Articles

  • Article |

    Triple-negative breast cancer is inhibited by depleting mitochondrial copper in mice.

    • Liyang Cui
    • , Arvin M. Gouw
    • , Edward L. LaGory
    • , Shenghao Guo
    • , Nabeel Attarwala
    • , Yao Tang
    • , Ji Qi
    • , Yun-Sheng Chen
    • , Zhou Gao
    • , Kerriann M. Casey
    • , Arkadiy A. Bazhin
    • , Min Chen
    • , Leeann Hu
    • , Jinghang Xie
    • , Mingxi Fang
    • , Cissy Zhang
    • , Qihua Zhu
    • , Zhiyuan Wang
    • , Amato J. Giaccia
    • , Sanjiv Sam Gambhir
    • , Weiping Zhu
    • , Dean W. Felsher
    • , Mark D. Pegram
    • , Elena A. Goun
    • , Anne Le
    •  & Jianghong Rao
  • Article |

    Interaction networks for any protein can be generated using a machine learning algorithm.

    • Joshua Broyde
    • , David R. Simpson
    • , Diana Murray
    • , Evan O. Paull
    • , Brennan W. Chu
    • , Somnath Tagore
    • , Sunny J. Jones
    • , Aaron T. Griffin
    • , Federico M. Giorgi
    • , Alexander Lachmann
    • , Peter Jackson
    • , E. Alejandro Sweet-Cordero
    • , Barry Honig
    •  & Andrea Califano
  • Article |

    An antibody-based method enables profiling of metabolic protein expression and regulation in single cells using mass spectrometry.

    • Felix J. Hartmann
    • , Dunja Mrdjen
    • , Erin McCaffrey
    • , David R. Glass
    • , Noah F. Greenwald
    • , Anusha Bharadwaj
    • , Zumana Khair
    • , Sanne G. S. Verberk
    • , Alex Baranski
    • , Reema Baskar
    • , William Graf
    • , David Van Valen
    • , Jan Van den Bossche
    • , Michael Angelo
    •  & Sean C. Bendall
  • Article |

    Of 12 serology assays tested, four detect antibodies in more than 80% of patients with COVID-19.

    • Jeffrey D. Whitman
    • , Joseph Hiatt
    • , Cody T. Mowery
    • , Brian R. Shy
    • , Ruby Yu
    • , Tori N. Yamamoto
    • , Ujjwal Rathore
    • , Gregory M. Goldgof
    • , Caroline Whitty
    • , Jonathan M. Woo
    • , Antonia E. Gallman
    • , Tyler E. Miller
    • , Andrew G. Levine
    • , David N. Nguyen
    • , Sagar P. Bapat
    • , Joanna Balcerek
    • , Sophia A. Bylsma
    • , Ana M. Lyons
    • , Stacy Li
    • , Allison Wai-yi Wong
    • , Eva Mae Gillis-Buck
    • , Zachary B. Steinhart
    • , Youjin Lee
    • , Ryan Apathy
    • , Mitchell J. Lipke
    • , Jennifer Anne Smith
    • , Tina Zheng
    • , Ian C. Boothby
    • , Erin Isaza
    • , Jackie Chan
    • , Dante D. Acenas II
    • , Jinwoo Lee
    • , Trisha A. Macrae
    • , Than S. Kyaw
    • , David Wu
    • , Dianna L. Ng
    • , Wei Gu
    • , Vanessa A. York
    • , Haig Alexander Eskandarian
    • , Perri C. Callaway
    • , Lakshmi Warrier
    • , Mary E. Moreno
    • , Justine Levan
    • , Leonel Torres
    • , Lila A. Farrington
    • , Rita P. Loudermilk
    • , Kanishka Koshal
    • , Kelsey C. Zorn
    • , Wilfredo F. Garcia-Beltran
    • , Diane Yang
    • , Michael G. Astudillo
    • , Bradley E. Bernstein
    • , Jeffrey A. Gelfand
    • , Edward T. Ryan
    • , Richelle C. Charles
    • , A. John Iafrate
    • , Jochen K. Lennerz
    • , Steve Miller
    • , Charles Y. Chiu
    • , Susan L. Stramer
    • , Michael R. Wilson
    • , Aashish Manglik
    • , Chun Jimmie Ye
    • , Nevan J. Krogan
    • , Mark S. Anderson
    • , Jason G. Cyster
    • , Joel D. Ernst
    • , Alan H. B. Wu
    • , Kara L. Lynch
    • , Caryn Bern
    • , Patrick D. Hsu
    •  & Alexander Marson
  • Article |

    Combining droplet-based ATAC-seq and mitochondrial DNA sequencing reveals clonal variation in human cells and tissues.

