Volume 16 Issue 9, September 2019

Volume 16 Issue 9

Secondary structure detection with deep learning

The deep-learning-based tool, Emap2sec, detects protein secondary structures in intermediate-resolution cryo-EM maps, as illustrated for the archaeal 20S proteasome.

See Maddhuri Venkata Subramaniya et al.

Image: Ella Marushchenko and Elina Karimullina; Ella Maru Studio, Inc. Cover design: Erin Dewalt.

Editorial

  • Editorial |

    There are many misconceptions about science journalism. We aim to provide some clarity on how journalists work and how to give interviews about your research.

This Month

  • This Month |

    Staying mobile and building a Toy-Story-related way to stitch terabyte-sized images in microscopy.

    • Vivien Marx
  • This Month |

    “Everything we see hides another thing, we always want to see what is hidden by what we see” — Rene Magritte

    • Jasleen K. Grewal
    • , Martin Krzywinski
    •  & Naomi Altman

Comment

  • Comment |

    Whole-body energy expenditure is the summed metabolic activities of tissues and, to remove the influence of body size, ratios of energy expenditure to body mass are often applied but can generate spurious differences. In 2011, a group of experts proposed adoption of ANCOVA for the analysis of metabolic rate but, seven years later, analyses based on ratios remain the most frequent. We discuss some of the barriers to adopting better analytical procedures.

    • Rodrigo Fernández-Verdejo
    • , Eric Ravussin
    • , John R. Speakman
    •  & Jose E. Galgani

Research Highlights

Technology Feature

News & Views

  • News & Views |

    Single objective light-sheet fluorescence microscopes combine the convenience of conventional sample mounting with sensitive subcellular and super-resolution imaging of cells and tissues.

    • Reto Fiolka

Perspectives

Analysis

  • Analysis | | Open Access

    In this DREAM challenge, 75 methods for the identification of disease-relevant modules from molecular networks are compared and validated with GWAS data. The authors provide practical guidelines for users and establish benchmarks for network analysis.

    • Sarvenaz Choobdar
    • , Mehmet E. Ahsen
    • , Jake Crawford
    • , Mattia Tomasoni
    • , Tao Fang
    • , David Lamparter
    • , Junyuan Lin
    • , Benjamin Hescott
    • , Xiaozhe Hu
    • , Johnathan Mercer
    • , Ted Natoli
    • , Rajiv Narayan
    • , Fabian Aicheler
    • , Nicola Amoroso
    • , Alex Arenas
    • , Karthik Azhagesan
    • , Aaron Baker
    • , Michael Banf
    • , Serafim Batzoglou
    • , Anaïs Baudot
    • , Roberto Bellotti
    • , Sven Bergmann
    • , Keith A. Boroevich
    • , Christine Brun
    • , Stanley Cai
    • , Michael Caldera
    • , Alberto Calderone
    • , Gianni Cesareni
    • , Weiqi Chen
    • , Christine Chichester
    • , Sarvenaz Choobdar
    • , Lenore Cowen
    • , Jake Crawford
    • , Hongzhu Cui
    • , Phuong Dao
    • , Manlio De Domenico
    • , Andi Dhroso
    • , Gilles Didier
    • , Mathew Divine
    • , Antonio del Sol
    • , Tao Fang
    • , Xuyang Feng
    • , Jose C. Flores-Canales
    • , Santo Fortunato
    • , Anthony Gitter
    • , Anna Gorska
    • , Yuanfang Guan
    • , Alain Guénoche
    • , Sergio Gómez
    • , Hatem Hamza
    • , András Hartmann
    • , Shan He
    • , Anton Heijs
    • , Julian Heinrich
    • , Benjamin Hescott
    • , Xiaozhe Hu
    • , Ying Hu
    • , Xiaoqing Huang
    • , V. Keith Hughitt
    • , Minji Jeon
    • , Lucas Jeub
    • , Nathan T. Johnson
    • , Keehyoung Joo
    • , InSuk Joung
    • , Sascha Jung
    • , Susana G. Kalko
    • , Piotr J. Kamola
    • , Jaewoo Kang
    • , Benjapun Kaveelerdpotjana
    • , Minjun Kim
    • , Yoo-Ah Kim
    • , Oliver Kohlbacher
    • , Dmitry Korkin
    • , Kiryluk Krzysztof
    • , Khalid Kunji
    • , Zoltàn Kutalik
    • , Kasper Lage
    • , David Lamparter
    • , Sean Lang-Brown
    • , Thuc Duy Le
    • , Jooyoung Lee
    • , Sunwon Lee
    • , Juyong Lee
    • , Dong Li
    • , Jiuyong Li
    • , Junyuan Lin
    • , Lin Liu
    • , Antonis Loizou
    • , Zhenhua Luo
    • , Artem Lysenko
    • , Tianle Ma
    • , Raghvendra Mall
    • , Daniel Marbach
    • , Tomasoni Mattia
    • , Mario Medvedovic
    • , Jörg Menche
    • , Johnathan Mercer
    • , Elisa Micarelli
    • , Alfonso Monaco
    • , Felix Müller
    • , Rajiv Narayan
    • , Oleksandr Narykov
    • , Ted Natoli
    • , Thea Norman
    • , Sungjoon Park
    • , Livia Perfetto
    • , Dimitri Perrin
    • , Stefano Pirrò
    • , Teresa M. Przytycka
    • , Xiaoning Qian
    • , Karthik Raman
    • , Daniele Ramazzotti
    • , Emilie Ramsahai
    • , Balaraman Ravindran
    • , Philip Rennert
    • , Julio Saez-Rodriguez
    • , Charlotta Schärfe
    • , Roded Sharan
    • , Ning Shi
    • , Wonho Shin
    • , Hai Shu
    • , Himanshu Sinha
    • , Donna K. Slonim
    • , Lionel Spinelli
    • , Suhas Srinivasan
    • , Aravind Subramanian
    • , Christine Suver
    • , Damian Szklarczyk
    • , Sabina Tangaro
    • , Suresh Thiagarajan
    • , Laurent Tichit
    • , Thorsten Tiede
    • , Beethika Tripathi
    • , Aviad Tsherniak
    • , Tatsuhiko Tsunoda
    • , Dénes Türei
    • , Ehsan Ullah
    • , Golnaz Vahedi
    • , Alberto Valdeolivas
    • , Jayaswal Vivek
    • , Christian von Mering
    • , Andra Waagmeester
    • , Bo Wang
    • , Yijie Wang
    • , Barbara A. Weir
    • , Shana White
    • , Sebastian Winkler
    • , Ke Xu
    • , Taosheng Xu
    • , Chunhua Yan
    • , Liuqing Yang
    • , Kaixian Yu
    • , Xiangtian Yu
    • , Gaia Zaffaroni
    • , Mikhail Zaslavskiy
    • , Tao Zeng
    • , Jitao D. Zhang
    • , Lu Zhang
    • , Weijia Zhang
    • , Lixia Zhang
    • , Xinyu Zhang
    • , Junpeng Zhang
    • , Xin Zhou
    • , Jiarui Zhou
    • , Hongtu Zhu
    • , Junjie Zhu
    • , Guido Zuccon
    • , Aravind Subramanian
    • , Jitao D. Zhang
    • , Gustavo Stolovitzky
    • , Zoltán Kutalik
    • , Kasper Lage
    • , Donna K. Slonim
    • , Julio Saez-Rodriguez
    • , Lenore J. Cowen
    • , Sven Bergmann
    •  & Daniel Marbach

