Search · four archives
Search · four archives
8 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…
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…
Anthony Christidis, Andrew Ghazi, Smriti Chawla, Nitesh Turaga + 2 more
Although cell type annotation has become an integral part of single-cell analysis workflows, the assessment of computational annotations remains challenging. Many annotation tools transfer labels from an annotated reference dataset to a new query dataset of interest, but blindly transferring labels from one dataset to…
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…
Maryam Majeed, Mara C.P. Rue, Aixin Zhang, Sabrina Cheng + 14 more
Parallel visual streams segregate information into pathways specialized for distinct computations, but how this segregation is achieved by anatomical segregation of primary visual cortex output remains unclear. This problem is complicated because individual neurons frequently send broadcasting projections to multiple…
Jinyao Wang, Shuang Li, Jingjing Zhou, Jing Yang + 2 more
Nonsmall cell lung cancer (NSCLC) is characterized by substantial heterogeneity in driver mutation backgrounds and tumor microenvironment (TME) phenotypes, yet the transcriptional regulatory states linking genotype context to immune-stromal variation remain incompletely defined. In this study, we integrated mutation…
Cheryl Kim, Denise Hinz, Aaron Middlebrook, Aaron J Tyznik + 4 more
Circulating cell-cell complexes (doublets) provide critical insights into in vivo immune interactions. Here, we leverage high-dimensional imaging spectral cytometry to systematically map the landscape of immune doublets in human peripheral blood. By integrating morphometric imaging features with a 22-color spectral…
Shaurav Bhattarai, Emma G. Foster, Rana Kadry, Yaman Lu + 9 more
Furthermore, neurons in dual pathology (Aβ+HIV-1) ROIs demonstrated altered expression of genes related to endosomal trafficking, cell organelle stress, and regulated cell death, including SORL1, RIPK1, ATG4, DTIT3, and BNIP5 (Figure [alz71807-fig-0008]). In particular, SORL1 regulates endosomal trafficking, including…