11 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…
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…
Zhida Luo, Cheng Wang, Yan Zhou, Tuhin Kumar Guha + 12 more
Human pregnancy unfolds in a unique mosaic tissue context. Embryonic/fetal placental and maternal uterine cells (decidua basalis) coalesce, forming the basal plate where immune tolerance is coordinated and the utero-placental circulation is initiated. The remaining approximately 70% of the maternal-fetal interface is…
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…
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…
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…
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…
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…
Colin Vullioud, Diana Geweiler, Joerg Melzheimer, Sonja Heinrich + 3 more
In populations with low genetic diversity, the capacity to adapt to environmental change is limited. While epigenetic mechanisms can generate phenotypic plasticity, their role in mediating adaptive life-history transitions in the wild is largely unknown. Here, we show that in adult Namibian cheetahs (Acinonyx jubatus…
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…
E. Kashuk, A. Tarakanova, A. Malygina, N. Kuzovkina + 4 more
SIRT6 is a NAD^+^-dependent sirtuin that plays central roles in chromatin regulation, DNA repair, telomere maintenance, metabolic homeostasis, and inflammatory control. Although SIRT6 have long been implicated in aging because of its association with several hallmarks of aging, the available evidence remains largely…