    • Caleb A. Lareau
    • , Leif S. Ludwig
    • , Christoph Muus
    • , Satyen H. Gohil
    • , Tongtong Zhao
    • , Zachary Chiang
    • , Karin Pelka
    • , Jeffrey M. Verboon
    • , Wendy Luo
    • , Elena Christian
    • , Daniel Rosebrock
    • , Gad Getz
    • , Genevieve M. Boland
    • , Fei Chen
    • , Jason D. Buenrostro
    • , Nir Hacohen
    • , Catherine J. Wu
    • , Martin J. Aryee
    • , Aviv Regev
    •  & Vijay G. Sankaran
  • Article |

    A system to express neoantigens in tumor cells and mice circumvents central T cell tolerance.

    • Martina Damo
    • , Brittany Fitzgerald
    • , Yisi Lu
    • , Mursal Nader
    • , Ivana William
    • , Julie F. Cheung
    • , Kelli A. Connolly
    • , Gena G. Foster
    • , Elliot Akama-Garren
    • , Da-Yae Lee
    • , Greg P. Chang
    • , Vasilena Gocheva
    • , Leah M. Schmidt
    • , Alice Boileve
    • , Josephine H. Wilson
    • , Can Cui
    • , Isabel Monroy
    • , Prashanth Gokare
    • , Peter Cabeceiras
    • , Tyler Jacks
    •  & Nikhil S. Joshi
  • Article |

    A blocking assay based on the recombinant receptor-binding domain of SARS-CoV-2 spike protein and human angiotensin-converting enzyme 2 receptor provides an alternative to conventional antibody neutralization assays requiring live virus.

    • Chee Wah Tan
    • , Wan Ni Chia
    • , Xijian Qin
    • , Pei Liu
    • , Mark I.-C. Chen
    • , Charles Tiu
    • , Zhiliang Hu
    • , Vivian Chih-Wei Chen
    • , Barnaby E. Young
    • , Wan Rong Sia
    • , Yee-Joo Tan
    • , Randy Foo
    • , Yongxiang Yi
    • , David C. Lye
    • , Danielle E. Anderson
    •  & Lin-Fa Wang
  • Article |

    Improved Cas12a variants and sgRNA design rules enhance genome-wide screens.

    • Peter C. DeWeirdt
    • , Kendall R. Sanson
    • , Annabel K. Sangree
    • , Mudra Hegde
    • , Ruth E. Hanna
    • , Marissa N. Feeley
    • , Audrey L. Griffith
    • , Teng Teng
    • , Samantha M. Borys
    • , Christine Strand
    • , J. Keith Joung
    • , Benjamin P. Kleinstiver
    • , Xuewen Pan
    • , Alan Huang
    •  & John G. Doench
  • Article |

    Off-the-shelf CAR T cells avoid immune rejection in mouse models of allogeneic cancer cell therapy.

    • Feiyan Mo
    • , Norihiro Watanabe
    • , Mary K. McKenna
    • , M. John Hicks
    • , Madhuwanti Srinivasan
    • , Diogo Gomes-Silva
    • , Erden Atilla
    • , Tyler Smith
    • , Pinar Ataca Atilla
    • , Royce Ma
    • , David Quach
    • , Helen E. Heslop
    • , Malcolm K. Brenner
    •  & Maksim Mamonkin
  • Article |

    Water contaminants are detected with freeze-dried, regulated in vitro transcription reactions.

    • Jaeyoung K. Jung
    • , Khalid K. Alam
    • , Matthew S. Verosloff
    • , Daiana A. Capdevila
    • , Morgane Desmau
    • , Phillip R. Clauer
    • , Jeong Wook Lee
    • , Peter Q. Nguyen
    • , Pablo A. Pastén
    • , Sandrine J. Matiasek
    • , Jean-François Gaillard
    • , David P. Giedroc
    • , James J. Collins
    •  & Julius B. Lucks
  • Article |

    Microscopy datasets are processed orders-of-magnitude faster with improved algorithms and deep learning.

