PhyloVelo, leverages monotonically expressed genes (MEGs) along cell divisions to quantify the transcriptomic velocity fields from lineage-resolved scRNA-seq data 2.A transcriptomic velocity field reconstructed by MEGs 他们这个方法一个很重要的一步是引入了monotonically expressed genes (MEGs) ,这个应该是...
Mapping transcriptomic vector fields of single cells. Cell 185, 690–711 (2022). Article Google Scholar Barile, M. et al. Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. Genome Biol. 22, 197 (2021). Gulati, G. S. et al. Single-cell ...
(MEGs) or genes with expression patterns that either increase or decrease, but do not cycle, through phylogenetic time. Through integration of scRNA-seq data with lineage information, PhyloVelo identifies MEGs and reconstructs a transcriptomic velocity field. We validate PhyloVelo using simulated ...
Previously, the most popular approach for visualizing RNA velocity has been the projection of the high-dimensional vector field onto a low-dimensional latent space representation7. With CellRank 2, we generalize this concept to any kernel based on ak-nearest-neighbor graph, that is, the Pseudotime...
Applied to lung cancer, we show that they align closely with patient survival, with histopathologically recognised tumor types and growth patterns, and with transcriptomic measures of immunophenotype. These properties are maintained in a multi-cancer study....
Transcriptomic approaches mapped detailed cell-type-specific mRNA splicing programs. However, it has been hard to probe the synapse-specific localization and function of the resulting protein splice isoforms, or “proteoforms,” in vivo. We here apply a proteoform-centric workflow in mice to test ...
So far, a great deal of efforts have been made to construct simulation models to predict glycan structures on proteins using kinetic, transcriptomic, and mass spectrometric information (Jimenez del Val et al., 2011; Krambeck et al., 2009; Krambeck and Betenbaugh, 2005; Kremkow and Lee, 2018...
vectorδi,jis the difference in gene expression between cells j and i. To assign probabilitypi,jto cell i transitioning to cell j in the neighborhoodNiof cell i, we transform correlations between the transcriptomic difference vectorsδi,jand the velocity vectorvi, essentially considering the ...
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high au...
Applied to lung cancer, we show that they align closely with patient survival, with histopathologically recognised tumor types and growth patterns, and with transcriptomic measures of immunophenotype. These properties are maintained in a multi-cancer study....