Latest Research

  • 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 |

    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
  • 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
  • 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
  • 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
  • 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
  • Author Correction |

    • 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
  • Brief Communication |

    The field synthesis method for generating any scanned light sheet is based on a new mathematical theorem in Fourier analysis and has important practical implications for simpler, multicolor lattice light-sheet microscopy.

    • Bo-Jui Chang
    • , Mark Kittisopikul
    • , Kevin M. Dean
    • , Philippe Roudot
    • , Erik S. Welf
    •  & Reto Fiolka
  • Author Correction |

    • 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
  • Article |

    Cpf1-mediated genome editing of CAR-T cells enables efficient multiple targeting, knocking in chimeric antigen receptors while removing immune-checkpoint genes.

    • Xiaoyun Dai
    • , Jonathan J. Park
    • , Yaying Du
    • , Hyunu R. Kim
    • , Guangchuan Wang
    • , Youssef Errami
    •  & Sidi Chen
  • Review Article |

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

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

    Acoustic scattering in a suspended microchannel resonator can be used to measure mechanical properties of single cells in a noninvasive manner. The approach is applied to follow stiffness changes of individual cells throughout the cell cycle.

    • Joon Ho Kang
    • , Teemu P. Miettinen
    • , Lynna Chen
    • , Selim Olcum
    • , Georgios Katsikis
    • , Patrick S. Doyle
    •  & Scott R. Manalis
  • Brief Communication |

    FIt-SNE, a sped-up version of t-SNE, enables visualization of rare cell types in large datasets by obviating the need for downsampling. One-dimensional t-SNE heatmaps allow simultaneous visualization of expression patterns from thousands of genes.

    • George C. Linderman
    • , Manas Rachh
    • , Jeremy G. Hoskins
    • , Stefan Steinerberger
    •  & Yuval Kluger
  • Article |

    Culturing human kidney organoids under fluidic shear conditions leads to robust vascularization and increased maturity. These kidney organoids should serve as a better model for kidney development than those developed in static culture.

    • Kimberly A. Homan
    • , Navin Gupta
    • , Katharina T. Kroll
    • , David B. Kolesky
    • , Mark Skylar-Scott
    • , Tomoya Miyoshi
    • , Donald Mau
    • , M. Todd Valerius
    • , Thomas Ferrante
    • , Joseph V. Bonventre
    • , Jennifer A. Lewis
    •  & Ryuji Morizane
  • Brief Communication |

    RNA-guided adenosine deaminases edit point mutations in in vivo mouse models for Duchenne muscular dystrophy and ornithine transcarbamylase deficiency.

    • Dhruva Katrekar
    • , Genghao Chen
    • , Dario Meluzzi
    • , Ashwin Ganesh
    • , Atharv Worlikar
    • , Yu-Ru Shih
    • , Shyni Varghese
    •  & Prashant Mali
  • Article |

    Engineered, bifunctional receptors present antigens and initiate signaling in response to binding to the cognate T cell receptor. Libraries built with SABRs can screen thousands of epitopes for the discovery of T cell target antigens.

    • Alok V. Joglekar
    • , Michael T. Leonard
    • , John D. Jeppson
    • , Margaret Swift
    • , Guideng Li
    • , Stephanie Wong
    • , Songming Peng
    • , Jesse M. Zaretsky
    • , James R. Heath
    • , Antoni Ribas
    • , Michael T. Bethune
    •  & David Baltimore
  • Article |

    Trogocytosis, the uptake of membrane proteins by an antigen-presenting cell from its cognate T cell, allows the identification of neoepitopes targeted by T cell receptors with high sensitivity.

    • Guideng Li
    • , Michael T. Bethune
    • , Stephanie Wong
    • , Alok V. Joglekar
    • , Michael T. Leonard
    • , Jessica K. Wang
    • , Jocelyn T. Kim
    • , Donghui Cheng
    • , Songming Peng
    • , Jesse M. Zaretsky
    • , Yapeng Su
    • , Yicheng Luo
    • , James R. Heath
    • , Antoni Ribas
    • , Owen N. Witte
    •  & David Baltimore
  • Brief Communication |

    NIR-GECO1, the first near-infrared genetically encoded calcium ion (Ca2+) indicator, enables improved Ca2+ imaging in conjunction with blue-light-activated optogenetic tools and multiplexed imaging in cell cultures and tissue slices.

    • Yong Qian
    • , Kiryl D. Piatkevich
    • , Benedict Mc Larney
    • , Ahmed S. Abdelfattah
    • , Sohum Mehta
    • , Mitchell H. Murdock
    • , Sven Gottschalk
    • , Rosana S. Molina
    • , Wei Zhang
    • , Yingche Chen
    • , Jiahui Wu
    • , Mikhail Drobizhev
    • , Thomas E. Hughes
    • , Jin Zhang
    • , Eric R. Schreiter
    • , Shy Shoham
    • , Daniel Razansky
    • , Edward S. Boyden
    •  & Robert E. Campbell
  • Perspective |

    An interactive online resource integrated in the GPCRdb hub presents tools to design GPCR constructs and determine appropriate experimental conditions for structural studies by crystallography and cryo-EM.

