Latest Research

  • Article |

    Segmental Duplication Assembler (SDA) uses long sequence reads to resolve segmental duplications that are collapsed in current genome assemblies. These assemblies correspond in total to the length of an average human chromosome.

    • Mitchell R. Vollger
    • , Philip C. Dishuck
    • , Melanie Sorensen
    • , AnneMarie E. Welch
    • , Vy Dang
    • , Max L. Dougherty
    • , Tina A. Graves-Lindsay
    • , Richard K. Wilson
    • , Mark J. P. Chaisson
    •  & Evan E. Eichler
  • Brief Communication |

    The length of the guide RNA for Cas12a-VPR determines whether a target gene is edited or activated and allows for multiplexed, combinatorial gene modifications.

    • Marco Breinig
    • , Anabel Y. Schweitzer
    • , Anna M. Herianto
    • , Steffie Revia
    • , Lisa Schaefer
    • , Lena Wendler
    • , Ana Cobos Galvez
    •  & Darjus F. Tschaharganeh
  • Article |

    Deep learning enables cross-modality super-resolution imaging, including confocal-to-STED and TIRF-to-TIRF-SIM image transformation. Imaging of a larger FOV and greater depth of field is possible with higher resolution and SNR at lower light doses.

    • Hongda Wang
    • , Yair Rivenson
    • , Yiyin Jin
    • , Zhensong Wei
    • , Ronald Gao
    • , Harun Günaydın
    • , Laurent A. Bentolila
    • , Comert Kural
    •  & Aydogan Ozcan
  • Brief Communication |

    DART-seq alters droplet sequencing in a simple and flexible way to simultaneously profile the transcriptome and multiplexed targeted RNAs, such as viral transcripts and immunoglobulin chains, in single cells.

    • Mridusmita Saikia
    • , Philip Burnham
    • , Sara H. Keshavjee
    • , Michael F. Z. Wang
    • , Michael Heyang
    • , Pablo Moral-Lopez
    • , Meleana M. Hinchman
    • , Charles G. Danko
    • , John S. L. Parker
    •  & Iwijn De Vlaminck
  • Brief Communication |

    A user-friendly ImageJ plugin enables the application and training of U-Nets for deep-learning-based image segmentation, detection and classification tasks with minimal labeling requirements.

    • Thorsten Falk
    • , Dominic Mai
    • , Robert Bensch
    • , Özgün Çiçek
    • , Ahmed Abdulkadir
    • , Yassine Marrakchi
    • , Anton Böhm
    • , Jan Deubner
    • , Zoe Jäckel
    • , Katharina Seiwald
    • , Alexander Dovzhenko
    • , Olaf Tietz
    • , Cristina Dal Bosco
    • , Sean Walsh
    • , Deniz Saltukoglu
    • , Tuan Leng Tay
    • , Marco Prinz
    • , Klaus Palme
    • , Matias Simons
    • , Ilka Diester
    • , Thomas Brox
    •  & Olaf Ronneberger
  • Brief Communication |

    U-ExM enables near-native expansion microscopy of samples in vitro and in cells. The combination of U-ExM with confocal microscopy and HyVolution revealed details of centriole chirality that were previously accessible only by electron microscopy.

    • Davide Gambarotto
    • , Fabian U. Zwettler
    • , Maeva Le Guennec
    • , Marketa Schmidt-Cernohorska
    • , Denis Fortun
    • , Susanne Borgers
    • , Jörn Heine
    • , Jan-Gero Schloetel
    • , Matthias Reuss
    • , Michael Unser
    • , Edward S. Boyden
    • , Markus Sauer
    • , Virginie Hamel
    •  & Paul Guichard
  • Article |

    The DNA-based, ratiometric fluorescent reporter CalipHluor enables quantitative imaging of pH and calcium in acidic organelles with single-organelle resolution. The probe was used to identify a lysosome-specific Ca2+ importer in animals.

    • Nagarjun Narayanaswamy
    • , Kasturi Chakraborty
    • , Anand Saminathan
    • , Elizabeth Zeichner
    • , KaHo Leung
    • , John Devany
    •  & Yamuna Krishnan
  • Article |

    fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

    • Oscar Esteban
    • , Christopher J. Markiewicz
    • , Ross W. Blair
    • , Craig A. Moodie
    • , A. Ilkay Isik
    • , Asier Erramuzpe
    • , James D. Kent
    • , Mathias Goncalves
    • , Elizabeth DuPre
    • , Madeleine Snyder
    • , Hiroyuki Oya
    • , Satrajit S. Ghosh
    • , Jessey Wright
    • , Joke Durnez
    • , Russell A. Poldrack
    •  & Krzysztof J. Gorgolewski
  • Article |

    An ex vivo 3D culture model of mycobacterial granulomas recapitulates the in vivo physiology of these structures and enables longitudinal imaging studies. The platform allows genetic and pharmacological manipulation of this key structure.

