Browse Articles

  • Article |

    Chemically inducible trimerization tools based on split FRB or FKBP with full-length FKBP or FRB, respectively, expand the chemogenetics toolbox. Their efficiency and fast kinetics enable new types of protein manipulation in live cells.

    • Helen D. Wu
    • , Masaki Kikuchi
    • , Onur Dagliyan
    • , Adam K. Aragaki
    • , Hideki Nakamura
    • , Nikolay V. Dokholyan
    • , Takashi Umehara
    •  & Takanari Inoue
  • Research Highlight |

    Tethering fluorescent proteins to ribosomes clears up background signals when imaging neural circuits.

    • Nina Vogt
  • Research Highlight |

    Intravital three-dimensional bioprinting enables the biofabrication of constructs in a pre-existing 3D matrix, such as inside tissues of live animals.

    • Lei Tang
  • Research Highlight |

    RIC-seq enables in situ mapping of intra- and intermolecular RNA–RNA interactions.

    • Lin Tang
  • Research Highlight |

    barRNAseq allows detailed explorations of signaling pathways that control embryonic differentiation.

    • Madhura Mukhopadhyay
  • Research Highlight |

    Direct imaging of carbohydrates using electrospray ion beam deposition and scanning tunneling microscopy.

    • Arunima Singh
  • Editorial |

    We’ve made some recent updates to our various content type offerings at Nature Methods. Here is a cheat sheet.

  • Article |

    Supervised machine-learning models trained using Drosophila epigenetic and STARR-seq data can be transferred to predict mouse and human enhancers.

    • Anurag Sethi
    • , Mengting Gu
    • , Emrah Gumusgoz
    • , Landon Chan
    • , Koon-Kiu Yan
    • , Joel Rozowsky
    • , Iros Barozzi
    • , Veena Afzal
    • , Jennifer A. Akiyama
    • , Ingrid Plajzer-Frick
    • , Chengfei Yan
    • , Catherine S. Novak
    • , Momoe Kato
    • , Tyler H. Garvin
    • , Quan Pham
    • , Anne Harrington
    • , Brandon J. Mannion
    • , Elizabeth A. Lee
    • , Yoko Fukuda-Yuzawa
    • , Axel Visel
    • , Diane E. Dickel
    • , Kevin Y. Yip
    • , Richard Sutton
    • , Len A. Pennacchio
    •  & Mark Gerstein
  • Article |

    A general tuning strategy is introduced for improving the utility of rhodamines for biological imaging applications. The strategy yielded bright, versatile and bioavailable far-red and near-infrared ‘Janelia Fluor’ dyes.

    • Jonathan B. Grimm
    • , Ariana N. Tkachuk
    • , Liangqi Xie
    • , Heejun Choi
    • , Boaz Mohar
    • , Natalie Falco
    • , Kathy Schaefer
    • , Ronak Patel
    • , Qinsi Zheng
    • , Zhe Liu
    • , Jennifer Lippincott-Schwartz
    • , Timothy A. Brown
    •  & Luke D. Lavis
  • Article |

    OligoFISSEQ combines Oligopaints with fluorescence in situ sequencing to enable the 3D mapping of many regions across the genome in human cells to interrogate genome organization at improved genomic resolution. OligoFISSEQ is compatible with immunochemistry and OligoSTORM for super-resolution imaging.

    • Huy Q. Nguyen
    • , Shyamtanu Chattoraj
    • , David Castillo
    • , Son C. Nguyen
    • , Guy Nir
    • , Antonios Lioutas
    • , Elliot A. Hershberg
    • , Nuno M. C. Martins
    • , Paul L. Reginato
    • , Mohammed Hannan
    • , Brian J. Beliveau
    • , George M. Church
    • , Evan R. Daugharthy
    • , Marc A. Marti-Renom
    •  & C.-ting Wu
  • Publisher Correction |

