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Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation.
Brief Bioinform
November 2024
School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P.R. China.
Single-cell RNA sequencing (scRNA-seq) offers remarkable insights into cellular development and differentiation by capturing the gene expression profiles of individual cells. The role of dimensionality reduction and visualization in the interpretation of scRNA-seq data has gained widely acceptance. However, current methods face several challenges, including incomplete structure-preserving strategies and high distortion in embeddings, which fail to effectively model complex cell trajectories with multiple branches.
View Article and Find Full Text PDFComparative Genomic Analysis Reveals the Emergence and Dissemination of Different serovar Gallinarum biovar Gallinarum Lineages in Brazil.
Avian Pathol
January 2025
Institute of Biotechnology, University of Caxias do Sul (UCS), Caxias do Sul, Rio Grande do Sul, Brazil, Rio Grande do Sul, Brazil.
serovar Gallinarum biovar Gallinarum is a pathogenic bacterium that causes fowl typhoid (FT), affecting chicken flocks worldwide. This study aimed to evaluate the emergence, dissemination and genomic profile of Gallinarum lineages from Brazil. Twelve whole-genomes sequences (WGS) of different .
View Article and Find Full Text PDFIntegrated single-cell RNA sequencing reveals the tumor heterogeneity and microenvironment landscape during liver metastasis in adenocarcinoma of esophagogastric junction.
Front Immunol
January 2025
Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China.
Background: Adenocarcinoma of the esophagogastric junction (AEGJ) is a highly aggressive tumor that frequently metastasizes to the liver. Understanding the cellular and molecular mechanisms that drive this process is essential for developing effective therapies.
Methods: We employed single-cell RNA sequencing to analyze the tumor heterogeneity and microenvironmental landscape in patients with AEGJ liver metastases.
Macrophage heterogeneity and oncogenic mechanisms in lung adenocarcinoma: insights from scRNA-seq analysis and predictive modeling.
Front Immunol
January 2025
Tianjin Chest Hospital, Tianjin University, Tianjin, China.
Background: Macrophages play a dual role in the tumor microenvironment(TME), capable of secreting pro-inflammatory factors to combat tumors while also promoting tumor growth through angiogenesis and immune suppression. This study aims to explore the characteristics of macrophages in lung adenocarcinoma (LUAD) and establish a prognostic model based on macrophage-related genes.
Method: We performed scRNA-seq analysis to investigate macrophage heterogeneity and their potential pseudotime evolutionary processes.
In recent years, DNA metabarcoding has been used for a more efficient assessment of bulk samples. However, there remains a paucity of studies examining potential disparities in species identification methodologies. Here, we explore the outcomes of diverse clustering and filtering techniques on data from a non-destructive metabarcoding approach, compared to species-level morphological identification of Brachycera (Diptera) and Hymenoptera of two bulk samples collected with Malaise traps.
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