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Consensus representation of multiple cell-cell graphs from gene signaling pathways for cell type annotation.
BMC Biol
January 2025
Research Office, City University of Hong Kong (Dongguan), Dongguan, 523000, China.
Background: Recent advancements in single-cell RNA sequencing have greatly expanded our knowledge of the heterogeneous nature of tissues. However, robust and accurate cell type annotation continues to be a major challenge, hindered by issues such as marker specificity, batch effects, and a lack of comprehensive spatial and interaction data. Traditional annotation methods often fail to adequately address the complexity of cellular interactions and gene regulatory networks.
View Article and Find Full Text PDFBAC-browser: the tool for synthetic biology.
BMC Bioinformatics
January 2025
Research Institute for Systems Biology and Medicine, Moscow, Russian Federation.
Background: Currently, synthetic genomics is a rapidly developing field. Its main tasks, such as the design of synthetic sequences and the assembly of DNA sequences from synthetic oligonucleotides, require specialized software. In this article, we present a program with a graphical interface that allows non-bioinformatics to perform the tasks needed in synthetic genomics.
View Article and Find Full Text PDFLarge language models vs human for classifying clinical documents.
Int J Med Inform
January 2025
College of Science and Engineering, James Cook University, Townsville, 4811, QLD, Australia. Electronic address:
Background: Accurate classification of medical records is crucial for clinical documentation, particularly when using the 10th revision of the International Classification of Diseases (ICD-10) coding system. The use of machine learning algorithms and Systematized Nomenclature of Medicine (SNOMED) mapping has shown promise in performing these classifications. However, challenges remain, particularly in reducing false negatives, where certain diagnoses are not correctly identified by either approach.
View Article and Find Full Text PDFLarge Language Models in Healthcare: A Bibliometric Analysis and Examination of Research Trends.
J Multidiscip Healthc
January 2025
Department of Computer Engineering, Afyon Kocatepe University, Faculty of Engineering, Afyonkarahisar, Turkey.
Background: The integration of large language models (LLMs) in healthcare has generated significant interest due to their potential to improve diagnostic accuracy, personalization of treatment, and patient care efficiency.
Objective: This study aims to conduct a comprehensive bibliometric analysis to identify current research trends, main themes and future directions regarding applications in the healthcare sector.
Methods: A systematic scan of publications until 08.
Mapping cells through time and space with moscot.
Nature
January 2025
Institute of Computational Biology, Helmholtz Center, Munich, Germany.
Single-cell genomic technologies enable the multimodal profiling of millions of cells across temporal and spatial dimensions. However, experimental limitations hinder the comprehensive measurement of cells under native temporal dynamics and in their native spatial tissue niche. Optimal transport has emerged as a powerful tool to address these constraints and has facilitated the recovery of the original cellular context.
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