Browse Articles

  • Article |

    Using primer-exchange reactions, SABER extends FISH probes with repetitive sequences that can accommodate multiple fluorescent imager strands, resulting in up to 450-fold signal amplification. SABER is showcased in DNA and RNA FISH experiments across a range of complex biological samples.

    • Jocelyn Y. Kishi
    • , Sylvain W. Lapan
    • , Brian J. Beliveau
    • , Emma R. West
    • , Allen Zhu
    • , Hiroshi M. Sasaki
    • , Sinem K. Saka
    • , Yu Wang
    • , Constance L. Cepko
    •  & Peng Yin
  • This Month |

    Bioluminescence lights her way to measure glucose uptake in vivo, and why a chemist travels outside her comfort zone.

    • Vivien Marx
  • Article |

    A bioluminescent glucose-uptake probe enables accurate, real-time, non-invasive longitudinal imaging of d-glucose absorption both in vitro and in vivo.

    • Tamara Maric
    • , Georgy Mikhaylov
    • , Pavlo Khodakivskyi
    • , Arkadiy Bazhin
    • , Riccardo Sinisi
    • , Nicolas Bonhoure
    • , Aleksey Yevtodiyenko
    • , Anthony Jones
    • , Vishaka Muhunthan
    • , Gihad Abdelhady
    • , David Shackelford
    •  & Elena Goun
  • Article |

    Light-sheet microscopy in the NIR-II window enables rapid volumetric imaging of tissues at impressive depths in vivo without invasive preparations owing to the reduced light scattering and tissue autofluorescence at these wavelengths.

    • Feifei Wang
    • , Hao Wan
    • , Zhuoran Ma
    • , Yeteng Zhong
    • , Qinchao Sun
    • , Ye Tian
    • , Liangqiong Qu
    • , Haotian Du
    • , Mingxi Zhang
    • , Lulin Li
    • , Huilong Ma
    • , Jian Luo
    • , Yongye Liang
    • , Wen Jung Li
    • , Guosong Hong
    • , Lianqing Liu
    •  & Hongjie Dai
  • Article |

    High-density arrays of optical fibers enable monitoring and manipulation of neural activity at large scale across many brain regions. The multi-fiber arrays can be used in head-fixed tasks, in freely behaving animals and during social interactions.

    • Yaroslav Sych
    • , Maria Chernysheva
    • , Lazar T. Sumanovski
    •  & Fritjof Helmchen
  • Perspective |

    Py-EM and SerialEM enable automated microscope control for high-throughput data acquisition in diverse transmission electron microscopy imaging experiments.

    • Martin Schorb
    • , Isabella Haberbosch
    • , Wim J. H. Hagen
    • , Yannick Schwab
    •  & David N. Mastronarde
  • Technology Feature |

    To apply machine learning, labs needn’t have years of computational expertise, but they do need a cautious mind-set.

    • Vivien Marx
  • Brief Communication |

    Epi-illumination SPIM enables fast, volumetric, high-resolution, subcellular imaging of any sample compatible with a standard inverted fluorescence microscope.

    • Bin Yang
    • , Xingye Chen
    • , Yina Wang
    • , Siyu Feng
    • , Veronica Pessino
    • , Nico Stuurman
    • , Nathan H. Cho
    • , Karen W. Cheng
    • , Samuel J. Lord
    • , Linfeng Xu
    • , Dan Xie
    • , R. Dyche Mullins
    • , Manuel D. Leonetti
    •  & Bo Huang
  • Research Highlight |

    A newly identified bacterial biosynthetic pathway enables the production of nonstandard amino acids.

    • Karin Kuehnel
  • Editorial |

    Dispelling stigmas and highlighting benefits of the Nature Research manuscript transfer service.

  • Research Highlight |

    An optimized chemogenetic tool enables highly specific and potent neuronal manipulations.

    • Nina Vogt
  • Research Highlight |

    Metabolic labeling enables researchers to spatiotemporally assess nascent protein deposition in 3D hydrogels and then study how nascent proteins influence cell behaviors.

    • Lei Tang
  • Research Highlight |

    Comparisons of genome organization in many individual cells with high-throughput FISH show extensive variation.

    • Nicole Rusk
  • Brief Communication |

    Iso-LFM enables rapid, instantaneous volumetric imaging of biological processes with isotropic and improved resolution by simultaneously capturing orthogonal light fields.

    • Nils Wagner
    • , Nils Norlin
    • , Jakob Gierten
    • , Gustavo de Medeiros
    • , Bálint Balázs
    • , Joachim Wittbrodt
    • , Lars Hufnagel
    •  & Robert Prevedel
  • Perspective |

    This paper reviews the cryo-EM technique of microcrystal electron diffraction (MicroED), providing a broad overview of the technique, the unique structures determined, and the opportunities for future development.

    • Brent L. Nannenga
    •  & Tamir Gonen
  • Article |

    Replication initiation is stochastic and obscured in population sequencing; D-NAscent reports the use of long nanopore reads to detect base analogs and thus to assess replication initiation at the individual molecule level.

    • Carolin A. Müller
    • , Michael A. Boemo
    • , Paolo Spingardi
    • , Benedikt M. Kessler
    • , Skirmantas Kriaucionis
    • , Jared T. Simpson
    •  & Conrad A. Nieduszynski
  • Brief Communication |

    ECCITE-seq combines the single-cell analysis of multiple modalities, for example transcriptome, immune cell receptors, cell surface proteins and single-guide RNAs.

