Articles

  • Article |

    The Ribosolve pipeline combines single-particle cryo-EM, M2-seq biochemical analysis and Rosetta auto-DRRAFTER modeling to guide three-dimensional RNA structure determination.

    • Kalli Kappel
    • , Kaiming Zhang
    • , Zhaoming Su
    • , Andrew M. Watkins
    • , Wipapat Kladwang
    • , Shanshan Li
    • , Grigore Pintilie
    • , Ved V. Topkar
    • , Ramya Rangan
    • , Ivan N. Zheludev
    • , Joseph D. Yesselman
    • , Wah Chiu
    •  & Rhiju Das
  • Article |

    Small vibrational tags (azide, 13C-edited carbonyl and deuterium-labeled probes) were introduced as metabolic probes for mid-infrared imaging. The tags allow unprecedented in situ visualization of metabolism in cells and animals with high information throughput.

    • Lixue Shi
    • , Xinwen Liu
    • , Lingyan Shi
    • , H. Ted Stinson
    • , Jeremy Rowlette
    • , Lisa J. Kahl
    • , Christopher R. Evans
    • , Chaogu Zheng
    • , Lars E. P. Dietrich
    •  & Wei Min
  • Article |

    PULSE is an optogenetic tool that consists of two modules with different wavelength sensitivities. Their interplay enables optogenetic access to gene expression in plants independently of ambient light.

    • Rocio Ochoa-Fernandez
    • , Nikolaj B. Abel
    • , Franz-Georg Wieland
    • , Jenia Schlegel
    • , Leonie-Alexa Koch
    • , J. Benjamin Miller
    • , Raphael Engesser
    • , Giovanni Giuriani
    • , Simon M. Brandl
    • , Jens Timmer
    • , Wilfried Weber
    • , Thomas Ott
    • , Rüdiger Simon
    •  & Matias D. Zurbriggen
  • Article |

    Multifocal flat illumination for field-independent imaging (mfFIFI) enables patterned illumination over an extended field of view. Integration with instant structured illumination microscope allowed for high-speed, multicolor, volumetric super-resolution imaging over 100 × 100 µm2.

    • Dora Mahecic
    • , Davide Gambarotto
    • , Kyle M. Douglass
    • , Denis Fortun
    • , Niccoló Banterle
    • , Khalid A. Ibrahim
    • , Maeva Le Guennec
    • , Pierre Gönczy
    • , Virginie Hamel
    • , Paul Guichard
    •  & Suliana Manley
  • Article |

    DeepSTORM3D uses deep learning for accurate localization of point emitters in densely labeled samples in three dimensions for volumetric localization microscopy with high temporal resolution, as well as for optimal point-spread function design.

    • Elias Nehme
    • , Daniel Freedman
    • , Racheli Gordon
    • , Boris Ferdman
    • , Lucien E. Weiss
    • , Onit Alalouf
    • , Tal Naor
    • , Reut Orange
    • , Tomer Michaeli
    •  & Yoav Shechtman
  • Article |

    Guide RNA selection plays an essential role in CRISPR screens, the Vienna Bioactivity CRISPR (VBC) scoring system provides an improved selection for sgRNAs that generate loss-of-function alleles.

    • Georg Michlits
    • , Julian Jude
    • , Matthias Hinterndorfer
    • , Melanie de Almeida
    • , Gintautas Vainorius
    • , Maria Hubmann
    • , Tobias Neumann
    • , Alexander Schleiffer
    • , Thomas Rainer Burkard
    • , Michaela Fellner
    • , Max Gijsbertsen
    • , Anna Traunbauer
    • , Johannes Zuber
    •  & Ulrich Elling
  • Article |

    Targeted sequencing of perturbation effects offers a sensitive approach to capture genes of interest in CRISPR-mediated screens, enabling genome-scale screens at higher scale and lower cost than whole-transcriptome Perturb-seq.

    • Daniel Schraivogel
    • , Andreas R. Gschwind
    • , Jennifer H. Milbank
    • , Daniel R. Leonce
    • , Petra Jakob
    • , Lukas Mathur
    • , Jan O. Korbel
    • , Christoph A. Merten
    • , Lars Velten
    •  & Lars M. Steinmetz
  • Article |

    Real-time 3D movement correction by tracking a fluorescent bead in the field of view enables functional imaging with 3D two-photon random-access microscopy in behaving mice and zebrafish.