    • Min Guo
    • , Yue Li
    • , Yijun Su
    • , Talley Lambert
    • , Damian Dalle Nogare
    • , Mark W. Moyle
    • , Leighton H. Duncan
    • , Richard Ikegami
    • , Anthony Santella
    • , Ivan Rey-Suarez
    • , Daniel Green
    • , Anastasia Beiriger
    • , Jiji Chen
    • , Harshad Vishwasrao
    • , Sundar Ganesan
    • , Victoria Prince
    • , Jennifer C. Waters
    • , Christina M. Annunziata
    • , Markus Hafner
    • , William A. Mohler
    • , Ajay B. Chitnis
    • , Arpita Upadhyaya
    • , Ted B. Usdin
    • , Zhirong Bao
    • , Daniel Colón-Ramos
    • , Patrick La Riviere
    • , Huafeng Liu
    • , Yicong Wu
    •  & Hari Shroff
  • Article |

    Transient p53 inhibition and induced cell-cycle progression increase clonal engraftment and homology-directed repair in hematopoietic stem cells.

    • Samuele Ferrari
    • , Aurelien Jacob
    • , Stefano Beretta
    • , Giulia Unali
    • , Luisa Albano
    • , Valentina Vavassori
    • , Davide Cittaro
    • , Dejan Lazarevic
    • , Chiara Brombin
    • , Federica Cugnata
    • , Anna Kajaste-Rudnitski
    • , Ivan Merelli
    • , Pietro Genovese
    •  & Luigi Naldini
  • Article |

    Single-cell analysis of COVID-19 patient samples identifies activated immune pathways that correlate with severe disease.

    • Robert Lorenz Chua
    • , Soeren Lukassen
    • , Saskia Trump
    • , Bianca P. Hennig
    • , Daniel Wendisch
    • , Fabian Pott
    • , Olivia Debnath
    • , Loreen Thürmann
    • , Florian Kurth
    • , Maria Theresa Völker
    • , Julia Kazmierski
    • , Bernd Timmermann
    • , Sven Twardziok
    • , Stefan Schneider
    • , Felix Machleidt
    • , Holger Müller-Redetzky
    • , Melanie Maier
    • , Alexander Krannich
    • , Sein Schmidt
    • , Felix Balzer
    • , Johannes Liebig
    • , Jennifer Loske
    • , Norbert Suttorp
    • , Jürgen Eils
    • , Naveed Ishaque
    • , Uwe Gerd Liebert
    • , Christof von Kalle
    • , Andreas Hocke
    • , Martin Witzenrath
    • , Christine Goffinet
    • , Christian Drosten
    • , Sven Laudi
    • , Irina Lehmann
    • , Christian Conrad
    • , Leif-Erik Sander
    •  & Roland Eils
  • Article |

    Gut microbiome composition is remodeled using small peptides.

    • Poshen B. Chen
    • , Audrey S. Black
    • , Adam L. Sobel
    • , Yannan Zhao
    • , Purba Mukherjee
    • , Bhuvan Molparia
    • , Nina E. Moore
    • , German R. Aleman Muench
    • , Jiejun Wu
    • , Weixuan Chen
    • , Antonio F. M. Pinto
    • , Bruce E. Maryanoff
    • , Alan Saghatelian
    • , Pejman Soroosh
    • , Ali Torkamani
    • , Luke J. Leman
    •  & M. Reza Ghadiri
  • Article |

    The genome-wide activity of Cas9 is measured in unprecedented detail.

    • Cicera R. Lazzarotto
    • , Nikolay L. Malinin
    • , Yichao Li
    • , Ruochi Zhang
    • , Yang Yang
    • , GaHyun Lee
    • , Eleanor Cowley
    • , Yanghua He
    • , Xin Lan
    • , Kasey Jividen
    • , Varun Katta
    • , Natalia G. Kolmakova
    • , Christopher T. Petersen
    • , Qian Qi
    • , Evgheni Strelcov
    • , Samantha Maragh
    • , Giedre Krenciute
    • , Jian Ma
    • , Yong Cheng
    •  & Shengdar Q. Tsai
  • Article |

    The location of genetic and epigenetic elements in mammalian nuclei is measured by gradual DNA fragmentation.

