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Authors compare RNA-seq aligners on mouse and human data sets using benchmarks such as alignment yield, splice junction accuracy and suitability for transcript reconstruction. The work highlights the strength of each program and discusses outstanding needs in RNA-seq analysis.
The Spinach2 RNA aptamer provides substantially improved imaging over its predecessor Spinach, enabling live-cell imaging of many tagged RNA species including toxic trinucleotide repeat–containing RNAs.
Dynamic changes to the 14-3-3 protein interactome are robustly followed over time using affinity-purification data-independent analysis–based mass spectrometry. Also in this issue, Lambert et al. describe a similar method.
Changes to protein interactomes as a result of mutations to the bait protein or addition of a pharmacological inhibitor are robustly monitored with affinity purification coupled with data-independent acquisition–based mass spectrometry and an automated data analysis pipeline. Also in this issue, Collins et al. describe a similar method.
A systematic evaluation of various single-cell RNA-seq approaches reports their sensitivity, accuracy and reproducibility and establishes the high performance of a high-throughput microfluidic method.
A method and software for profiling microbial communities from shotgun sequence data uses universal single-copy marker sequences for accurate species-level assignment. The method can classify species lacking a reference genome sequence, making it possible to analyze the large fraction of unknown microbes in the human gut.
This paper describes a platform for high-throughput image-based profiling of human pluripotent stem cells (hPSCs). It is used to quantify differentiation bias and endogenous signaling levels in hPSC lines.
Amphipols, bicelles and nanodiscs are used to study intact membrane protein complexes by mass spectrometry, with better preservation of oligomeric complexes than traditional detergent micelles.
A simple method for preparing entirely monovalent quantum dots is described. These reagents can be targeted to protein and lipid tags and used as imaging probes in live cells.
A database of known drug-gene interactions, with information derived from many public sources, allows the identification of genes that are currently targeted by a drug and the membership of genes in a category, such as kinase genes, that have a high potential for drug development.
This paper introduces and benchmarks a statistic, the hierarchical interaction score, a statistic for measuring functional interactions between genes from large-scale data, and provides accessible methods for calculating this score.
An automated experimental and software pipeline for large-scale FISH enables spatial transcriptomics in thousands of single human cells at single-molecule resolution.
An analog implementation of structured illumination using matched microlens and pinhole arrays allows up to 100-Hz 3D two-color imaging with 145-nm lateral and 350-nm axial resolution.
An approach combining the sampling methodology and energy function of Rosetta with the X-ray refinement methodology of Phenix enables improved low-resolution crystallographic refinement.
The metagenomeSeq tool robustly detects the differential abundance of microbes in marker-based microbial surveys by tackling the problems of data sparsity and undersampling common to these data sets.
A set of Cas9 endonucleases orthogonal to the Streptococcus pyogenes enzyme is identified. This will enable simultaneous addressing of multiple RNA-guided activities to different genomic target sites with the CRISPR-Cas9 system.