FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3150951911> ?p ?o ?g. }

• W3150951911 endingPage "e1008218" @default.
• W3150951911 startingPage "e1008218" @default.
• W3150951911 abstract "High-throughput spatial-transcriptomics RNA sequencing (sptRNA-seq) based on in-situ capturing technologies has recently been developed to spatially resolve transcriptome-wide mRNA expressions mapped to the captured locations in a tissue sample. Due to the low RNA capture efficiency by in-situ capturing and the complication of tissue section preparation, sptRNA-seq data often only provides an incomplete profiling of the gene expressions over the spatial regions of the tissue. In this paper, we introduce a graph-regularized tensor completion model for imputing the missing mRNA expressions in sptRNA-seq data, namely FIST, Fast Imputation of Spatially-resolved transcriptomes by graph-regularized Tensor completion. We first model sptRNA-seq data as a 3-way sparse tensor in genes ( p -mode) and the ( x , y ) spatial coordinates ( x -mode and y -mode) of the observed gene expressions, and then consider the imputation of the unobserved entries or fibers as a tensor completion problem in Canonical Polyadic Decomposition (CPD) form. To improve the imputation of highly sparse sptRNA-seq data, we also introduce a protein-protein interaction network to add prior knowledge of gene functions, and a spatial graph to capture the the spatial relations among the capture spots. The tensor completion model is then regularized by a Cartesian product graph of protein-protein interaction network and the spatial graph to capture the high-order relations in the tensor. In the experiments, FIST was tested on ten 10x Genomics Visium spatial transcriptomic datasets of different tissue sections with cross-validation among the known entries in the imputation. FIST significantly outperformed the state-of-the-art methods for single-cell RNAseq data imputation. We also demonstrate that both the spatial graph and PPI network play an important role in improving the imputation. In a case study, we further analyzed the gene clusters obtained from the imputed gene expressions to show that the imputations by FIST indeed capture the spatial characteristics in the gene expressions and reveal functions that are highly relevant to three different kinds of tissues in mouse kidney." @default.
• W3150951911 created "2021-04-13" @default.
• W3150951911 creator A5010172507 @default.
• W3150951911 creator A5057134657 @default.
• W3150951911 creator A5066338313 @default.
• W3150951911 creator A5078337006 @default.
• W3150951911 date "2021-04-07" @default.
• W3150951911 modified "2023-10-16" @default.
• W3150951911 title "Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion" @default.
• W3150951911 cites W1511885491 @default.
• W3150951911 cites W1988391018 @default.
• W3150951911 cites W1992690823 @default.
• W3150951911 cites W1993101011 @default.
• W3150951911 cites W2024165284 @default.
• W3150951911 cites W2034590976 @default.
• W3150951911 cites W2035618305 @default.
• W3150951911 cites W2049588365 @default.
• W3150951911 cites W2069089843 @default.
• W3150951911 cites W2071010503 @default.
• W3150951911 cites W2080338559 @default.
• W3150951911 cites W2102212449 @default.
• W3150951911 cites W2109890799 @default.
• W3150951911 cites W2110649308 @default.
• W3150951911 cites W2116040960 @default.
• W3150951911 cites W2120901716 @default.
• W3150951911 cites W2124363222 @default.
• W3150951911 cites W2126537932 @default.
• W3150951911 cites W2135937351 @default.
• W3150951911 cites W2142678478 @default.
• W3150951911 cites W2149964263 @default.
• W3150951911 cites W2151013106 @default.
• W3150951911 cites W2152692691 @default.
• W3150951911 cites W2157109450 @default.
• W3150951911 cites W2165685007 @default.
• W3150951911 cites W2167913971 @default.
• W3150951911 cites W2225856091 @default.
• W3150951911 cites W2428018828 @default.
• W3150951911 cites W2467652252 @default.
• W3150951911 cites W2471536144 @default.
• W3150951911 cites W2527836113 @default.
• W3150951911 cites W2529957613 @default.
• W3150951911 cites W2604438238 @default.
• W3150951911 cites W2612502013 @default.
• W3150951911 cites W2612639002 @default.
• W3150951911 cites W2770694377 @default.
• W3150951911 cites W2783644856 @default.
• W3150951911 cites W2808465642 @default.
• W3150951911 cites W2915536738 @default.
• W3150951911 cites W2915848182 @default.
• W3150951911 cites W2950479715 @default.
• W3150951911 cites W2952459265 @default.
• W3150951911 cites W2963191549 @default.
• W3150951911 cites W2972983657 @default.
• W3150951911 cites W3003385342 @default.
• W3150951911 cites W331119053 @default.
• W3150951911 cites W4239055654 @default.
• W3150951911 doi "https://doi.org/10.1371/journal.pcbi.1008218" @default.
• W3150951911 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8055040" @default.
• W3150951911 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/33826608" @default.
• W3150951911 hasPublicationYear "2021" @default.
• W3150951911 type Work @default.
• W3150951911 sameAs 3150951911 @default.
• W3150951911 citedByCount "18" @default.
• W3150951911 countsByYear W31509519112021 @default.
• W3150951911 countsByYear W31509519112022 @default.
• W3150951911 countsByYear W31509519112023 @default.
• W3150951911 crossrefType "journal-article" @default.
• W3150951911 hasAuthorship W3150951911A5010172507 @default.
• W3150951911 hasAuthorship W3150951911A5057134657 @default.
• W3150951911 hasAuthorship W3150951911A5066338313 @default.
• W3150951911 hasAuthorship W3150951911A5078337006 @default.
• W3150951911 hasBestOaLocation W31509519111 @default.
• W3150951911 hasConcept C119857082 @default.
• W3150951911 hasConcept C124101348 @default.
• W3150951911 hasConcept C132525143 @default.
• W3150951911 hasConcept C153180895 @default.
• W3150951911 hasConcept C154945302 @default.
• W3150951911 hasConcept C41008148 @default.
• W3150951911 hasConcept C58041806 @default.
• W3150951911 hasConcept C70721500 @default.
• W3150951911 hasConcept C80444323 @default.
• W3150951911 hasConcept C86803240 @default.
• W3150951911 hasConcept C9357733 @default.
• W3150951911 hasConceptScore W3150951911C119857082 @default.
• W3150951911 hasConceptScore W3150951911C124101348 @default.
• W3150951911 hasConceptScore W3150951911C132525143 @default.
• W3150951911 hasConceptScore W3150951911C153180895 @default.
• W3150951911 hasConceptScore W3150951911C154945302 @default.
• W3150951911 hasConceptScore W3150951911C41008148 @default.
• W3150951911 hasConceptScore W3150951911C58041806 @default.
• W3150951911 hasConceptScore W3150951911C70721500 @default.
• W3150951911 hasConceptScore W3150951911C80444323 @default.
• W3150951911 hasConceptScore W3150951911C86803240 @default.
• W3150951911 hasConceptScore W3150951911C9357733 @default.
• W3150951911 hasFunder F4320332161 @default.
• W3150951911 hasIssue "4" @default.
• W3150951911 hasLocation W31509519111 @default.
• W3150951911 hasLocation W31509519112 @default.

• next