    • Mark R. Cronan
    • , Molly A. Matty
    • , Allison F. Rosenberg
    • , Landry Blanc
    • , Charlie J. Pyle
    • , Scott T. Espenschied
    • , John F. Rawls
    • , Véronique Dartois
    •  & David M. Tobin
  • Article |

    Imaging of neuronal activity across the whole zebrafish brain in combination with online analysis allows for manipulating neuronal activity according to function. This approach is used to ablate or activate neurons in fictively swimming zebrafish larvae.

    • Nikita Vladimirov
    • , Chen Wang
    • , Burkhard Höckendorf
    • , Avinash Pujala
    • , Masashi Tanimoto
    • , Yu Mu
    • , Chao-Tsung Yang
    • , Jason D. Wittenbach
    • , Jeremy Freeman
    • , Stephan Preibisch
    • , Minoru Koyama
    • , Philipp J. Keller
    •  & Misha B. Ahrens
  • Brief Communication |

    The combination of positive and negative selection strategies, paired with the use of shRNAs to avoid random integration, allows efficient and scarless CRISPR-based homologous recombination.

    • Kazuya Ikeda
    • , Nobuko Uchida
    • , Toshinobu Nishimura
    • , Joseph White
    • , Renata M. Martin
    • , Hiromitsu Nakauchi
    • , Vittorio Sebastiano
    • , Kenneth I. Weinberg
    •  & Matthew H. Porteus
  • Article |

    A particle-filter algorithm for single-particle cryo-electron microscopy, implemented in a tool called THUNDER, provides high-dimensional parameter estimation, improving the obtainable resolution for several protein structures.

    • Mingxu Hu
    • , Hongkun Yu
    • , Kai Gu
    • , Zhao Wang
    • , Huabin Ruan
    • , Kunpeng Wang
    • , Siyuan Ren
    • , Bing Li
    • , Lin Gan
    • , Shizhen Xu
    • , Guangwen Yang
    • , Yuan Shen
    •  & Xueming Li
  • Article |

    scVI is a ready-to-use generative deep learning tool for large-scale single-cell RNA-seq data that enables raw data processing and a wide range of rapid and accurate downstream analyses.

    • Romain Lopez
    • , Jeffrey Regier
    • , Michael B. Cole
    • , Michael I. Jordan
    •  & Nir Yosef
  • 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
  • Article |

    YETI puts individual -omics experiments in the context of public genomics data by creating an integrated dataset-specific functional network, thus allowing more thorough interpretation of the data.

    • Young-suk Lee
    • , Aaron K. Wong
    • , Alicja Tadych
    • , Boris M. Hartmann
    • , Christopher Y. Park
    • , Veronica A. DeJesus
    • , Irene Ramos
    • , Elena Zaslavsky
    • , Stuart C. Sealfon
    •  & Olga G. Troyanskaya
  • Article |

    Content-aware image restoration (CARE) uses deep learning to improve microscopy images. CARE bypasses the trade-offs between imaging speed, resolution, and maximal light exposure that limit fluorescence imaging to enable discovery.

    • Martin Weigert
    • , Uwe Schmidt
    • , Tobias Boothe
    • , Andreas Müller
    • , Alexandr Dibrov
    • , Akanksha Jain
    • , Benjamin Wilhelm
    • , Deborah Schmidt
    • , Coleman Broaddus
    • , Siân Culley
    • , Mauricio Rocha-Martins
    • , Fabián Segovia-Miranda
    • , Caren Norden
    • , Ricardo Henriques
    • , Marino Zerial
    • , Michele Solimena
    • , Jochen Rink
    • , Pavel Tomancak
    • , Loic Royer
    • , Florian Jug
    •  & Eugene W. Myers
  • Article |

    The machine learning approach FIT leverages public mouse and human expression data to improve the translation of mouse model results to analogous human disease.

    • Rachelly Normand
    • , Wenfei Du
    • , Mayan Briller
    • , Renaud Gaujoux
    • , Elina Starosvetsky
    • , Amit Ziv-Kenet
    • , Gali Shalev-Malul
    • , Robert J. Tibshirani
    •  & Shai S. Shen-Orr
  • Brief Communication |

    An AAV-based platform achieves sparse yet bright labeling of neurons with cell-type specificity. This technology will facilitate the reconstruction of neurons in the mouse brain.

