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…
Emma C. Murray, Namya Manoj, Lynn Ziegler, Gillian M. Hodge + 9 more
Genetic variations in the MYO9B gene have been associated with Crohn’s disease, celiac disease, and ulcerative colitis. These diseases have been characterized as primarily immune disorders. However, the overall molecular basis for the influence of Myo9b in these diseases remains poorly understood. Using in vivo small…
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…
Megan Sholomiski, Victor Yon, Franziska Mudlaff, Aparna Suvrathan
The cerebellum supports a wide range of motor and non-motor behaviors, yet the specific cerebellar regions and neuronal populations underlying this functional diversity remain poorly understood. Here, we mapped patterns of immediate early gene activation in the cerebellar cortex during the accelerating rotarod task, an…
Yuqiao Liu, Siyu Yi, Hengchuang Yin, Wei Ju
Single-cell RNA sequencing profiles cellular heterogeneity at atlas scale, making automated annotation essential. However, target datasets often contain novel cell types missing from incomplete references. We present scOLAR, an ontology-guided open-set framework that learns prototypes over the Cell Ontology and uses…
Peng Wang, Zixiong Fan, Haoyu Wu, Kaijiao Wang + 4 more
Accurate preoperative segmentation of colorectal cancer lymph node metastasis holds significant clinical value for formulating individualized surgical strategies. However, accurate segmentation remains a formidable challenge due to the complex backgrounds, small sizes, irregular shapes, and indistinct boundaries…
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…