    • Gabriele Girelli
    • , Joaquin Custodio
    • , Tomasz Kallas
    • , Federico Agostini
    • , Erik Wernersson
    • , Bastiaan Spanjaard
    • , Ana Mota
    • , Solrun Kolbeinsdottir
    • , Eleni Gelali
    • , Nicola Crosetto
    •  & Magda Bienko
  • Article
    | Open Access

    High contiguity human genomes can be assembled de novo in 6 h using nanopore long-read sequences and the Shasta toolkit.

    • Kishwar Shafin
    • , Trevor Pesout
    • , Ryan Lorig-Roach
    • , Marina Haukness
    • , Hugh E. Olsen
    • , Colleen Bosworth
    • , Joel Armstrong
    • , Kristof Tigyi
    • , Nicholas Maurer
    • , Sergey Koren
    • , Fritz J. Sedlazeck
    • , Tobias Marschall
    • , Simon Mayes
    • , Vania Costa
    • , Justin M. Zook
    • , Kelvin J. Liu
    • , Duncan Kilburn
    • , Melanie Sorensen
    • , Katy M. Munson
    • , Mitchell R. Vollger
    • , Jean Monlong
    • , Erik Garrison
    • , Evan E. Eichler
    • , Sofie Salama
    • , David Haussler
    • , Richard E. Green
    • , Mark Akeson
    • , Adam Phillippy
    • , Karen H. Miga
    • , Paolo Carnevali
    • , Miten Jain
    •  & Benedict Paten
  • Article |

    Markers that distinguish pancreatic and hepatic progenitors improve stem-cell differentiation to pancreatic β cells.

    • Pallavi U. Mahaddalkar
    • , Katharina Scheibner
    • , Sandra Pfluger
    • , Ansarullah
    • , Michael Sterr
    • , Julia Beckenbauer
    • , Martin Irmler
    • , Johannes Beckers
    • , Sebastian Knöbel
    •  & Heiko Lickert
  • Article |

    Adenine base editors are evolved to be more efficient and more compatible with Cas9 variants.

    • Nicole M. Gaudelli
    • , Dieter K. Lam
    • , Holly A. Rees
    • , Noris M. Solá-Esteves
    • , Luis A. Barrera
    • , David A. Born
    • , Aaron Edwards
    • , Jason M. Gehrke
    • , Seung-Joo Lee
    • , Alexander J. Liquori
    • , Ryan Murray
    • , Michael S. Packer
    • , Conrad Rinaldi
    • , Ian M. Slaymaker
    • , Jonathan Yen
    • , Lauren E. Young
    •  & Giuseppe Ciaramella
  • Article |

    Mosquitoes are nearly eradicated in three suburbs of California using accurately sorted sterile male mosquitoes.

    • Jacob E. Crawford
    • , David W. Clarke
    • , Victor Criswell
    • , Mark Desnoyer
    • , Devon Cornel
    • , Brittany Deegan
    • , Kyle Gong
    • , Kaycie C. Hopkins
    • , Paul Howell
    • , Justin S. Hyde
    • , Josh Livni
    • , Charlie Behling
    • , Renzo Benza
    • , Willa Chen
    • , Karen L. Dobson
    • , Craig Eldershaw
    • , Daniel Greeley
    • , Yi Han
    • , Bridgette Hughes
    • , Evdoxia Kakani
    • , Joe Karbowski
    • , Angus Kitchell
    • , Erika Lee
    • , Teresa Lin
    • , Jianyi Liu
    • , Martin Lozano
    • , Warren MacDonald
    • , James W. Mains
    • , Matty Metlitz
    • , Sara N. Mitchell
    • , David Moore
    • , Johanna R. Ohm
    • , Kathleen Parkes
    • , Alexandra Porshnikoff
    • , Chris Robuck
    • , Martin Sheridan
    • , Robert Sobecki
    • , Peter Smith
    • , Jessica Stevenson
    • , Jordan Sullivan
    • , Brian Wasson
    • , Allison M. Weakley
    • , Mark Wilhelm
    • , Joshua Won
    • , Ari Yasunaga
    • , William C. Chan
    • , Jodi Holeman
    • , Nigel Snoad
    • , Linus Upson
    • , Tiantian Zha
    • , Stephen L. Dobson
    • , F. Steven Mulligan
    • , Peter Massaro
    •  & Bradley J. White
  • Article |

    A continuously evolved adenine base editor is compatible with various Cas proteins and mediates efficient A•T-to-G•C base conversions at a wide variety of PAM sites.

