Review Articles

  • Review Article |

    This Review discusses the principles, advantages and limitations of Brillouin microscopy, a non-invasive tool for measuring mechanical properties of biological samples in three dimensions.

    • Robert Prevedel
    • , Alba Diz-Muñoz
    • , Giancarlo Ruocco
    •  & Giuseppe Antonacci
  • Review Article |

    A Review on applications of deep machine learning in image analysis that offers practical guidance for biologists.

    • Erick Moen
    • , Dylan Bannon
    • , Takamasa Kudo
    • , William Graf
    • , Markus Covert
    •  & David Van Valen
  • Review Article |

    This Review discusses the strengths and limitations of methods to probe RNA–protein interactions.

    • Muthukumar Ramanathan
    • , Douglas F. Porter
    •  & Paul A. Khavari
  • Review Article |

    This review discusses and contrasts different acoustic-tweezer technologies and their applications in biology.

    • Adem Ozcelik
    • , Joseph Rufo
    • , Feng Guo
    • , Yuyang Gu
    • , Peng Li
    • , James Lata
    •  & Tony Jun Huang
  • Review Article |

    A review of cellular barcoding fundamentals and applications, including powerful approaches for lineage reconstruction, genetic screening, and the recording of cellular activity and neuroanatomy.

    • Justus M. Kebschull
    •  & Anthony M. Zador
  • Review Article |

    This review outlines experimental considerations, advances and challenges in microbial single-cell genome sequencing and discusses the applications and scientific questions that this approach enabled.

    • Tanja Woyke
    • , Devin F R Doud
    •  & Frederik Schulz
  • Review Article
    | Open Access

    This Review covers the steps required to create high-quality image-based profiles from high-throughput microscopy images.

    • Juan C Caicedo
    • , Sam Cooper
    • , Florian Heigwer
    • , Scott Warchal
    • , Peng Qiu
    • , Csaba Molnar
    • , Aliaksei S Vasilevich
    • , Joseph D Barry
    • , Harmanjit Singh Bansal
    • , Oren Kraus
    • , Mathias Wawer
    • , Lassi Paavolainen
    • , Markus D Herrmann
    • , Mohammad Rohban
    • , Jane Hung
    • , Holger Hennig
    • , John Concannon
    • , Ian Smith
    • , Paul A Clemons
    • , Shantanu Singh
    • , Paul Rees
    • , Peter Horvath
    • , Roger G Linington
    •  & Anne E Carpenter
  • Review Article |

    Yang and Yuste review currently available technologies for optical imaging of neural circuits, comparing them to help researchers choose optimal ones for their applications.

    • Weijian Yang
    •  & Rafael Yuste
  • Review Article |

    This Review discusses key aspects of experimental design to evaluate intergenerational and transgenerational epigenetic inheritance. It describes advantages of patrilineal and matrilineal design, and it offers advice for selecting animals for breeding and for determining the weaning scheme and group size.

    • Johannes Bohacek
    •  & Isabelle M Mansuy
  • Review Article |

    In this Review, the authors compare commonly used chromosome conformation capture techniques, describing their respective strengths and weaknesses, and provide advice for the end user on which approach and analysis method to use.

    • James O J Davies
    • , A Marieke Oudelaar
    • , Douglas R Higgs
    •  & Jim R Hughes
  • Review Article |

    Photoacoustic imaging (PAI) can bridge the gap between high resolution optical imaging and deep tissue imaging applications. This Review introduces PAI as well as various implementations for a range of biological applications.

    • Lihong V Wang
    •  & Junjie Yao
  • Review Article |

    This Review covers genetically encoded and exogenous contrast agents for photoacoustic imaging and offers guidance for choosing optimal probes for biological applications on the basis of photophysical properties, targeting and performance.

    • Judith Weber
    • , Paul C Beard
    •  & Sarah E Bohndiek
  • Review Article |

    There is a growing appreciation that mechanical forces have important roles in many aspects of biology. This review provides a survey of methods for measuring the forces exerted by cells and discusses technical barriers to their implementation.

    • William J Polacheck
    •  & Christopher S Chen
  • Review Article |

    Applications of focused ion beams for biological ultrastructure and chemical imaging, with a particular emphasis on the coupling of this technology with scanning electron microscopy, are discussed in this Review.

    • Kedar Narayan
    •  & Sriram Subramaniam
  • Review Article |

    Correlated light and electron microscopy (CLEM) gives context to biomolecules studied with fluorescence microscopy. This Review discusses recent improvements and guides readers on probes, instrumentation and sample preparation to implement CLEM.

    • Pascal de Boer
    • , Jacob P Hoogenboom
    •  & Ben N G Giepmans
  • Review Article |

    A proteogenomic approach to analyzing mass spectrometry–based proteomic data enables the discovery of novel peptides, provides peptide-level evidence of gene expression, and assists in refining gene models. Strategies for building custom sequence databases, applications benefitting from a proteogenomic approach, and challenges in interpreting data are discussed in this Review. Also in this issue, Alfaro et al. discuss the use of proteogenomic approaches for studying cancer biology.

    • Alexey I Nesvizhskii
  • Review Article |

    This Review introduces tools to build transcriptional circuits and explains how the choice of different tools can affect circuit behavior and how its operation can be affected by the cellular host.

    • Jennifer A N Brophy
    •  & Christopher A Voigt
  • Review Article |

    This first of two review articles provides an overview and practical introduction to the precise and accurate localization of single emitters for single-particle tracking and super-resolution localization microscopy.

