Reviews & Analysis

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  • A diagnostic fragment ion in tandem mass spectrometry enables confident protein lactylation assignment and the discovery of broad lysine modification beyond histones.

    • Xiaofeng Wu
    • W. Andy Tao
    News & Views
  • Evidence for at least one protein product from 80% of all mouse genes is reported in a comprehensive proteomic analysis of 41 adult mouse tissues. Comparison of tissue profiles between mouse and human suggests that the fundamental biology of this important model organism is even more different from our own than we thought.

    • Leonard J. Foster
    News & Views
  • Bioluminescent phasor is a new technology for multiplexed, excitation-free imaging at the microscale using luciferase–luciferin pairs. This platform can readily unmix the broad, overlapping emission spectra of bioluminescent reporters, making possible the dynamic tracking of cellular and molecular features over prolonged time periods.

    Research Briefing
  • Adenosine-to-inosine RNA editing is a common post-transcriptional modification, but can be challenging to identify correctly from Illumina data. We show that Oxford Nanopore RNA sequencing, combined with deep learning models, can be used to accurately detect inosine-containing sites in native transcriptomes and to estimate the modification rate of each site.

    Research Briefing
  • Determining the functional properties of a protein from its structure is challenging. This study presents an interpretable deep learning model that directly learns function-bearing structural motifs from raw data, allowing accurate mapping of protein binding sites and antibody epitopes onto a protein structure.

    Research Briefing
  • Repository-scale analysis of hundreds of millions to billions of mass spectra is a challenging endeavor due to the complexity and volume of associated data. A deep neural network embedding method is presented that enables large-scale investigation of repeatedly observed yet consistently unidentified mass spectra.

    Research Briefing
  • De novo structure generation from tandem mass spectrometry data will advance annotation of unknown metabolomic signals.

    • Corey D. Broeckling
    News & Views
  • This Perspective focuses on experimental techniques developed for circRNA studies, and provides practical guidelines for performing circRNA research.

    • Anne F. Nielsen
    • Albrecht Bindereif
    • Jørgen Kjems
    Perspective
  • A repeat-aware pipeline corrects structural assembly errors and polishes assembly sequences in large repeats without overcorrection.

    • Li Fang
    • Kai Wang
    News & Views
  • A novel bright near-infrared fluorescent protein inserted into a nanobody enables visualization of native proteins inside living cells and specific manipulation of cell function, including Boolean protein-based operators.

    • Theodorus W. J. Gadella
    News & Views
  • DiMeLo-seq leverages immunotethered DNA methyltransferases with long-read sequencing to map the locations of chromatin proteins in their natural context.

    • Kami Ahmad
    News & Views
  • A novel approach to probabilistically align adjacent multiple tissue slices from spatially resolved transcriptomics data provides unprecedented depth for the investigation of tissue architecture and paves the way for new developments in 3D spatial analytics.

    • Yingxin Lin
    • Jean Y. H. Yang
    News & Views
  • Tangram, gimVI and SpaGE outperformed other integration methods for predicting the spatial distributions of RNA transcripts, while Cell2location, SpatialDWLS and RCTD were the top-performing methods for the cell type deconvolution of spots in histological sections.

    Research Briefing
  • Neuromechanical simulations enable the study of how interactions between organisms and their physical surroundings give rise to behavior. NeuroMechFly is an open-source neuromechanical model of adult Drosophila, with data-driven morphological biorealism that enables a synergistic cross-talk between computational and experimental neuroscience.

    Research Briefing
  • A flexible open-top light-sheet microscope has been developed that can perform deep three-dimensional imaging on all clearing protocols with low and high optical resolution.

    • Shigeaki Kanatani
    • Per Uhlén
    News & Views
  • Counting of RNA molecules using unique molecular identifiers (UMIs) is ubiquitous in single-cell sequencing. Here, we introduce molecular spikes, a new type of RNA spike-ins with in-built UMIs. These versatile molecular spikes have many uses in experimental and computational method development and routine biological applications.

    Research Briefing
  • Two new toolkits that leverage deep-learning approaches can track the positions of multiple animals and estimate poses in different experimental paradigms.

    • Sena Agezo
    • Gordon J. Berman
    News & Views