    • Eleni P. Mimitou
    • , Anthony Cheng
    • , Antonino Montalbano
    • , Stephanie Hao
    • , Marlon Stoeckius
    • , Mateusz Legut
    • , Timothy Roush
    • , Alberto Herrera
    • , Efthymia Papalexi
    • , Zhengqing Ouyang
    • , Rahul Satija
    • , Neville E. Sanjana
    • , Sergei B. Koralov
    •  & Peter Smibert
  • Article |

    A method for protein binder selection and identification, NestLink, uses barcoding peptides detectable by mass spectrometry to select and biophysically characterize thousands of binders without requiring the handling of individual clones.

    • Pascal Egloff
    • , Iwan Zimmermann
    • , Fabian M. Arnold
    • , Cedric A. J. Hutter
    • , Damien Morger
    • , Lennart Opitz
    • , Lucy Poveda
    • , Hans-Anton Keserue
    • , Christian Panse
    • , Bernd Roschitzki
    •  & Markus A. Seeger
  • Brief Communication |

    A mass-spectrometry-compatible surfactant called Azo effectively solubilizes proteins, is rapidly degraded by ultraviolet irradiation and enables top-down proteomic analysis of membrane proteins.

    • Kyle A. Brown
    • , Bifan Chen
    • , Tania M. Guardado-Alvarez
    • , Ziqing Lin
    • , Leekyoung Hwang
    • , Serife Ayaz-Guner
    • , Song Jin
    •  & Ying Ge
  • Brief Communication |

    To address the issue of intra-tissue heterogeneity in cancer genomics, we developed Texomer, which enables joint analysis of bulk DNA and RNA sequencing data for allele-specific deconvolution and quantification of tumor heterogeneity.

    • Fang Wang
    • , Shaojun Zhang
    • , Tae-Beom Kim
    • , Yu-yu Lin
    • , Ramiz Iqbal
    • , Zixing Wang
    • , Vakul Mohanty
    • , Kanishka Sircar
    • , Jose A. Karam
    • , Michael C. Wendl
    • , Funda Meric-Bernstam
    • , John N. Weinstein
    • , Li Ding
    • , Gordon B. Mills
    •  & Ken Chen
  • Article |

    Ribonucleotidyl transferases tethered to an RNA reporter add untemplated RNA tails. TRAID-seq identifies the activities of 22 enzymes, including the addition of poly(UG).

    • Melanie A. Preston
    • , Douglas F. Porter
    • , Fan Chen
    • , Natascha Buter
    • , Christopher P. Lapointe
    • , Sunduz Keles
    • , Judith Kimble
    •  & Marvin Wickens
  • This Month |

    His enhancer-discovery tool cisTopic is both wet-lab and dry-lab. John Coltrane matters, too.

    • Vivien Marx
  • Analysis |

    Among 17 measures of association tested, measures of proportionality consistently performed well for inference of gene and cellular networks, cell clusters and links to disease from scRNA-seq data. In contrast, several widely used measures of association performed well on only a subset of tasks.

    • Michael A. Skinnider
    • , Jordan W. Squair
    •  & Leonard J. Foster
  • Analysis |

    This study reports results from the second community-wide single-molecule localization microscopy software challenge, which tested over 30 software packages on realistic simulated data for multiple popular 3D image acquisition modes, as well as 2D localization microscopy.

    • Daniel Sage
    • , Thanh-An Pham
    • , Hazen Babcock
    • , Tomas Lukes
    • , Thomas Pengo
    • , Jerry Chao
    • , Ramraj Velmurugan
    • , Alex Herbert
    • , Anurag Agrawal
    • , Silvia Colabrese
    • , Ann Wheeler
    • , Anna Archetti
    • , Bernd Rieger
    • , Raimund Ober
    • , Guy M. Hagen
    • , Jean-Baptiste Sibarita
    • , Jonas Ries
    • , Ricardo Henriques
    • , Michael Unser
    •  & Seamus Holden
  • Brief Communication |

    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.

    • Ryan D. Chow
    • , Guangchuan Wang
    • , Lupeng Ye
    • , Adan Codina
    • , Hyunu Ray Kim
    • , Li Shen
    • , Matthew B. Dong
    • , Youssef Errami
    •  & Sidi Chen
  • Brief Communication |

    As an unsupervised Bayesian framework, cisTopic classifies regions in scATAC-seq data into regulatory topics, which are used for clustering.

    • Carmen Bravo González-Blas
    • , Liesbeth Minnoye
    • , Dafni Papasokrati
    • , Sara Aibar
    • , Gert Hulselmans
    • , Valerie Christiaens
    • , Kristofer Davie
    • , Jasper Wouters
    •  & Stein Aerts
  • Brief Communication |

    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.

    • Hiroshi Tsugawa
    • , Ryo Nakabayashi
    • , Tetsuya Mori
    • , Yutaka Yamada
    • , Mikiko Takahashi
    • , Amit Rai
    • , Ryosuke Sugiyama
    • , Hiroyuki Yamamoto
    • , Taiki Nakaya
    • , Mami Yamazaki
    • , Rik Kooke
    • , Johanna A. Bac-Molenaar
    • , Nihal Oztolan-Erol
    • , Joost J. B. Keurentjes
    • , Masanori Arita
    •  & Kazuki Saito
  • Research Highlight |

    An eight-letter genetic alphabet can form a double helix resembling natural DNA and can be transcribed into RNA.

    • Irene Jarchum
  • Brief Communication |

    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.

    • Kathleen M. Chen
    • , Evan M. Cofer
    • , Jian Zhou
    •  & Olga G. Troyanskaya