This can be achieved by removing the diagonal constraint from Problem 3 and replacing the matrix product by the Hadamard product (element-wise product). For every entry in the expression matrix, Ai,j, this formulation matches an optimization variable Fi,j. Therefore, the enhanced gene expression...
We report these 73 spatially significant peaks as a reference for future MCAO regulatory element studies. Moran’s I spatial autocorrelation analysis We performed a Moran’s I test to assess spatial autocorrelation between punch locations, wherein a higher Moran’s I value signifies a higher chance...
where ⊙ is the Hadamard (element-wise) product, and x represents the N− dimensional vector on the graph, i.e. the gene expression values of a cell in this work. Λh(Λ) is a diagonal matrix that is denoted as the convolution kernel of the transformation. In general, the designation...
unsupervised analysis based on iterative differential expression (DE) between small clusters of cells. To computeZ-scores, we exploit a probabilistic model of the noise that considers all sources of variability in single-cell data. Thereby, this approach can detect correlations that would otherwise b...
in theVNSfamily, the master regulators of vessel element differentiation [15], and the expansin gene (Potri.001G240900) are also expressed in this fusiform cell lineage (Fig.1Q, Additional file1: Fig. S13D, S13F, S15A). In addition, two paralogous MYB transcription factors in poplar, ...
Calibration beads, EQ™ Four Element Fluidigm Cat#201078; RRID: N/A UltraComp eBeads beads eBioscience Cat# 01-2222-42; RRID: N/A Seahorse XF Base RPMI pH 7.4 Agilent Technologies Part#103576-100; RRID: N/A TrueStain FcX (anti-mouse CD16/32 antibody (clone 93) BioLegend Cat#10132...
During mouse embryonic development, pluripotent cells rapidly divide and diversify, yet the regulatory programs that define the cell repertoire for each organ remain ill-defined. To delineate comprehensive chromatin landscapes during early organogenesis,
Dissecting the cellular heterogeneity embedded in single-cell transcriptomic data is challenging. Although many methods and approaches exist, identifying cell states and their underlying topology is still a major challenge. Here, we introduce the concept of multiresolution cell-state decomposition as a pr...
As used herein “another” or “other” may mean at least a second or more of the same or different claim element or components thereof. As used herein, the term “functional SWNT” refers to a single wall nanotube (SWNT) that has a functional pendant moiety or handle, such as a ...
Throughout this specification the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, ...