologies are increasingly common but usually lack single-cell resolution. This leaves unanswered whether spatially variable isoforms reflect variability within one cell type or differences in region-specific cell-type composition. Here, we developed Spl-ISO-Seq2 (500-nm resolution) and…
A. Nieto-Quero, J. Munoz-Martin, M. I. Infantes-López, S. Tabbai + 6 more
Effective stress regulation is essential for emotional health, whereas maladaptive stress responses contribute to neuropsychiatric disorders such as depression and post-traumatic stress disorder. Because neuron-microglia interactions are increasingly recognized as key modulators of neuroplasticity under physiological…
Jackie Rao, Muntadher Jihad, Giulia Biffi, Paul D.W. Kirk
Identifying cell types from single-cell RNA sequencing (scRNA-seq) data typically requires several separate and often uninterpretable steps: dimensionality reduction, batch-correction, clustering, marker-gene identification and the discovery of finer-grained structure. Here we introduce scFLAME (single-cell Factor…
Raphael Mostov, Greyson Lewis, Gabriel Sturm, Wallace F. Marshall
This paper addresses the increasing need for comprehensive mathematical descriptions of cell organization by examining the algebraic structure of mitochondrial network dynamics. Mitochondria are cellular structures involved in metabolism that take the form of a network of membrane-based tubes that undergo continuous…