Articles

  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Article |

    LFADS, a deep learning method for analyzing neural population activity, can extract neural dynamics from single-trial recordings, stitch separate datasets into a single model, and infer perturbations, for example, from behavioral choices to these dynamics.

    • Chethan Pandarinath
    • , Daniel J. O’Shea
    • , Jasmine Collins
    • , Rafal Jozefowicz
    • , Sergey D. Stavisky
    • , Jonathan C. Kao
    • , Eric M. Trautmann
    • , Matthew T. Kaufman
    • , Stephen I. Ryu
    • , Leigh R. Hochberg
    • , Jaimie M. Henderson
    • , Krishna V. Shenoy
    • , L. F. Abbott
    •  & David Sussillo
  • Article |

    REVOLVER uses transfer learning on multi-region tumor sequencing data to jointly infer tumor evolution models in multiple individuals and to detect repeated evolutionary trajectories. Repeated evolution can be used to stratify the cohort.

    • Giulio Caravagna
    • , Ylenia Giarratano
    • , Daniele Ramazzotti
    • , Ian Tomlinson
    • , Trevor A. Graham
    • , Guido Sanguinetti
    •  & Andrea Sottoriva
  • Article |

    Insertion of a bivalent linker between two regions of interest allows chromatin contacts to be probed without proximity ligation.

    • Binbin Lai
    • , Qingsong Tang
    • , Wenfei Jin
    • , Gangqing Hu
    • , Darawalee Wangsa
    • , Kairong Cui
    • , Benjamin Z. Stanton
    • , Gang Ren
    • , Yi Ding
    • , Ming Zhao
    • , Shuai Liu
    • , Jiuzhou Song
    • , Thomas Ried
    •  & Keji Zhao
  • Article |

    This paper describes modifications to standard culture conditions that permit the growth of naive human pluripotent stem cells with reduced genomic instability.

    • Bruno Di Stefano
    • , Mai Ueda
    • , Shan Sabri
    • , Justin Brumbaugh
    • , Aaron J. Huebner
    • , Anna Sahakyan
    • , Kendell Clement
    • , Katie J. Clowers
    • , Alison R. Erickson
    • , Keiko Shioda
    • , Steven P. Gygi
    • , Hongcang Gu
    • , Toshi Shioda
    • , Alexander Meissner
    • , Yasuhiro Takashima
    • , Kathrin Plath
    •  & Konrad Hochedlinger
  • Article |

    Spinal cord neural stem cells are generated from human pluripotent stem cells via a chemically defined, xeno-free method, and exhibit efficient and functional engraftment in rat spinal cord lesions.

    • Hiromi Kumamaru
    • , Ken Kadoya
    • , Andrew F. Adler
    • , Yoshio Takashima
    • , Lori Graham
    • , Giovanni Coppola
    •  & Mark H. Tuszynski
  • Article |

    Humanized mouse models are useful for studies of human hematopoiesis and immunity. Li et al. report an improved model that harbors lymph nodes and therefore permits investigation of local human adaptive immune processes in secondary lymphoid tissue.

    • Yan Li
    • , Guillemette Masse-Ranson
    • , Zacarias Garcia
    • , Timothée Bruel
    • , Ayrin Kök
    • , Helene Strick-Marchand
    • , Gregory Jouvion
    • , Nicolas Serafini
    • , Ai Ing Lim
    • , Mathilde Dusseaux
    • , Thierry Hieu
    • , Franck Bourgade
    • , Antoine Toubert
    • , Daniela Finke
    • , Olivier Schwartz
    • , Philippe Bousso
    • , Hugo Mouquet
    •  & James P. Di Santo
  • Article |

    A method for generating cortical spheroids from human pluripotent stem cells produces maturing oligodendrocytes that can myelinate axons and model myelin disease and drug effects.

    • Mayur Madhavan
    • , Zachary S. Nevin
    • , H. Elizabeth Shick
    • , Eric Garrison
    • , Cheryl Clarkson-Paredes
    • , Molly Karl
    • , Benjamin L. L. Clayton
    • , Daniel C. Factor
    • , Kevin C. Allan
    • , Lilianne Barbar
    • , Tanya Jain
    • , Panagiotis Douvaras
    • , Valentina Fossati
    • , Robert H. Miller
    •  & Paul J. Tesar
  • Article |

    Cerebral organoids are developed into in vitro models of human brain cancer by CRISPR–Cas9- and/or transposon-mediated introduction of oncogenic mutations.

    • Shan Bian
    • , Marko Repic
    • , Zhenming Guo
    • , Anoop Kavirayani
    • , Thomas Burkard
    • , Joshua A. Bagley
    • , Christian Krauditsch
    •  & Jürgen A. Knoblich
  • Article |

    The fusion of dead Cas9 with KRAB and the transcriptional repressor domain of the chromatin modifier MeCP2 leads to an efficient transcriptional silencer that can be applied to genome-scale screens and genetic circuits.

    • Nan Cher Yeo
    • , Alejandro Chavez
    • , Alissa Lance-Byrne
    • , Yingleong Chan
    • , David Menn
    • , Denitsa Milanova
    • , Chih-Chung Kuo
    • , Xiaoge Guo
    • , Sumana Sharma
    • , Angela Tung
    • , Ryan J. Cecchi
    • , Marcelle Tuttle
    • , Swechchha Pradhan
    • , Elaine T. Lim
    • , Noah Davidsohn
    • , Mo R. Ebrahimkhani
    • , James J. Collins
    • , Nathan E. Lewis
    • , Samira Kiani
    •  & George M. Church
  • Article |

    Flood-filling networks are a deep-learning-based pipeline for reconstruction of neurons from electron microscopy datasets. The approach results in exceptionally low error rates, thereby reducing the need for extensive human proofreading.

    • Michał Januszewski
    • , Jörgen Kornfeld
    • , Peter H. Li
    • , Art Pope
    • , Tim Blakely
    • , Larry Lindsey
    • , Jeremy Maitin-Shepard
    • , Mike Tyka
    • , Winfried Denk
    •  & Viren Jain
  • Article |

    A genome-wide collection of N-terminally tagged yeast libraries allows easy swapping of tags and exploration of the yeast proteome.

    • 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
  • Article |

    The ProximID approach generates single-cell expression profiles and a network of enriched physical cellular interactions within a tissue.

    • Jean-Charles Boisset
    • , Judith Vivié
    • , Dominic Grün
    • , Mauro J. Muraro
    • , Anna Lyubimova
    •  & Alexander van Oudenaarden