    • Ismael Rodríguez-Espigares
    • , Mariona Torrens-Fontanals
    • , Johanna K. S. Tiemann
    • , David Aranda-García
    • , Juan Manuel Ramírez-Anguita
    • , Tomasz Maciej Stepniewski
    • , Nathalie Worp
    • , Alejandro Varela-Rial
    • , Adrián Morales-Pastor
    • , Brian Medel-Lacruz
    • , Gáspár Pándy-Szekeres
    • , Eduardo Mayol
    • , Toni Giorgino
    • , Jens Carlsson
    • , Xavier Deupi
    • , Slawomir Filipek
    • , Marta Filizola
    • , José Carlos Gómez-Tamayo
    • , Angel Gonzalez
    • , Hugo Gutiérrez-de-Terán
    • , Mireia Jiménez-Rosés
    • , Willem Jespers
    • , Jon Kapla
    • , George Khelashvili
    • , Peter Kolb
    • , Dorota Latek
    • , Maria Marti-Solano
    • , Pierre Matricon
    • , Minos-Timotheos Matsoukas
    • , Przemyslaw Miszta
    • , Mireia Olivella
    • , Laura Perez-Benito
    • , Davide Provasi
    • , Santiago Ríos
    • , Iván R. Torrecillas
    • , Jessica Sallander
    • , Agnieszka Sztyler
    • , Silvana Vasile
    • , Harel Weinstein
    • , Ulrich Zachariae
    • , Peter W. Hildebrand
    • , Gianni De Fabritiis
    • , Ferran Sanz
    • , David E. Gloriam
    • , Arnau Cordomi
    • , Ramon Guixà-González
    •  & Jana Selent
  • This Month |

    A platform for exploring GPCR secrets, powered by community, music and sports.

    • Vivien Marx
  • Article |

    NanoLuc substrates with improved solubility and bioavailability, hydrofurimazine and fluorofurimazine, strongly enhance bioluminescence signals in vivo and enable bright dual-color bioluminescent imaging with AkaLuc and AkaLumine.

    • Yichi Su
    • , Joel R. Walker
    • , Yunhee Park
    • , Thomas P. Smith
    • , Lan Xiang Liu
    • , Mary P. Hall
    • , Louai Labanieh
    • , Robin Hurst
    • , David C. Wang
    • , Lance P. Encell
    • , Namdoo Kim
    • , Feijie Zhang
    • , Mark A. Kay
    • , Kerriann M. Casey
    • , Robbie G. Majzner
    • , Jennifer R. Cochran
    • , Crystal L. Mackall
    • , Thomas A. Kirkland
    •  & Michael Z. Lin
  • Resource |

    GPCRmd is a community-driven online platform to visualize, analyze and share G-protein-coupled receptor (GPCR) molecular dynamics data. It currently contains simulation data representing 100% of GPCR classes, 71% of receptor subtypes and 80% of GPCR families.

    • Ismael Rodríguez-Espigares
    • , Mariona Torrens-Fontanals
    • , Johanna K. S. Tiemann
    • , David Aranda-García
    • , Juan Manuel Ramírez-Anguita
    • , Tomasz Maciej Stepniewski
    • , Nathalie Worp
    • , Alejandro Varela-Rial
    • , Adrián Morales-Pastor
    • , Brian Medel-Lacruz
    • , Gáspár Pándy-Szekeres
    • , Eduardo Mayol
    • , Toni Giorgino
    • , Jens Carlsson
    • , Xavier Deupi
    • , Slawomir Filipek
    • , Marta Filizola
    • , José Carlos Gómez-Tamayo
    • , Angel Gonzalez
    • , Hugo Gutiérrez-de-Terán
    • , Mireia Jiménez-Rosés
    • , Willem Jespers
    • , Jon Kapla
    • , George Khelashvili
    • , Peter Kolb
    • , Dorota Latek
    • , Maria Marti-Solano
    • , Pierre Matricon
    • , Minos-Timotheos Matsoukas
    • , Przemyslaw Miszta
    • , Mireia Olivella
    • , Laura Perez-Benito
    • , Davide Provasi
    • , Santiago Ríos
    • , Iván R. Torrecillas
    • , Jessica Sallander
    • , Agnieszka Sztyler
    • , Silvana Vasile
    • , Harel Weinstein
    • , Ulrich Zachariae
    • , Peter W. Hildebrand
    • , Gianni De Fabritiis
    • , Ferran Sanz
    • , David E. Gloriam
    • , Arnau Cordomi
    • , Ramon Guixà-González
    •  & Jana Selent
  • Article |

    ZipSeq uses patterned illumination and photocaged oligonucleotides to serially print barcodes onto live, intact tissues for spatially mapping single cell transcriptomes.

    • Kenneth H. Hu
    • , John P. Eichorst
    • , Chris S. McGinnis
    • , David M. Patterson
    • , Eric D. Chow
    • , Kelly Kersten
    • , Stephen C. Jameson
    • , Zev J. Gartner
    • , Arjun A. Rao
    •  & Matthew F. Krummel
  • Review Article |

    A review on recent method development for discovering T cell antigens.