    • Victoria A. Griffiths
    • , Antoine M. Valera
    • , Joanna YN. Lau
    • , Hana Roš
    • , Thomas J. Younts
    • , Bóris Marin
    • , Chiara Baragli
    • , Diccon Coyle
    • , Geoffrey J. Evans
    • , George Konstantinou
    • , Theo Koimtzis
    • , K. M. Naga Srinivas Nadella
    • , Sameer A. Punde
    • , Paul A. Kirkby
    • , Isaac H. Bianco
    •  & R. Angus Silver
  • Article |

    CRISPR-based microraft followed by guide RNA identification (CRaft-ID) combines microraft arrays, microscopy and CRISPR–Cas9 technology for high-content image-based phenotyping. CRaft-ID was used to identify proteins involved in stress granule formation.

    • Emily C. Wheeler
    • , Anthony Q. Vu
    • , Jaclyn M. Einstein
    • , Matthew DiSalvo
    • , Noorsher Ahmed
    • , Eric L. Van Nostrand
    • , Alexander A. Shishkin
    • , Wenhao Jin
    • , Nancy L. Allbritton
    •  & Gene W. Yeo
  • Article |

    In situ point spread function (PSF) retrieval (INSPR) enables precise single-molecule localization in 3D single-molecule localization microscopy of whole cells and tissues. It directly determines PSF from a single-molecule blinking dataset, removing errors associated with sample-induced aberrations.

    • Fan Xu
    • , Donghan Ma
    • , Kathryn P. MacPherson
    • , Sheng Liu
    • , Ye Bu
    • , Yu Wang
    • , Yu Tang
    • , Cheng Bi
    • , Tim Kwok
    • , Alexander A. Chubykin
    • , Peng Yin
    • , Sarah Calve
    • , Gary E. Landreth
    •  & Fang Huang
  • Article |

    M-CREATE is an in vivo screening strategy for identifying recombinant AAVs with desired tropism. The approach involves both positive and negative selection and yields vectors with diversified cell-type tropism that can cross the blood–brain barrier in adult mice across strains when delivered intravenously.

    • Sripriya Ravindra Kumar
    • , Timothy F. Miles
    • , Xinhong Chen
    • , David Brown
    • , Tatyana Dobreva
    • , Qin Huang
    • , Xiaozhe Ding
    • , Yicheng Luo
    • , Pétur H. Einarsson
    • , Alon Greenbaum
    • , Min J. Jang
    • , Benjamin E. Deverman
    •  & Viviana Gradinaru
  • Article |

    Light-dependent variants of Cre, Dre and Flp enable targeted sparse or single-cell labeling in mouse and zebrafish.

    • Shenqin Yao
    • , Peng Yuan
    • , Ben Ouellette
    • , Thomas Zhou
    • , Marty Mortrud
    • , Pooja Balaram
    • , Soumya Chatterjee
    • , Yun Wang
    • , Tanya L. Daigle
    • , Bosiljka Tasic
    • , Xiuli Kuang
    • , Hui Gong
    • , Qingming Luo
    • , Shaoqun Zeng
    • , Andrew Curtright
    • , Ajay Dhaka
    • , Anat Kahan
    • , Viviana Gradinaru
    • , Radosław Chrapkiewicz
    • , Mark Schnitzer
    • , Hongkui Zeng
    •  & Ali Cetin
  • Article |

    A set of isobaric labeling reagents called TMTpro enables deep quantitative comparisons of proteome measurements across 16 samples.

    • Jiaming Li
    • , Jonathan G. Van Vranken
    • , Laura Pontano Vaites
    • , Devin K. Schweppe
    • , Edward L. Huttlin
    • , Chris Etienne
    • , Premchendar Nandhikonda
    • , Rosa Viner
    • , Aaron M. Robitaille
    • , Andrew H. Thompson
    • , Karsten Kuhn
    • , Ian Pike
    • , Ryan D. Bomgarden
    • , John C. Rogers
    • , Steven P. Gygi
    •  & Joao A. Paulo
  • Article |

    3D ATAC-PALM integrates ATAC with super-resolution imaging for nanoscale views of the accessible genome. When combined with FISH, protein fluorescence and genetic perturbation, the method enables investigation of accessible chromatin in situ.

    • Liangqi Xie
    • , Peng Dong
    • , Xingqi Chen
    • , Tsung-Han S. Hsieh
    • , Sambashiva Banala
    • , Margherita De Marzio
    • , Brian P. English
    • , Yifeng Qi
    • , Seol Kyoung Jung
    • , Kyong-Rim Kieffer-Kwon
    • , Wesley R. Legant
    • , Anders S. Hansen
    • , Anton Schulmann
    • , Rafael Casellas
    • , Bin Zhang
    • , Eric Betzig
    • , Luke D. Lavis
    • , Howard Y. Chang
    • , Robert Tjian
    •  & Zhe Liu
  • Article |

    DNA-based FluoroCubes are ~6 nm small, monovalent probes that contain six organic dyes, which confer dramatic photostability relative to single dyes and offer more uniform signal compared to quantum dots for extended biological imaging.

