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Peer review is at the heart of publishing scientific papers. In this first installment of a two-part Editorial, we explain how we manage the process at Nature Methods.
Diploid assembly is a difficult task that requires several types of genomic sequencing data, including — but not limited to — HiFi reads and parental sequences. Hypo-assembler, an assembly algorithm, uses high quality solid k-mers extracted from Illumina data alongside Nanopore reads to produce a high-quality diploid assembly using only Nanopore and Illumina data.
Square and rectangular beams made with new condenser apertures enable more efficient image capture in low-dose transmission electron microscopy with no compromise to image quality in single-particle cryoelectron microscopy.
This work introduces two polishers for refining the draft genome generated from nanopore long reads, as well as an assembler pipeline for producing telomere-to-telomere diploid genome with low error rate.
An optogenetic system enables the controlled release of soluble and transmembrane proteins for precise exploration of cellular protein function at the single-molecule level and streamlined single-molecule imaging.
Implementation of ultralong transients on an Orbitrap mass spectrometer improves mass resolution, sensitivity and accuracy of charge determination in the analysis of large macromolecular ions.
Deng et al. expand the toolbox of neurotransmitter sensors with high-sensitivity green and red genetically encoded serotonin sensors. These are suitable for in vivo applications, as demonstrated in a variety of applications in mice.
A copper(II)-functionalized Mycobacteriumsmegmatis porin A nanopore enables direct identification of all 20 proteinogenic amino acids, one unnatural amino acid and two post-translational modifications, and shows potential for peptide discrimination and sequencing.
Effortless landmark detection is an unsupervised deep learning-based approach that addresses key challenges in landmark detection and image registration for accurate performance across diverse tissue imaging datasets.
Collaborations between researchers and companies can progress swimmingly and teams quickly validate findings and mature methods. All too often, things can’t advance and the ‘Valley of Death’ looms. New ways to collaborate, underpinned by computational muscle, can help.
mBaoJin is a monomeric derivative of the bright and photostable green fluorescent protein StayGold. mBaoJin offers favorable photophysical properties for use in diverse protein tagging and subcellular labeling applications.
Pretrained using over 33 million single-cell RNA-sequencing profiles, scGPT is a foundation model facilitating a broad spectrum of downstream single-cell analysis tasks by transfer learning.
Multi-sheet RESOLFT combines the speed and optical sectioning of light-sheet fluorescence microscopy with reversibly photoswitchable fluorescent proteins to enable fast, volumetric super-resolution imaging in live cells.
A-SOiD is a computational platform for behavioral annotation whose training includes elements of supervised and unsupervised learning. The approach is demonstrated on mouse, macaque and human datasets.
Targeting coalescent analysis (TarCA) is a statistical method that quantifies the number of progenitor cells of a given population using single-cell phylogenetic data.
We developed a high-content profiling method named vibrational painting (VIBRANT) for single-cell drug response measurements, combining vibrational imaging, multiplexed vibrational probes and machine learning. VIBRANT showed high performance in predicting drug mechanisms of action, discovering novel compounds and assessing drug combinations, demonstrating great promise for phenotypic drug discovery.
We introduce a biomimetic antigen-presenting system that uses hexapod heterostructures for specific T cell recognition at the single-molecule and single-cell levels. The system enables high-resolution T cell activation, uses magnetic forces to increase immune responses, and offers flexible and precise identification of antigen-specific T cell receptors, aiding the study of T cell recognition and immune cell mechanics.