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Massively parallel Cpf1 array profiling (MCAP) targets genes and gene pairs that are candidate drivers of metastasis in cancer. In vivo profiling of single and double gene knockouts enables quantitative mapping of the genes’ contribution to metastatic phenotypes.
Selene is a deep learning library that enables the expansion of existing deep learning models to new data, the development of new model architectures, and the evaluation of these new models on biological sequence data.
Covalent linking of a histone-modification-specific antibody to MNase allows for the isolation of fragments with the desired histone mark, which can be amplified and sequenced. This approach is sensitive enough to profile histone modifications in single cells.
A computational approach facilitates molecular formula, metabolite class, and structure assignment for plant metabolites on the basis of LC–MS analysis of fully 13C-labeled and unlabeled plants.
DARTS first uses public domain data to train a deep neural network to predict differential alternative splicing; the predictions are then combined with observed RNA-seq data in a Bayesian framework to infer changes in alternative splicing between biological samples.
SNAC-tags allow for versatile sequence-specific cleavage of soluble and membrane proteins with Ni2+ under biocompatible conditions, bypassing enzymatic cleavage and enabling cleavage in situations where commonly used enzymes fail.
Cell Population Mapping (CPM) leverages single-cell RNA-seq data as a rich reference to predict the composition of cell types and cell states from bulk RNA-seq data.
An active atlas for automatic alignment of brains to a reference atlas is presented. The method uses the fine-scale pattern of tissue. The atlas is refined by each new brain and can inform on the structural variability between different brains.
The development of 19F-13C TROSY provides a new avenue for the collection of high-sensitivity, background-free information about the structure and dynamics of challenging biomolecular systems by NMR spectroscopy.
The solid media portable cell killing assay uses metabolism-sensitive staining to illuminate the killing of antibiotic-tolerant bacteria under resource-depleted conditions, thereby enabling multiplex, genome-scale analyses for the identification of target strains.
The field synthesis method for generating any scanned light sheet is based on a new mathematical theorem in Fourier analysis and has important practical implications for simpler, multicolor lattice light-sheet microscopy.
FIt-SNE, a sped-up version of t-SNE, enables visualization of rare cell types in large datasets by obviating the need for downsampling. One-dimensional t-SNE heatmaps allow simultaneous visualization of expression patterns from thousands of genes.
Culturing human kidney organoids under fluidic shear conditions leads to robust vascularization and increased maturity. These kidney organoids should serve as a better model for kidney development than those developed in static culture.
Acoustic scattering in a suspended microchannel resonator can be used to measure mechanical properties of single cells in a noninvasive manner. The approach is applied to follow stiffness changes of individual cells throughout the cell cycle.
RNA-guided adenosine deaminases edit point mutations in in vivo mouse models for Duchenne muscular dystrophy and ornithine transcarbamylase deficiency.
Trogocytosis, the uptake of membrane proteins by an antigen-presenting cell from its cognate T cell, allows the identification of neoepitopes targeted by T cell receptors with high sensitivity.