    • Stefan Niekamp
    • , Nico Stuurman
    •  & Ronald D. Vale
  • Article |

    Cardelino leverages variant information from single-cell RNA-seq data for inferring clonal tree configuration and mapping cells to their clone of origin.

    • Davis J. McCarthy
    • , Raghd Rostom
    • , Yuanhua Huang
    • , Daniel J. Kunz
    • , Petr Danecek
    • , Marc Jan Bonder
    • , Tzachi Hagai
    • , Ruqian Lyu
    • , Helena Kilpinen
    • , Angela Goncalves
    • , Andreas Leha
    • , Vackar Afzal
    • , Kaur Alasoo
    • , Sofie Ashford
    • , Sendu Bala
    • , Dalila Bensaddek
    • , Marc Jan Bonder
    • , Francesco Paolo Casale
    • , Oliver J. Culley
    • , Anna Cuomo
    • , Petr Danecek
    • , Adam Faulconbridge
    • , Peter W. Harrison
    • , Annie Kathuria
    • , Davis J. McCarthy
    • , Shane A. McCarthy
    • , Ruta Meleckyte
    • , Yasin Memari
    • , Bogdan Mirauta
    • , Nathalie Moens
    • , Filipa Soares
    • , Alice Mann
    • , Daniel Seaton
    • , Ian Streeter
    • , Chukwuma A. Agu
    • , Alex Alderton
    • , Rachel Nelson
    • , Sarah Harper
    • , Minal Patel
    • , Alistair White
    • , Sharad R. Patel
    • , Laura Clarke
    • , Reena Halai
    • , Christopher M. Kirton
    • , Anja KolbKokocinski
    • , Philip Beales
    • , Ewan Birney
    • , Davide Danovi
    • , Angus I. Lamond
    • , Willem H. Ouwehand
    • , Ludovic Vallier
    • , Fiona M. Watt
    • , Richard Durbin
    • , Oliver Stegle
    • , Daniel J. Gaffney
    • , Wenyi Wang
    • , Daniel J. Gaffney
    • , Benjamin D. Simons
    • , Oliver Stegle
    •  & Sarah A. Teichmann
  • Article |

    VesSAP is a tissue clearing- and deep learning-based pipeline for comprehensively analyzing mouse vasculature, from large vessels to small capillaries.

    • Mihail Ivilinov Todorov
    • , Johannes Christian Paetzold
    • , Oliver Schoppe
    • , Giles Tetteh
    • , Suprosanna Shit
    • , Velizar Efremov
    • , Katalin Todorov-Völgyi
    • , Marco Düring
    • , Martin Dichgans
    • , Marie Piraud
    • , Bjoern Menze
    •  & Ali Ertürk
  • Article |

    The TooManyCells approach to scRNA-seq data facilitates efficient and unbiased identification and visualization of cell clades and rare subpopulations. Application of TooManyCells to drug-resistant leukemia cells identifies a rare resistant-like subpopulation of treatment-naive cells.

    • Gregory W. Schwartz
    • , Yeqiao Zhou
    • , Jelena Petrovic
    • , Maria Fasolino
    • , Lanwei Xu
    • , Sydney M. Shaffer
    • , Warren S. Pear
    • , Golnaz Vahedi
    •  & Robert B. Faryabi
  • Article |

    Mass cytometry in combination with a thiol-reactive barcoding strategy allows analysis and comparison of cell-type-specific signaling networks in organoids.

    • Xiao Qin
    • , Jahangir Sufi
    • , Petra Vlckova
    • , Pelagia Kyriakidou
    • , Sophie E. Acton
    • , Vivian S. W. Li
    • , Mark Nitz
    •  & Christopher J. Tape
  • Article |

    SMAC-seq combines long-read sequencing with open chromatin methylation by DNA methyltransferases to enable mapping of nucleosome position and chromatin accessibility.

    • Zohar Shipony
    • , Georgi K. Marinov
    • , Matthew P. Swaffer
    • , Nicholas A. Sinnott-Armstrong
    • , Jan M. Skotheim
    • , Anshul Kundaje
    •  & William J. Greenleaf
  • Article |

    Ubiquitous mammalian enzymes can scavenge uracil analogs, leading to non-specific background in cell-type-specific RNA labeling. This work reveals the enzymes involved and describes the uridine/cytidine kinase 2 and 2′-azidouridine pair as a highly specific and non-toxic alternative.

