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Graph contrastive learning of subcellular-resolution spatial transcriptomics improves cell type annotation and reveals critical molecular pathways.
Brief Bioinform
November 2024
School of Artificial Intelligence, Jilin University, Qianjin Street 2699, 130010 Changchun, China.
Imaging-based spatial transcriptomics (iST), such as MERFISH, CosMx SMI, and Xenium, quantify gene expression level across cells in space, but more importantly, they directly reveal the subcellular distribution of RNA transcripts at the single-molecule resolution. The subcellular localization of RNA molecules plays a crucial role in the compartmentalization-dependent regulation of genes within individual cells. Understanding the intracellular spatial distribution of RNA for a particular cell type thus not only improves the characterization of cell identity but also is of paramount importance in elucidating unique subcellular regulatory mechanisms specific to the cell type.
View Article and Find Full Text PDFA comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions.
Brief Bioinform
November 2024
Department of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong, 999077, China.
The complexity of T cell receptor (TCR) sequences, particularly within the complementarity-determining region 3 (CDR3), requires efficient embedding methods for applying machine learning to immunology. While various TCR CDR3 embedding strategies have been proposed, the absence of their systematic evaluations created perplexity in the community. Here, we extracted CDR3 embedding models from 19 existing methods and benchmarked these models with four curated datasets by accessing their impact on the performance of TCR downstream tasks, including TCR-epitope binding affinity prediction, epitope-specific TCR identification, TCR clustering, and visualization analysis.
View Article and Find Full Text PDFAdvancing High-Throughput Cellular Atomic Force Microscopy with Automation and Artificial Intelligence.
ACS Nano
January 2025
Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
Atomic force microscopy (AFM) has reached a significant level of maturity in biology, demonstrated by the diversity of modes for obtaining not only topographical images but also insightful mechanical and adhesion data by performing force measurements on delicate samples with a controlled environment (e.g., liquid, temperature, pH).
View Article and Find Full Text PDFPrediction of dry matter intake in growing Black Bengal goats using artificial neural networks.
Trop Anim Health Prod
January 2025
Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243 122, India.
Dry matter intake (DMI) determination is essential for effective management of meat goats, especially in optimizing feed utilization and production efficiency. Unfortunately, farmers often face challenges in accurately predicting DMI which leads to wastage of feed and an increase in the cost of production. This investigation aimed to predict DMI in Black Bengal goats by using body weight (BW), body condition score (BCS), average daily gain (ADG), and metabolic body weight (MBW) by applying an artificial neural network (ANN) model.
View Article and Find Full Text PDFStrategies to increase the robustness of microbial cell factories.
Adv Biotechnol (Singap)
March 2024
State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
Engineering microbial cell factories have achieved much progress in producing fuels, natural products and bulk chemicals. However, in industrial fermentation, microbial cells often face various predictable and stochastic disturbances resulting from intermediate metabolites or end product toxicity, metabolic burden and harsh environment. These perturbances can potentially decrease productivity and titer.
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