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In her seminal paper in which the three types of human corneal cells were used to generate an artificial cornea, May Griffith (Griffith et al., 1999) obtained the “best results” through the use of immortalized epithelial cell lines that had been screened for biochemical, electrophysiological, ...
We present Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an algorithm that unifies these two spatial clustering problems by embedding cells in a product space of their own and the local neighborhood transcriptome, representing cell state and microenvironment, respectively...
Bulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet curren...
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To enhance the clinical utility of mass spectrometry (MS), lengthy dwell times on less informative regions of patient specimens (e.g., adipose tissue in breast) must be minimized. Additionally, a promising variant of MS known as picosecond infrared laser MS (PIRL-MS) faces further challenges,...
Moreover, the bulk RNA-seq data would suggest that the Tspan2 CArG box acts locally to control the Tspan2/Tspan2os gene pair and not at a distal target gene. It will be of major interest to ascertain whether these observations extend to other CArG-dependent mRNA-LncRNA gene pairs. ...
The VESPERS beamline uses a pink beam which operates in the energy range of 6–30 keV and uses Si (111) crystal monochromator, Kirkpatrick-Baez focusing mirror, and Vortex ®-ME4 4-element (bulk spectroscopy) or 1-element (mapping) dispersive silicon drift detector (Hitachi, Troy, MI, ...
The color of the bars indicates the cell types in each linking method. Extended Data Fig. 8 Causal variant enrichment for GWAS and comparison with published bulk methods and single-cell methods. a. Comparison of the mean causal variant enrichment for FinnGen GWAS (y-axis) among SCENT (teal)...
Tabulated data to reproduce all the plots in the main Figures and Supplementary Figs. are available as a Source Data file. The TCGA data that we used here can be downloaded from https://www.cbioportal.org/study/cnSegments?id=prad_tcga. Source data are provided with this paper. Code ...