    • Rui Lin
    • , Ruiyu Wang
    • , Jing Yuan
    • , Qiru Feng
    • , Youtong Zhou
    • , Shaoqun Zeng
    • , Miao Ren
    • , Siqi Jiang
    • , Hong Ni
    • , Can Zhou
    • , Hui Gong
    •  & Minmin Luo
  • Article |

    VARNAM is a red-shifted genetically encoded voltage sensor based on the Ace opsin. It is applied in Drosophila, mouse brain slices and behaving mice. It can be readily combined with blue-light-sensitive tools for dual-color applications.

    • Madhuvanthi Kannan
    • , Ganesh Vasan
    • , Cheng Huang
    • , Simon Haziza
    • , Jin Zhong Li
    • , Hakan Inan
    • , Mark J. Schnitzer
    •  & Vincent A. Pieribone
  • Brief Communication |

    A closed-loop all-optical strategy allows manipulation of neurons on the basis of their ongoing activity and can be used to clamp neuronal activity to a preset level, boost sensory-evoked activity or yoke together the activity of trigger and target neurons.

    • Zihui Zhang
    • , Lloyd E. Russell
    • , Adam M. Packer
    • , Oliver M. Gauld
    •  & Michael Häusser
  • Brief Communication |

    FLIRT enables spatiotemporally precise control of protein function in C. elegans by harnessing existing temperature-sensitive mutations. Proteins can be inactivated at desired sites by infrared laser light targeted to the region(s) of interest.

    • Sophia M. Hirsch
    • , Sriramkumar Sundaramoorthy
    • , Tim Davies
    • , Yelena Zhuravlev
    • , Jennifer C. Waters
    • , Mimi Shirasu-Hiza
    • , Julien Dumont
    •  & Julie C. Canman
  • Brief Communication |

    osmFISH applies automated cycles of single-molecule fluorescence in situ hybridization without barcoding to provide spatial gene expression in tissue sections at high sensitivity, accuracy and throughput.

    • Simone Codeluppi
    • , Lars E. Borm
    • , Amit Zeisel
    • , Gioele La Manno
    • , Josina A. van Lunteren
    • , Camilla I. Svensson
    •  & Sten Linnarsson
  • Brief Communication |

    This paper describes a platform for carrying out antibody-based capture and mass spectrometry in parallel, and tests the feasibility of this platform for high-throughput validation of antibodies.

    • Krzysztof Sikorski
    • , Adi Mehta
    • , Marit Inngjerdingen
    • , Flourina Thakor
    • , Simon Kling
    • , Tomas Kalina
    • , Tuula A. Nyman
    • , Maria Ekman Stensland
    • , Wei Zhou
    • , Gustavo A. de Souza
    • , Lars Holden
    • , Jan Stuchly
    • , Markus Templin
    •  & Fridtjof Lund-Johansen
  • Brief Communication |

    A data-collection strategy using a fixed-target crystallography chip allows time-resolved serial synchrotron crystallography experiments to determine enzyme intermediate structures with time resolutions of milliseconds to seconds.

    • Eike C. Schulz
    • , Pedram Mehrabi
    • , Henrike M. Müller-Werkmeister
    • , Friedjof Tellkamp
    • , Ajay Jha
    • , William Stuart
    • , Elke Persch
    • , Raoul De Gasparo
    • , François Diederich
    • , Emil F. Pai
    •  & R. J. Dwayne Miller
  • Article |

    BLINK2 is a light-activated potassium channel for optogenetic inhibition of neuronal activity. Alberio et al. apply the tool in systems as diverse as cultured rat neurons, mouse brain slices, behaving zebrafish and a rat model of neuropathic pain.

    • Laura Alberio
    • , Andrea Locarno
    • , Andrea Saponaro
    • , Edoardo Romano
    • , Valérie Bercier
    • , Shahad Albadri
    • , Federica Simeoni
    • , Silvia Moleri
    • , Silvia Pelucchi
    • , Alessandro Porro
    • , Elena Marcello
    • , Noemi Barsotti
    • , Kerri Kukovetz
    • , Arjen J. Boender
    • , Andrea Contestabile
    • , Shizhen Luo
    • , Aubin Moutal
    • , Yingshi Ji
    • , Giulia Romani
    • , Monica Beltrame
    • , Filippo Del Bene
    • , Monica Di Luca
    • , Rajesh Khanna
    • , Henry M. Colecraft
    • , Massimo Pasqualetti
    • , Gerhard Thiel
    • , Raffaella Tonini
    •  & Anna Moroni
  • 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
  • Resource |

    A library of mutant mouse lung endothelial cells expressing a comprehensive repertoire of heparin sulfate structure modifications enables studies of the structure–function relationships of this complex polysaccharide.

