Search the literature by keyword, topic, or author. Filter to articles with full text available.
1073 results
We present SCITE-RNA, a novel phylogenetic tree inference method designed for single-cell RNA sequencing data which takes reference and alternative read counts of single-nucleotide variants as input. Our approach uses a maximum-likelihood random-scan greedy search …
Read PDFAs novel technologies for single-cell lineage tracing emerge, phylogenetic and phylodynamic tools are increasingly being used to study developmental processes. However, traditional phylodynamic methods rely on assumptions that are difficult to justify in developmental contexts. …
Read PDFAt the transcriptomic level, several molecular subtyping schemes have been established to elucidate the intrinsic heterogeneity of urothelial carcinoma and to inform prognostic assessment and therapeutic guidance. However, a unified molecular classification scheme characterizing genomic …
Read PDFReference-based annotation tools have become standard for cell type assignment in single-cell RNA sequencing, leveraging large-scale atlases to transfer labels to new datasets. However, a substantial fraction of cells often receive uncertain or ambiguous annotations-low …
Read PDF<h4>Motivation</h4>Throughout the years, single-cell RNA sequencing (scRNA-seq) has become a standard approach for characterising transcriptomic changes associated with diseases and other biological conditions. However, the rapid expansion of tools and algorithms developed in various programming …
Read PDF<h4>Summary</h4>New advances in single-cell multi-omics experiments have allowed biologists to examine how various biological factors regulate processes in concert on the cellular level. However, measuring multiple cellular features for a single cell can be quite …
Read PDFThe potential health hazards caused by microwave exposure have attracted increasing attention. Microwave radiation has been reported to induce oxidative stress in neural tissues, which is considered one of the primary mechanisms underlying its adverse …
Read PDFSepsis is a life-threatening systemic inflammatory syndrome often associated with immune dysregulation, multi-organ dysfunction, and high mortality. In recent years, single-cell transcriptomics has generated a wealth of data on immune cell heterogeneity, lineage reprogramming, and …
Read PDFSingle-cell 3D genome technologies provide unprecedented views of chromatin architecture, but the extreme sparsity and noise of contact maps limit robust detection of chromatin loops at the individual cell level. Here we present CellLoop, a …
Read PDFBenign prostatic hyperplasia (BPH) is characterized by excessive cell proliferation and inflammation and affects most aging men. The development of new therapies for BPH requires a deeper understanding of the underlying pathophysiology and cellular components …
Read PDFTumour heterogeneity is a key factor in cancer progression, with immune responses within the tumour microenvironment (TME) contributing significantly to treatment resistance and immunotherapy outcomes. Recent advances in single-cell RNA sequencing (scRNA-seq) have provided unprecedented …
Read PDFCell type annotation is a fundamental task in single-cell genomics. Although various methods have been developed for automatic annotation, they often function as black-box models lacking explainability, proper uncertainty estimation, and robustness for rare cell …
Read PDFThe isolation of single plant cells from complex tissues is prone to selective enrichment and sampling biases, which complicates accurate profiling of the large diversity in cell types. Optimizing methodologies for cell enrichment and single-cell …
Read PDFPreeclampsia (PE) is a multisystem syndrome that manifests after 20 weeks of gestation, with a global incidence of 2%-8%, and is one of the leading causes of maternal and perinatal mortality. Its etiology is complex, …
Read PDFThyroid cancer exhibits pronounced cellular heterogeneity, yet the mechanisms underlying epithelial-mesenchymal transition (EMT) and tumor microenvironment (TME) remodeling remain incompletely understood. In this study, single-cell RNA sequencing of 92,849 cells from 20 thyroid tissue samples …
Read PDF<b>Aim:</b> Osteosarcoma remains aggressive with poor prognosis, particularly in chemotherapy-resistant cases. This study aimed to characterize transcriptional features of chemoresistant osteosarcoma cells, establish a prognostic resistance signature, and identify therapeutic vulnerabilities. <b>Methods:</b> Single-cell RNA sequencing …
Read PDFChildren with Down syndrome have a 150-fold increased risk of developing myeloid leukaemia (ML-DS). Unusually for a childhood leukaemia, ML-DS arises from a preleukaemic state, termed transient abnormal myelopoiesis (TAM), via a conserved sequence of …
Read PDF