Applications of transformer-based language models in bioinformatics: a survey
The transformer-based language models, including vanilla transformer, BERT and GPT-3,
have achieved revolutionary breakthroughs in the field of natural language processing …
have achieved revolutionary breakthroughs in the field of natural language processing …
A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics
Spatial transcriptomics technologies are used to profile transcriptomes while preserving
spatial information, which enables high-resolution characterization of transcriptional patterns …
spatial information, which enables high-resolution characterization of transcriptional patterns …
SONAR enables cell type deconvolution with spatially weighted Poisson-Gamma model for spatial transcriptomics
Recent advancements in spatial transcriptomic technologies have enabled the
measurement of whole transcriptome profiles with preserved spatial context. However …
measurement of whole transcriptome profiles with preserved spatial context. However …
Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges
Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the
measurement of the expression of all genes in each individual cell contained in a sample …
measurement of the expression of all genes in each individual cell contained in a sample …
Delineating the early dissemination mechanisms of acral melanoma by integrating single-cell and spatial transcriptomic analyses
C Wei, W Sun, K Shen, J Zhong, W Liu, Z Gao… - Nature …, 2023 - nature.com
Acral melanoma (AM) is a rare subtype of melanoma characterized by a high incidence of
lymph node (LN) metastasis, a critical factor in tumor dissemination and therapeutic decision …
lymph node (LN) metastasis, a critical factor in tumor dissemination and therapeutic decision …
EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning
Motivation Spatially resolved gene expression profiles are the key to exploring the cell type
spatial distributions and understanding the architecture of tissues. Many spatially resolved …
spatial distributions and understanding the architecture of tissues. Many spatially resolved …
Cell composition inference and identification of layer-specific spatial transcriptional profiles with POLARIS
Spatial transcriptomics (ST) technology, providing spatially resolved transcriptional profiles,
facilitates advanced understanding of key biological processes related to health and …
facilitates advanced understanding of key biological processes related to health and …
Deep learning in spatially resolved transcriptomics: A comprehensive technical view
Spatially resolved transcriptomics (SRT) has evolved rapidly through various technologies,
enabling scientists to investigate both morphological contexts and gene expression profiling …
enabling scientists to investigate both morphological contexts and gene expression profiling …
Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection
CD4 T cell help is critical to sustain effector CD8 T cell responses during chronic infection,
notably via T follicular helper (Tfh)-derived interleukin-21 (IL-21). Conversely, CD4 depletion …
notably via T follicular helper (Tfh)-derived interleukin-21 (IL-21). Conversely, CD4 depletion …
Simulating multiple variability in spatially resolved transcriptomics with scCube
A pressing challenge in spatially resolved transcriptomics (SRT) is to benchmark the
computational methods. A widely-used approach involves utilizing simulated data. However …
computational methods. A widely-used approach involves utilizing simulated data. However …