A computational study of density-dependent individual movement and the formation of population clusters in two-dimensional spatial domains.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of theoretical biology"
DOI: 10.1016/j.jtbi.2020.110421
Abstract: The patterns of collective behaviour in a population emerging from individual animal movement has long been of interest to ecologists, as has the emergence of heterogeneous patterns among a population. In this paper we will… read more here.
Keywords: density dependent; movement; spatial domains; formation ... See more keywords
Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder.
Sign Up to like & getrecommendations! Published in 2022 at "Nature communications"
DOI: 10.1038/s41467-022-29439-6
Abstract: Recent advances in spatially resolved transcriptomics have enabled comprehensive measurements of gene expression patterns while retaining the spatial context of the tissue microenvironment. Deciphering the spatial context of spots in a tissue needs to use… read more here.
Keywords: spatially resolved; resolved transcriptomics; spatial domains; attention ... See more keywords
Nonparametric Density Estimation for Data Scattered on Irregular Spatial Domains: A Likelihood-Based Approach Using Bivariate Penalized Spline Smoothing.
Sign Up to like & getrecommendations! Published in 2024 at "Journal of nonparametric statistics"
DOI: 10.1080/10485252.2025.2497541
Abstract: Accurately estimating data density is crucial for making informed decisions and modeling in various fields. This paper presents a novel nonparametric density estimation procedure that utilizes bivariate penalized spline smoothing over triangulation for data scattered… read more here.
Keywords: spatial domains; bivariate penalized; nonparametric density; density estimation ... See more keywords
Graph deep learning enabled spatial domains identification for spatial transcriptomics.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbad146
Abstract: Advancing spatially resolved transcriptomics (ST) technologies help biologists comprehensively understand organ function and tissue microenvironment. Accurate spatial domain identification is the foundation for delineating genome heterogeneity and cellular interaction. Motivated by this perspective, a graph… read more here.
Keywords: learning enabled; enabled spatial; deep learning; graph deep ... See more keywords
ST-SCSR: identifying spatial domains in spatial transcriptomics data via structure correlation and self-representation
Sign Up to like & getrecommendations! Published in 2024 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbae437
Abstract: Abstract Recent advances in spatial transcriptomics (ST) enable measurements of transcriptome within intact biological tissues by preserving spatial information, offering biologists unprecedented opportunities to comprehensively understand tissue micro-environment, where spatial domains are basic units of… read more here.
Keywords: spatial domains; spatial transcriptomics; correlation self; self representation ... See more keywords
A multi-modality and multi-granularity collaborative learning framework for identifying spatial domains and spatially variable genes
Sign Up to like & getrecommendations! Published in 2024 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btae607
Abstract: Abstract Motivation Recent advances in spatial transcriptomics technologies have provided multi-modality data integrating gene expression, spatial context, and histological images. Accurately identifying spatial domains and spatially variable genes is crucial for understanding tissue structures and… read more here.
Keywords: spatial domains; domains spatially; modality; multi modality ... See more keywords
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts
Sign Up to like & getrecommendations! Published in 2025 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaf254
Abstract: Motivation Gene expression varies across a tissue due to both the organization of the tissue into spatial domains, i.e. discrete regions of a tissue with distinct cell type composition, and continuous spatial gradients of gene… read more here.
Keywords: spatial domains; gene expression; spatial gradients; model ... See more keywords
MVST: Identifying spatial domains of spatial transcriptomes from multiple views using multi-view graph convolutional networks
Sign Up to like & getrecommendations! Published in 2024 at "PLOS Computational Biology"
DOI: 10.1371/journal.pcbi.1012409
Abstract: Spatial transcriptome technology can parse transcriptomic data at the spatial level to detect high-throughput gene expression and preserve information regarding the spatial structure of tissues. Identifying spatial domains, that is identifying regions with similarities in… read more here.
Keywords: spatial domains; information; graph convolutional; spatial transcriptome ... See more keywords