    • Christian Munk
    • , Eshita Mutt
    • , Vignir Isberg
    • , Louise F. Nikolajsen
    • , Janne M. Bibbe
    • , Tilman Flock
    • , Michael A. Hanson
    • , Raymond C. Stevens
    • , Xavier Deupi
    •  & David E. Gloriam
  • Brief Communication |

    A single-photon detector array enables robust and versatile image scanning microscopy (ISM) on any confocal microscope. This implementation makes super-resolution FLIM possible and eases a transition from confocal microscopy to ISM.

    • Marco Castello
    • , Giorgio Tortarolo
    • , Mauro Buttafava
    • , Takahiro Deguchi
    • , Federica Villa
    • , Sami Koho
    • , Luca Pesce
    • , Michele Oneto
    • , Simone Pelicci
    • , Luca Lanzanó
    • , Paolo Bianchini
    • , Colin J. R. Sheppard
    • , Alberto Diaspro
    • , Alberto Tosi
    •  & Giuseppe Vicidomini
  • Author Correction |

    • Uri Weill
    • , Ido Yofe
    • , Ehud Sass
    • , Bram Stynen
    • , Dan Davidi
    • , Janani Natarajan
    • , Reut Ben-Menachem
    • , Zohar Avihou
    • , Omer Goldman
    • , Nofar Harpaz
    • , Silvia Chuartzman
    • , Kiril Kniazev
    • , Barbara Knoblach
    • , Janina Laborenz
    • , Felix Boos
    • , Jacqueline Kowarzyk
    • , Shifra Ben-Dor
    • , Einat Zalckvar
    • , Johannes M. Herrmann
    • , Richard A. Rachubinski
    • , Ophry Pines
    • , Doron Rapaport
    • , Stephen W. Michnick
    • , Emmanuel D. Levy
    •  & Maya Schuldiner
  • Publisher Correction |

    • 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
  • Brief Communication |

    A protocol adapted to xeno- and feeder-free conditions is shown to generate reliable and consistent cortical brain organoids across differentiations and source stem cell lines, making it suitable for disease modeling and other applications.

    • Se-Jin Yoon
    • , Lubayna S. Elahi
    • , Anca M. Pașca
    • , Rebecca M. Marton
    • , Aaron Gordon
    • , Omer Revah
    • , Yuki Miura
    • , Elisabeth M. Walczak
    • , Gwendolyn M. Holdgate
    • , H. Christina Fan
    • , John R. Huguenard
    • , Daniel H. Geschwind
    •  & Sergiu P. Pașca
  • Article |

    LEAP is a deep-learning-based approach for the analysis of animal pose. LEAP’s graphical user interface facilitates training of the deep network. The authors illustrate the method by analyzing Drosophila and mouse behavior.

    • Talmo D. Pereira
    • , Diego E. Aldarondo
    • , Lindsay Willmore
    • , Mikhail Kislin
    • , Samuel S.-H. Wang
    • , Mala Murthy
    •  & Joshua W. Shaevitz
  • Article |

    A transcriptional analysis of kidney organoids reveals batch effects as the key drivers of variation, mainly through differences in maturity, and provides a list of highly variable genes and a method for estimating differentiation stage for improved disease modeling.

    • Belinda Phipson
    • , Pei X. Er
    • , Alexander N. Combes
    • , Thomas A. Forbes
    • , Sara E. Howden
    • , Luke Zappia
    • , Hsan-Jan Yen
    • , Kynan T. Lawlor
    • , Lorna J. Hale
    • , Jane Sun
    • , Ernst Wolvetang
    • , Minoru Takasato
    • , Alicia Oshlack
    •  & Melissa H. Little
  • Analysis |

    kBET informs attempts at single-cell RNA-seq data integration by quantifying batch effects and determining how well batch regression and normalization approaches remove technical variation while preserving biological variability.

    • Maren Büttner
    • , Zhichao Miao
    • , F. Alexander Wolf
    • , Sarah A. Teichmann
    •  & Fabian J. Theis
  • Perspective |

    Expansion microscopy allows super-resolution images of diverse samples to be acquired on conventional microscopes, thus democratizing super-resolution imaging. This Perspective reviews available methods and provides practical guidance for users.

    • Asmamaw T. Wassie
    • , Yongxin Zhao
    •  & Edward S. Boyden
  • Article |

    A compressed sensing approach enables the identification of key neurons involved in a particular behavior with few measurements, using genetic tools with limited specificity. The approach is demonstrated in the C. elegans interneuron circuitry.

    • Jeffrey B. Lee
    • , Abdullah Yonar
    • , Timothy Hallacy
    • , Ching-Han Shen
    • , Josselin Milloz
    • , Jagan Srinivasan
    • , Askin Kocabas
    •  & Sharad Ramanathan
  • 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