    • Hendrik Deschout
    • , Francesca Cella Zanacchi
    • , Michael Mlodzianoski
    • , Alberto Diaspro
    • , Joerg Bewersdorf
    • , Samuel T Hess
    •  & Kevin Braeckmans
  • Review Article |

    Fourteen scientists who participated in a recent workshop to identify and address challenges of epigenome-wide association studies summarize their recommendations in this Review.

    • Karin B Michels
    • , Alexandra M Binder
    • , Sarah Dedeurwaerder
    • , Charles B Epstein
    • , John M Greally
    • , Ivo Gut
    • , E Andres Houseman
    • , Benedetta Izzi
    • , Karl T Kelsey
    • , Alexander Meissner
    • , Aleksandar Milosavljevic
    • , Kimberly D Siegmund
    • , Christoph Bock
    •  & Rafael A Irizarry
  • Review Article |

    This Review of force-distance curve-based atomic force microscopy highlights the unique capabilities of the technique to simultaneously image the architecture of complex biological systems and map their physical, chemical and biological properties at nanometer resolution.

    • Yves F Dufrêne
    • , David Martínez-Martín
    • , Izhar Medalsy
    • , David Alsteens
    •  & Daniel J Müller
  • Review Article |

    At macroscopic scales, the human connectome comprises anatomically distinct brain areas, the structural pathways connecting them and their functional interactions. Annotation of phenotypic associations with variation in the connectome and cataloging of neurophenotypes promise to transform our understanding of the human brain. In this Review, we provide a survey of magnetic resonance imaging–based measurements of functional and structural connectivity. We highlight emerging areas of development and inquiry and emphasize the importance of integrating structural and functional perspectives on brain architecture.

    • R Cameron Craddock
    • , Saad Jbabdi
    • , Chao-Gan Yan
    • , Joshua T Vogelstein
    • , F Xavier Castellanos
    • , Adriana Di Martino
    • , Clare Kelly
    • , Keith Heberlein
    • , Stan Colcombe
    •  & Michael P Milham
  • Review Article |

    The beginning of the 21st century has seen a renaissance in light microscopy and anatomical tract tracing that together are rapidly advancing our understanding of the form and function of neuronal circuits. The introduction of instruments for automated imaging of whole mouse brains, new cell type–specific and trans-synaptic tracers, and computational methods for handling the whole-brain data sets has opened the door to neuroanatomical studies at an unprecedented scale. We present an overview of the present state and future opportunities in charting long-range and local connectivity in the entire mouse brain and in linking brain circuits to function.

    • Pavel Osten
    •  & Troy W Margrie
  • Review Article |

    A review of zymography techniques is presented. Zymography approaches yield valuable information about enzyme forms and localization of activity in tissues or in whole organisms.

    • Jennifer Vandooren
    • , Nathalie Geurts
    • , Erik Martens
    • , Philippe E Van den Steen
    •  & Ghislain Opdenakker
  • Review Article |

    Representative members of the bioimage informatics community review the computational steps and some of the primary software tools available to biologists who are acquiring and analyzing microscopy-based digital image data, with a focus on open-source options.

    • Kevin W Eliceiri
    • , Michael R Berthold
    • , Ilya G Goldberg
    • , Luis Ibáñez
    • , B S Manjunath
    • , Maryann E Martone
    • , Robert F Murphy
    • , Hanchuan Peng
    • , Anne L Plant
    • , Badrinath Roysam
    • , Nico Stuurman
    • , Jason R Swedlow
    • , Pavel Tomancak
    •  & Anne E Carpenter
  • Review Article |

    In this Review, the authors take the reader through the steps needed to analyze bisulfite-treated DNA, pointing out different considerations for data in base or color space, to ensure high-quality methylome analysis.

    • Felix Krueger
    • , Benjamin Kreck
    • , Andre Franke
    •  & Simon R Andrews
  • Review Article |

    This Review covers recent technological developments to label and manipulate genes in selected populations of cells in Drosophila melanogaster. The Review is intended as a user guide to help with the selection of the best expression systems and clonal analysis techniques for developmental studies in the fly.

    • Alberto del Valle Rodríguez
    • , Dominic Didiano
    •  & Claude Desplan
  • Review Article |

    In this Review, the authors thoroughly discuss solution-state NMR spectroscopy methods used for characterizing the dynamic structure landscape of RNA molecules, from picosecond to second timescale motions.

    • Jameson R Bothe
    • , Evgenia N Nikolova
    • , Catherine D Eichhorn
    • , Jeetender Chugh
    • , Alexandar L Hansen
    •  & Hashim M Al-Hashimi
  • Review Article |

    • Nils Gehlenborg
    • , Seán I O'Donoghue
    • , Nitin S Baliga
    • , Alexander Goesmann
    • , Matthew A Hibbs
    • , Hiroaki Kitano
    • , Oliver Kohlbacher
    • , Heiko Neuweger
    • , Reinhard Schneider
    • , Dan Tenenbaum
    •  & Anne-Claude Gavin
  • Review Article |

    • Seán I O'Donoghue
    • , David S Goodsell
    • , Achilleas S Frangakis
    • , Fabrice Jossinet
    • , Roman A Laskowski
    • , Michael Nilges
    • , Helen R Saibil
    • , Andrea Schafferhans
    • , Rebecca C Wade
    • , Eric Westhof
    •  & Arthur J Olson
  • Review Article |

    • Thomas Walter
    • , David W Shattuck
    • , Richard Baldock
    • , Mark E Bastin
    • , Anne E Carpenter
    • , Suzanne Duce
    • , Jan Ellenberg
    • , Adam Fraser
    • , Nicholas Hamilton
    • , Steve Pieper
    • , Mark A Ragan
    • , Jurgen E Schneider
    • , Pavel Tomancak
    •  & Jean-Karim Hériché