    • Michelle F. Richter
    • , Kevin T. Zhao
    • , Elliot Eton
    • , Audrone Lapinaite
    • , Gregory A. Newby
    • , Benjamin W. Thuronyi
    • , Christopher Wilson
    • , Luke W. Koblan
    • , Jing Zeng
    • , Daniel E. Bauer
    • , Jennifer A. Doudna
    •  & David R. Liu
  • Article |

    T cell receptors are identified in large-scale screening of T cell repertoires cloned from primary human T cells.

    • Matthew J. Spindler
    • , Ayla L. Nelson
    • , Ellen K. Wagner
    • , Natasha Oppermans
    • , John S. Bridgeman
    • , James M. Heather
    • , Adam S. Adler
    • , Michael A. Asensio
    • , Robert C. Edgar
    • , Yoong Wearn Lim
    • , Everett H. Meyer
    • , Robert E. Hawkins
    • , Mark Cobbold
    •  & David S. Johnson
  • Article |

    PIC-seq characterizes cellular crosstalk by sorting and sequencing physically interacting cells.

    • Amir Giladi
    • , Merav Cohen
    • , Chiara Medaglia
    • , Yael Baran
    • , Baoguo Li
    • , Mor Zada
    • , Pierre Bost
    • , Ronnie Blecher-Gonen
    • , Tomer-Meir Salame
    • , Johannes U. Mayer
    • , Eyal David
    • , Franca Ronchese
    • , Amos Tanay
    •  & Ido Amit
  • Article |

    The protein complexes associated with specific chromatin marks in living cells are identified using engineered binding proteins.

    • Rodrigo Villaseñor
    • , Ramon Pfaendler
    • , Christina Ambrosi
    • , Stefan Butz
    • , Sara Giuliani
    • , Elana Bryan
    • , Thomas W. Sheahan
    • , Annika L. Gable
    • , Nina Schmolka
    • , Massimiliano Manzo
    • , Joël Wirz
    • , Christian Feller
    • , Christian von Mering
    • , Ruedi Aebersold
    • , Philipp Voigt
    •  & Tuncay Baubec
  • Article |

    Nematode bacterial symbionts were evolved in vitro to resist insect-sequestered plant toxins to improve the insect-killing efficacy of their nematode host.

    • Ricardo A. R. Machado
    • , Lisa Thönen
    • , Carla C. M. Arce
    • , Vanitha Theepan
    • , Fausto Prada
    • , Daniel Wüthrich
    • , Christelle A. M. Robert
    • , Evangelia Vogiatzaki
    • , Yi-Ming Shi
    • , Olivier P. Schaeren
    • , Matheus Notter
    • , Rémy Bruggmann
    • , Siegfried Hapfelmeier
    • , Helge B. Bode
    •  & Matthias Erb
  • Article |

    The efficacy of an antidepressant is predicted from an EEG signature.

    • Wei Wu
    • , Yu Zhang
    • , Jing Jiang
    • , Molly V. Lucas
    • , Gregory A. Fonzo
    • , Camarin E. Rolle
    • , Crystal Cooper
    • , Cherise Chin-Fatt
    • , Noralie Krepel
    • , Carena A. Cornelssen
    • , Rachael Wright
    • , Russell T. Toll
    • , Hersh M. Trivedi
    • , Karen Monuszko
    • , Trevor L. Caudle
    • , Kamron Sarhadi
    • , Manish K. Jha
    • , Joseph M. Trombello
    • , Thilo Deckersbach
    • , Phil Adams
    • , Patrick J. McGrath
    • , Myrna M. Weissman
    • , Maurizio Fava
    • , Diego A. Pizzagalli
    • , Martijn Arns
    • , Madhukar H. Trivedi
    •  & Amit Etkin
  • Article |

    PAM sequences without G bases can be edited with SpCas9 variants that were continuously evolved in the laboratory.

    • Shannon M. Miller
    • , Tina Wang
    • , Peyton B. Randolph
    • , Mandana Arbab
    • , Max W. Shen
    • , Tony P. Huang
    • , Zaneta Matuszek
    • , Gregory A. Newby
    • , Holly A. Rees
    •  & David R. Liu