    • Hong Qiu
    • , Songshan Shi
    • , Jingwen Yue
    • , Meng Xin
    • , Alison V. Nairn
    • , Lei Lin
    • , Xinyue Liu
    • , Guoyun Li
    • , Stephanie A. Archer-Hartmann
    • , Mitche Dela Rosa
    • , Melina Galizzi
    • , Shunchun Wang
    • , Fuming Zhang
    • , Parastoo Azadi
    • , Toin H. van Kuppevelt
    • , Wellington V. Cardoso
    • , Koji Kimata
    • , Xingbin Ai
    • , Kelley W. Moremen
    • , Jeffrey D. Esko
    • , Robert J. Linhardt
    •  & Lianchun Wang
  • Brief Communication |

    Variants of the genetically encoded sensor iGluSnFR extend the range of conditions under which glutamate neurotransmission can be visualized. In addition, chromatic variants of iGluSnFR improve compatibility with various illumination schemes.

    • Jonathan S. Marvin
    • , Benjamin Scholl
    • , Daniel E. Wilson
    • , Kaspar Podgorski
    • , Abbas Kazemipour
    • , Johannes Alexander Müller
    • , Susanne Schoch
    • , Francisco José Urra Quiroz
    • , Nelson Rebola
    • , Huan Bao
    • , Justin P. Little
    • , Ariana N. Tkachuk
    • , Edward Cai
    • , Adam W. Hantman
    • , Samuel S.-H. Wang
    • , Victor J. DePiero
    • , Bart G. Borghuis
    • , Edwin R. Chapman
    • , Dirk Dietrich
    • , David A. DiGregorio
    • , David Fitzpatrick
    •  & Loren L. Looger
  • Article |

    HUMAnN2 uses a tiered sequence search to provide rapid and accurate species-level functional profiles of microbial communities from metagenomic and metatranscriptomic data.

    • Eric A. Franzosa
    • , Lauren J. McIver
    • , Gholamali Rahnavard
    • , Luke R. Thompson
    • , Melanie Schirmer
    • , George Weingart
    • , Karen Schwarzberg Lipson
    • , Rob Knight
    • , J. Gregory Caporaso
    • , Nicola Segata
    •  & Curtis Huttenhower
  • Brief Communication |

    Multiple MS2 loops inserted in the first loop of an sgRNA after the spacer sequence stabilize the sgRNA and allow recruitment of multicolor fluorescent proteins for imaging of low-repeat genomic loci.

    • Hanhui Ma
    • , Li-Chun Tu
    • , Ardalan Naseri
    • , Yu-Chieh Chung
    • , David Grunwald
    • , Shaojie Zhang
    •  & Thoru Pederson
  • Brief Communication |

    The deep neural network smNet extracts multiplexed parameters such as 3D position, orientation and wavefront distortion from emission patterns of single molecules.

    • Peiyi Zhang
    • , Sheng Liu
    • , Abhishek Chaurasia
    • , Donghan Ma
    • , Michael J. Mlodzianoski
    • , Eugenio Culurciello
    •  & Fang Huang
  • Brief Communication |

    CASANOVA uses LOV and blue light to regulate CRISPR activity.

    • Felix Bubeck
    • , Mareike D. Hoffmann
    • , Zander Harteveld
    • , Sabine Aschenbrenner
    • , Andreas Bietz
    • , Max C. Waldhauer
    • , Kathleen Börner
    • , Julia Fakhiri
    • , Carolin Schmelas
    • , Laura Dietz
    • , Dirk Grimm
    • , Bruno E. Correia
    • , Roland Eils
    •  & Dominik Niopek
  • Publisher Correction |

