Volume 16 Issue 4, April 2019

Volume 16 Issue 4

Tools for metabolomics

A computational tool facilitates molecular formula, metabolite class and structure assignment of plant metabolites from LC-MS data.

See Tsugawa et al.

Cover design: Erin Dewalt.

Editorial

  • Editorial |

    Different methods have contributed to a better understanding of the malaria parasite, but improvements are still needed to uncover basic Plasmodium biology.

This Month

  • This Month |

    A spin-jock’s path to biomolecular dynamics with NMR, and why solitude matters.

    • Vivien Marx

Correspondence

Research Highlights

Technology Feature

News & Views

  • News & Views |

    Light-sheet fluorescence microscopes are making it possible to follow subcellular dynamics with unprecedented detail, but they are complex to build and maintain. A new method that can generate arbitrary light sheets provides much-needed simplicity and additional versatility.

    • Manu Forero-Shelton

Brief Communications

  • 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
  • Brief Communication |

    The solid media portable cell killing assay uses metabolism-sensitive staining to illuminate the killing of antibiotic-tolerant bacteria under resource-depleted conditions, thereby enabling multiplex, genome-scale analyses for the identification of target strains.

    • Jonathan M. Stokes
    • , Arnaud Gutierrez
    • , Allison J. Lopatkin
    • , Ian W. Andrews
    • , Shawn French
    • , Ivan Matic
    • , Eric D. Brown
    •  & James J. Collins
  • Brief Communication |

    DARTS first uses public domain data to train a deep neural network to predict differential alternative splicing; the predictions are then combined with observed RNA-seq data in a Bayesian framework to infer changes in alternative splicing between biological samples.

    • Zijun Zhang
    • , Zhicheng Pan
    • , Yi Ying
    • , Zhijie Xie
    • , Samir Adhikari
    • , John Phillips
    • , Russ P. Carstens
    • , Douglas L. Black
    • , Yingnian Wu
    •  & Yi Xing
  • 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
  • Brief Communication |

    SNAC-tags allow for versatile sequence-specific cleavage of soluble and membrane proteins with Ni2+ under biocompatible conditions, bypassing enzymatic cleavage and enabling cleavage in situations where commonly used enzymes fail.

    • Bobo Dang
    • , Marco Mravic
    • , Hailin Hu
    • , Nathan Schmidt
    • , Bruk Mensa
    •  & William F. DeGrado
  • Brief Communication |

    Covalent linking of a histone-modification-specific antibody to MNase allows for the isolation of fragments with the desired histone mark, which can be amplified and sequenced. This approach is sensitive enough to profile histone modifications in single cells.

    • Wai Lim Ku
    • , Kosuke Nakamura
    • , Weiwu Gao
    • , Kairong Cui
    • , Gangqing Hu
    • , Qingsong Tang
    • , Bing Ni
    •  & Keji Zhao

Articles

  • Article |

    Cell Population Mapping (CPM) leverages single-cell RNA-seq data as a rich reference to predict the composition of cell types and cell states from bulk RNA-seq data.

    • Amit Frishberg
    • , Naama Peshes-Yaloz
    • , Ofir Cohn
    • , Diana Rosentul
    • , Yael Steuerman
    • , Liran Valadarsky
    • , Gal Yankovitz
    • , Michal Mandelboim
    • , Fuad A. Iraqi
    • , Ido Amit
    • , Lior Mayo
    • , Eran Bacharach
    •  & Irit Gat-Viks
  • Article |

    The development of 19F-13C TROSY provides a new avenue for the collection of high-sensitivity, background-free information about the structure and dynamics of challenging biomolecular systems by NMR spectroscopy.

    • Andras Boeszoermenyi
    • , Sandeep Chhabra
    • , Abhinav Dubey
    • , Denitsa L. Radeva
    • , Nikola T. Burdzhiev
    • , Christo D. Chanev
    • , Ognyan I. Petrov
    • , Vladimir M. Gelev
    • , Meng Zhang
    • , Clemens Anklin
    • , Helena Kovacs
    • , Gerhard Wagner
    • , Ilya Kuprov
    • , Koh Takeuchi
    •  & Haribabu Arthanari
  • Article |

    An active atlas for automatic alignment of brains to a reference atlas is presented. The method uses the fine-scale pattern of tissue. The atlas is refined by each new brain and can inform on the structural variability between different brains.

    • Yuncong Chen
    • , Lauren E. McElvain
    • , Alexander S. Tolpygo
    • , Daniel Ferrante
    • , Beth Friedman
    • , Partha P. Mitra
    • , Harvey J. Karten
    • , Yoav Freund
    •  & David Kleinfeld

Amendments & Corrections