    • Sarah Nainar
    • , Bonnie J. Cuthbert
    • , Nathan M. Lim
    • , Whitney E. England
    • , Ke Ke
    • , Kanika Sophal
    • , Robert Quechol
    • , David L. Mobley
    • , Celia W. Goulding
    •  & Robert C. Spitale
  • Article |

    Advances in MINFLUX nanoscopy enable multicolor imaging over large fields of view, bringing true nanometer-scale fluorescence imaging to labeled structures in fixed and living cells.

    • Klaus C. Gwosch
    • , Jasmin K. Pape
    • , Francisco Balzarotti
    • , Philipp Hoess
    • , Jan Ellenberg
    • , Jonas Ries
    •  & Stefan W. Hell
  • Article |

    Phenotypic earth mover’s distance (PhEMD) facilitates the comparison of single-cell experimental conditions, each of which is a high-dimensional dataset, and identifies axes of variation among multicellular biospecimens.

    • William S. Chen
    • , Nevena Zivanovic
    • , David van Dijk
    • , Guy Wolf
    • , Bernd Bodenmiller
    •  & Smita Krishnaswamy
  • Article |

    4Pi single-molecule switching microscopy combined with ‘salvaged fluorescence’ enables improved ratiometric imaging that bypasses chromatic aberrations and allows for multicolor whole-cell imaging with sub-10-nm localization precision.

    • Yongdeng Zhang
    • , Lena K. Schroeder
    • , Mark D. Lessard
    • , Phylicia Kidd
    • , Jeeyun Chung
    • , Yuanbin Song
    • , Lorena Benedetti
    • , Yiming Li
    • , Jonas Ries
    • , Jonathan B. Grimm
    • , Luke D. Lavis
    • , Pietro De Camilli
    • , James E. Rothman
    • , David Baddeley
    •  & Joerg Bewersdorf
  • Article |

    An optogenetic strategy enables selection of proteases with improved catalytic rates. The developed TEV protease variants are well suited for biotechnology applications, including FLARE assays with substantially improved temporal resolution.

    • Mateo I. Sanchez
    •  & Alice Y. Ting
  • Article |

    The unique advantages of single-particle cryo-electron microscopy and cryo-electron tomography are combined in a method called TYGRESS, here applied to determine the structure of the intact ciliary axoneme at a resolution of 12 Å.

    • Kangkang Song
    • , Zhiguo Shang
    • , Xiaofeng Fu
    • , Xiaochu Lou
    • , Nikolaus Grigorieff
    •  & Daniela Nicastro
  • Article |

    An approach combining cryo-electron microscopy and mass spectrometry analysis of protein complexes enriched directly from cells enables structure determination of unknown complexes at atomic resolution.

    • Chi-Min Ho
    • , Xiaorun Li
    • , Mason Lai
    • , Thomas C. Terwilliger
    • , Josh R. Beck
    • , James Wohlschlegel
    • , Daniel E. Goldberg
    • , Anthony W. P. Fitzpatrick
    •  & Z. Hong Zhou
  • Article |

    Single-cell isolation following time-lapse imaging (SIFT) enables high-throughput screening of complex and dynamic phenotypes from pooled bacterial libraries. SIFT was used to generate ultraprecise synthetic gene oscillators.

    • Scott Luro
    • , Laurent Potvin-Trottier
    • , Burak Okumus
    •  & Johan Paulsson
  • Article |

    A new method of autophagy measurement is based on the detection of phospho-ATG16L1, a conserved early marker of autophagy. Sensitive detection can be achieved in multiple biological systems and assays with advantages over standard methods.

    • Wensheng Tian
    • , Reham Alsaadi
    • , Zhihao Guo
    • , Alena Kalinina
    • , Micaël Carrier
    • , Marie-Eve Tremblay
    • , Baptiste Lacoste
    • , Diane Lagace
    •  & Ryan C. Russell
  • Article |

    European XFEL allows investigation of the picosecond time range in the photocycle of photoactive yellow protein.