    • Björn Hellenkamp
    • , Sonja Schmid
    • , Olga Doroshenko
    • , Oleg Opanasyuk
    • , Ralf Kühnemuth
    • , Soheila Rezaei Adariani
    • , Benjamin Ambrose
    • , Mikayel Aznauryan
    • , Anders Barth
    • , Victoria Birkedal
    • , Mark E. Bowen
    • , Hongtao Chen
    • , Thorben Cordes
    • , Tobias Eilert
    • , Carel Fijen
    • , Christian Gebhardt
    • , Markus Götz
    • , Giorgos Gouridis
    • , Enrico Gratton
    • , Taekjip Ha
    • , Pengyu Hao
    • , Christian A. Hanke
    • , Andreas Hartmann
    • , Jelle Hendrix
    • , Lasse L. Hildebrandt
    • , Verena Hirschfeld
    • , Johannes Hohlbein
    • , Boyang Hua
    • , Christian G. Hübner
    • , Eleni Kallis
    • , Achillefs N. Kapanidis
    • , Jae-Yeol Kim
    • , Georg Krainer
    • , Don C. Lamb
    • , Nam Ki Lee
    • , Edward A. Lemke
    • , Brié Levesque
    • , Marcia Levitus
    • , James J. McCann
    • , Nikolaus Naredi-Rainer
    • , Daniel Nettels
    • , Thuy Ngo
    • , Ruoyi Qiu
    • , Nicole C. Robb
    • , Carlheinz Röcker
    • , Hugo Sanabria
    • , Michael Schlierf
    • , Tim Schröder
    • , Benjamin Schuler
    • , Henning Seidel
    • , Lisa Streit
    • , Johann Thurn
    • , Philip Tinnefeld
    • , Swati Tyagi
    • , Niels Vandenberk
    • , Andrés Manuel Vera
    • , Keith R. Weninger
    • , Bettina Wünsch
    • , Inna S. Yanez-Orozco
    • , Jens Michaelis
    • , Claus A. M. Seidel
    • , Timothy D. Craggs
    •  & Thorsten Hugel
  • Article |

    The combination of transparency, small brain size and genetic access positions Danionella translucida as a promising model organism for functional imaging of neuronal circuits, especially during complex behaviors in adults.

    • Lisanne Schulze
    • , Jörg Henninger
    • , Mykola Kadobianskyi
    • , Thomas Chaigne
    • , Ana Isabel Faustino
    • , Nahid Hakiy
    • , Shahad Albadri
    • , Markus Schuelke
    • , Leonard Maler
    • , Filippo Del Bene
    •  & Benjamin Judkewitz
  • Article |

    Guide Swap challenges the hypothesis that Cas9–sgRNA binding is irreversible. The authors find that instead, nontargeting sgRNAs are swapped for targeting sgRNAs in the Cas9 complex. The method allows genome-scale functional screens in primary cells

    • Pamela Y. Ting
    • , Albert E. Parker
    • , J. Scott Lee
    • , Chris Trussell
    • , Orzala Sharif
    • , Fabio Luna
    • , Glenn Federe
    • , S. Whitney Barnes
    • , John R. Walker
    • , Julie Vance
    • , Mu-Yun Gao
    • , Heath E. Klock
    • , Scott Clarkson
    • , Carsten Russ
    • , Loren J. Miraglia
    • , Michael P. Cooke
    • , Anthony E. Boitano
    • , Peter McNamara
    • , John Lamb
    • , Christian Schmedt
    •  & Jennifer L. Snead
  • Article |

    A charge-integrating pixel-array detector called JUNGFRAU enables the collection of highly accurate X-ray crystallography data at synchrotron sources at unprecedented speeds.

    • Filip Leonarski
    • , Sophie Redford
    • , Aldo Mozzanica
    • , Carlos Lopez-Cuenca
    • , Ezequiel Panepucci
    • , Karol Nass
    • , Dmitry Ozerov
    • , Laura Vera
    • , Vincent Olieric
    • , Dominik Buntschu
    • , Roman Schneider
    • , Gemma Tinti
    • , Erik Froejdh
    • , Kay Diederichs
    • , Oliver Bunk
    • , Bernd Schmitt
    •  & Meitian Wang
  • Brief Communication |

    The Qiita web platform provides access to large amounts of public microbial multi-omic data and enables easy analysis and meta-analysis of standardized private and public data.

    • Antonio Gonzalez
    • , Jose A. Navas-Molina
    • , Tomasz Kosciolek
    • , Daniel McDonald
    • , Yoshiki Vázquez-Baeza
    • , Gail Ackermann
    • , Jeff DeReus
    • , Stefan Janssen
    • , Austin D. Swafford
    • , Stephanie B. Orchanian
    • , Jon G. Sanders
    • , Joshua Shorenstein
    • , Hannes Holste
    • , Semar Petrus
    • , Adam Robbins-Pianka
    • , Colin J. Brislawn
    • , Mingxun Wang
    • , Jai Ram Rideout
    • , Evan Bolyen
    • , Matthew Dillon
    • , J. Gregory Caporaso
    • , Pieter C. Dorrestein
    •  & Rob Knight