    • Alok V. Joglekar
    •  & Guideng Li
  • Research Highlight |

    Proteins that control the optical properties of cephalopod skin cells can modulate the transparency of mammalian cells.

    • Rita Strack
  • Research Highlight |

    Sequencing gradually digested chromatin along the nuclear radius enables the mapping of radial organization of chromatin in human cells.

    • Lei Tang
  • Research Highlight |

    In situ labeling with azido sugars enables in vivo immunomodulation of dendritic cells.

    • Madhura Mukhopadhyay
  • News & Views |

    Producing reliable atomic- or close-to-atomic-resolution structures of RNA-only molecules has been a formidable task. Ribosolve can solve sub-nanometer-resolution cryo-EM structures of unbound RNA molecules with unprecedented accuracy and speed.

    • Jane S. Richardson
  • Editorial |

    Systemic racism has held back under-represented minorities, especially Black people, in scientific research. We’re committed in our roles as journal editors to help correct this inequality.

  • Article |

    The Ribosolve pipeline combines single-particle cryo-EM, M2-seq biochemical analysis and Rosetta auto-DRRAFTER modeling to guide three-dimensional RNA structure determination.

    • Kalli Kappel
    • , Kaiming Zhang
    • , Zhaoming Su
    • , Andrew M. Watkins
    • , Wipapat Kladwang
    • , Shanshan Li
    • , Grigore Pintilie
    • , Ved V. Topkar
    • , Ramya Rangan
    • , Ivan N. Zheludev
    • , Joseph D. Yesselman
    • , Wah Chiu
    •  & Rhiju Das
  • Brief Communication |

    Hundred-fold-faster DNA-PAINT imaging is enabled by the introduction of concatenated, periodic DNA sequence motifs in the docking strand. Six orthogonal sequences are described for speed-optimized and highly multiplexed cellular imaging.

    • Sebastian Strauss
    •  & Ralf Jungmann
  • Article |

    Small vibrational tags (azide, 13C-edited carbonyl and deuterium-labeled probes) were introduced as metabolic probes for mid-infrared imaging. The tags allow unprecedented in situ visualization of metabolism in cells and animals with high information throughput.

    • Lixue Shi
    • , Xinwen Liu
    • , Lingyan Shi
    • , H. Ted Stinson
    • , Jeremy Rowlette
    • , Lisa J. Kahl
    • , Christopher R. Evans
    • , Chaogu Zheng
    • , Lars E. P. Dietrich
    •  & Wei Min
  • Article |

    PULSE is an optogenetic tool that consists of two modules with different wavelength sensitivities. Their interplay enables optogenetic access to gene expression in plants independently of ambient light.

    • Rocio Ochoa-Fernandez
    • , Nikolaj B. Abel
    • , Franz-Georg Wieland
    • , Jenia Schlegel
    • , Leonie-Alexa Koch
    • , J. Benjamin Miller
    • , Raphael Engesser
    • , Giovanni Giuriani
    • , Simon M. Brandl
    • , Jens Timmer
    • , Wilfried Weber
    • , Thomas Ott
    • , Rüdiger Simon
    •  & Matias D. Zurbriggen
  • Brief Communication |

    CARPID uses CRISPR technology to navigate biotin ligase to specific lncRNAs, which allows proximal labeling and thus the querying of RNA–protein interactions in living cells.

    • Wenkai Yi
    • , Jingyu Li
    • , Xiaoxuan Zhu
    • , Xi Wang
    • , Ligang Fan
    • , Wenju Sun
    • , Linbu Liao
    • , Jilin Zhang
    • , Xiaoyu Li
    • , Jing Ye
    • , Fulin Chen
    • , Jussi Taipale
    • , Kui Ming Chan
    • , Liang Zhang
    •  & Jian Yan
  • Article |

    Multifocal flat illumination for field-independent imaging (mfFIFI) enables patterned illumination over an extended field of view. Integration with instant structured illumination microscope allowed for high-speed, multicolor, volumetric super-resolution imaging over 100 × 100 µm2.

    • Dora Mahecic
    • , Davide Gambarotto
    • , Kyle M. Douglass
    • , Denis Fortun
    • , Niccoló Banterle
    • , Khalid A. Ibrahim
    • , Maeva Le Guennec
    • , Pierre Gönczy
    • , Virginie Hamel
    • , Paul Guichard
    •  & Suliana Manley
  • This Month |

    A yellow fluorescent sensor to study the brain, and the joy and pain of climbing.

    • Vivien Marx