Brief Communications

  • Brief Communication |

    Single-molecule oblique-plane microscopy (obSTORM) enables deep volumetric super-resolution imaging in a light-sheet microscopy platform that is convenient for standard tissues and small intact animals.

    • Jeongmin Kim
    • , Michal Wojcik
    • , Yuan Wang
    • , Seonah Moon
    • , Emilia A. Zin
    • , Nadia Marnani
    • , Zachary L. Newman
    • , John G. Flannery
    • , Ke Xu
    •  & Xiang Zhang
  • Brief Communication |

    By embedding DNA sequences that are known to bind transcription factors in vitro together with labels for the TFs in a high-dimensional space, the machine learning approach BindSpace distinguishes between the binding preferences of even closely related TFs.

    • Han Yuan
    • , Meghana Kshirsagar
    • , Lee Zamparo
    • , Yuheng Lu
    •  & Christina S. Leslie
  • Brief Communication |

    Pepper, an RNA aptamer that prevents degradation of degron-tagged fluorescent proteins, enables fully genetically encoded fluorescence imaging of mRNA in living cells.

    • Jiahui Wu
    • , Sara Zaccara
    • , Deepak Khuperkar
    • , Hyaeyeong Kim
    • , Marvin E. Tanenbaum
    •  & Samie R. Jaffrey
  • Brief Communication |

    BigStitcher enables fast and accurate alignment and reconstruction of terabyte-sized imaging datasets of cleared and expanded samples.

    • David Hörl
    • , Fabio Rojas Rusak
    • , Friedrich Preusser
    • , Paul Tillberg
    • , Nadine Randel
    • , Raghav K. Chhetri
    • , Albert Cardona
    • , Philipp J. Keller
    • , Hartmann Harz
    • , Heinrich Leonhardt
    • , Mathias Treier
    •  & Stephan Preibisch
  • Brief Communication |

    SAVER-X trains a deep neural network for transfer learning that improves the quality of scRNA-seq data using prior information learnt from existing public studies.

    • Jingshu Wang
    • , Divyansh Agarwal
    • , Mo Huang
    • , Gang Hu
    • , Zilu Zhou
    • , Chengzhong Ye
    •  & Nancy R. Zhang

Articles

Amendments & Corrections