    • Suraj Pandey
    • , Richard Bean
    • , Tokushi Sato
    • , Ishwor Poudyal
    • , Johan Bielecki
    • , Jorvani Cruz Villarreal
    • , Oleksandr Yefanov
    • , Valerio Mariani
    • , Thomas A. White
    • , Christopher Kupitz
    • , Mark Hunter
    • , Mohamed H. Abdellatif
    • , Saša Bajt
    • , Valerii Bondar
    • , Austin Echelmeier
    • , Diandra Doppler
    • , Moritz Emons
    • , Matthias Frank
    • , Raimund Fromme
    • , Yaroslav Gevorkov
    • , Gabriele Giovanetti
    • , Man Jiang
    • , Daihyun Kim
    • , Yoonhee Kim
    • , Henry Kirkwood
    • , Anna Klimovskaia
    • , Juraj Knoska
    • , Faisal H. M. Koua
    • , Romain Letrun
    • , Stella Lisova
    • , Luis Maia
    • , Victoria Mazalova
    • , Domingo Meza
    • , Thomas Michelat
    • , Abbas Ourmazd
    • , Guido Palmer
    • , Marco Ramilli
    • , Robin Schubert
    • , Peter Schwander
    • , Alessandro Silenzi
    • , Jolanta Sztuk-Dambietz
    • , Alexandra Tolstikova
    • , Henry N. Chapman
    • , Alexandra Ros
    • , Anton Barty
    • , Petra Fromme
    • , Adrian P. Mancuso
    •  & Marius Schmidt
  • Article |

    Harmony, for the integration of single-cell transcriptomic data, identifies broad and fine-grained populations, scales to large datasets, and can integrate sequencing- and imaging-based data.

    • Ilya Korsunsky
    • , Nghia Millard
    • , Jean Fan
    • , Kamil Slowikowski
    • , Fan Zhang
    • , Kevin Wei
    • , Yuriy Baglaenko
    • , Michael Brenner
    • , Po-ru Loh
    •  & Soumya Raychaudhuri
  • Article |

    Directly sequencing RNA strands through a nanopore retains the full length of the transcript and allows for analysis of polyA tail length, transcript haplotypes and base modifications.

    • Rachael E. Workman
    • , Alison D. Tang
    • , Paul S. Tang
    • , Miten Jain
    • , John R. Tyson
    • , Roham Razaghi
    • , Philip C. Zuzarte
    • , Timothy Gilpatrick
    • , Alexander Payne
    • , Joshua Quick
    • , Norah Sadowski
    • , Nadine Holmes
    • , Jaqueline Goes de Jesus
    • , Karen L. Jones
    • , Cameron M. Soulette
    • , Terrance P. Snutch
    • , Nicholas Loman
    • , Benedict Paten
    • , Matthew Loose
    • , Jared T. Simpson
    • , Hugh E. Olsen
    • , Angela N. Brooks
    • , Mark Akeson
    •  & Winston Timp
  • Article |

    DuMPLING (dynamic μ-fluidic microscopy phenotyping of a library before in situ genotyping) enables screening of dynamic phenotypes in strain libraries and was used here to study genes that coordinate replication and cell division in Escherichia coli.

    • Daniel Camsund
    • , Michael J. Lawson
    • , Jimmy Larsson
    • , Daniel Jones
    • , Spartak Zikrin
    • , David Fange
    •  & Johan Elf
  • Article |

    Probabilistic cell typing by in situ sequencing (pciSeq), leverages previous single-cell RNA sequencing classification and multiplexed in situ RNA detection to spatially map cell types accurately in the mouse hippocampus and isocortex.

    • Xiaoyan Qian
    • , Kenneth D. Harris
    • , Thomas Hauling
    • , Dimitris Nicoloutsopoulos
    • , Ana B. Muñoz-Manchado
    • , Nathan Skene
    • , Jens Hjerling-Leffler
    •  & Mats Nilsson
  • Article |

    Deep-Z uses deep learning to go from a two-dimensional snapshot to three-dimensional fluorescence images. The method improves imaging speed while reducing light dose, and was shown to be useful for accurate structural and functional imaging of neurons in Caenorhabditis elegans.

    • Yichen Wu
    • , Yair Rivenson
    • , Hongda Wang
    • , Yilin Luo
    • , Eyal Ben-David
    • , Laurent A. Bentolila
    • , Christian Pritz
    •  & Aydogan Ozcan
  • Article |

    mmvec, a neural-network-based algorithm, uses paired multiomics data (microbial sequence counts and metabolite abundances) to compute the conditional probability of observing a metabolite in the presence of a specific microorganism.

    • James T. Morton
    • , Alexander A. Aksenov
    • , Louis Felix Nothias
    • , James R. Foulds
    • , Robert A. Quinn
    • , Michelle H. Badri
    • , Tami L. Swenson
    • , Marc W. Van Goethem
    • , Trent R. Northen
    • , Yoshiki Vazquez-Baeza
    • , Mingxun Wang
    • , Nicholas A. Bokulich
    • , Aaron Watters
    • , Se Jin Song
    • , Richard Bonneau
    • , Pieter C. Dorrestein
    •  & Rob Knight