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Two DNA nanodevices, RatiNa and pHlicker, provide precise mapping of sodium levels in acidic organelles and potassium activity at a single-organelle resolution.
Using an experimental and computational framework inspired by compressed sensing, we greatly reduced the number of measurements needed to run Perturb-seq. Our compressed Perturb-seq strategy relies on collecting measurements comprising random linear combinations of genetic perturbations, followed by deconvolving the perturbation effects on the transcriptome using sparsity-exploiting algorithms.
We designed a method for fast aptamer selection by integrating biomaterials science, engineering principles and biology. Aptamer candidates dynamically interacting with immobilized targets in a three-dimensional, non-fouling and macroporous polyethylene glycol hydrogel were rapidly enriched and selected with high affinity against five protein targets.
Most features of a cell are determined by gene programs — sets of co-expressed genes that execute a specific function. By incorporating existing knowledge about gene programs and cell types, the Spectra factor analysis method improves how we decode single-cell transcriptomic data and offers insights into challenging tumor immune contexts.
The detection of mobile genetic elements is crucial for exploring the ecology and evolution of microbial communities, and it has diverse implications in biotechnology and public health. geNomad is a computational framework that enables researchers to precisely identifiy and annotate plasmids and viruses in sequencing data on a large scale.