Brief Communications

  • Brief Communication |

    Optogenetic control of neural activity in the deep brain is achieved without intracranial surgery using ChRmine.

    • Ritchie Chen
    • , Felicity Gore
    • , Quynh-Anh Nguyen
    • , Charu Ramakrishnan
    • , Sneha Patel
    • , Soo Hyun Kim
    • , Misha Raffiee
    • , Yoon Seok Kim
    • , Brian Hsueh
    • , Esther Krook-Magnusson
    • , Ivan Soltesz
    •  & Karl Deisseroth
  • Brief Communication |

    Gut microbiome composition is associated with phenotypes as revealed by a dimensionality reduction tool.

    • Cameron Martino
    • , Liat Shenhav
    • , Clarisse A. Marotz
    • , George Armstrong
    • , Daniel McDonald
    • , Yoshiki Vázquez-Baeza
    • , James T. Morton
    • , Lingjing Jiang
    • , Maria Gloria Dominguez-Bello
    • , Austin D. Swafford
    • , Eran Halperin
    •  & Rob Knight
  • Brief Communication |

    Cell clones in lineage-tracing studies can be isolated for functional experiments.

    • Christian Umkehrer
    • , Felix Holstein
    • , Laura Formenti
    • , Julian Jude
    • , Kimon Froussios
    • , Tobias Neumann
    • , Shona M. Cronin
    • , Lisa Haas
    • , Jesse J. Lipp
    • , Thomas R. Burkard
    • , Michaela Fellner
    • , Thomas Wiesner
    • , Johannes Zuber
    •  & Anna C. Obenauf
  • Brief Communication |

    The cell types affected by biological perturbations in complex tissues are uncovered by single-cell analysis.

    • Michael A. Skinnider
    • , Jordan W. Squair
    • , Claudia Kathe
    • , Mark A. Anderson
    • , Matthieu Gautier
    • , Kaya J. E. Matson
    • , Marco Milano
    • , Thomas H. Hutson
    • , Quentin Barraud
    • , Aaron A. Phillips
    • , Leonard J. Foster
    • , Gioele La Manno
    • , Ariel J. Levine
    •  & Grégoire Courtine
  • Brief Communication |

    Mass spectral fragmentations of lipids across 117 lipid subclasses are presented in a lipidome atlas.

    • Hiroshi Tsugawa
    • , Kazutaka Ikeda
    • , Mikiko Takahashi
    • , Aya Satoh
    • , Yoshifumi Mori
    • , Haruki Uchino
    • , Nobuyuki Okahashi
    • , Yutaka Yamada
    • , Ipputa Tada
    • , Paolo Bonini
    • , Yasuhiro Higashi
    • , Yozo Okazaki
    • , Zhiwei Zhou
    • , Zheng-Jiang Zhu
    • , Jeremy Koelmel
    • , Tomas Cajka
    • , Oliver Fiehn
    • , Kazuki Saito
    • , Masanori Arita
    •  & Makoto Arita
  • Brief Communication |

    Base editors that modify both adenosine and cytosine broaden the potential applications of base editing.

    • Rina C. Sakata
    • , Soh Ishiguro
    • , Hideto Mori
    • , Mamoru Tanaka
    • , Kenji Tatsuno
    • , Hiroki Ueda
    • , Shogo Yamamoto
    • , Motoaki Seki
    • , Nanami Masuyama
    • , Keiji Nishida
    • , Hiroshi Nishimasu
    • , Kazuharu Arakawa
    • , Akihiko Kondo
    • , Osamu Nureki
    • , Masaru Tomita
    • , Hiroyuki Aburatani
    •  & Nozomu Yachie
  • Brief Communication |

    Base editors that modify both adenine and cytosine broaden the potential applications of base editing.

    • Xiaohui Zhang
    • , Biyun Zhu
    • , Liang Chen
    • , Ling Xie
    • , Weishi Yu
    • , Ying Wang
    • , Linxi Li
    • , Shuming Yin
    • , Lei Yang
    • , Handan Hu
    • , Honghui Han
    • , Yongmei Li
    • , Liren Wang
    • , Geng Chen
    • , Xueyun Ma
    • , Hongquan Geng
    • , Wanfeng Huang
    • , Xiufeng Pang
    • , Zuozhen Yang
    • , Yuxuan Wu
    • , Stefan Siwko
    • , Ryo Kurita
    • , Yukio Nakamura
    • , Li Yang
    • , Mingyao Liu
    •  & Dali Li
  • Brief Communication |

    A hybrid CRISPR–Cas9 variant is able to specifically and efficiently target a larger proportion of the genome.

    • Pranam Chatterjee
    • , Noah Jakimo
    • , Jooyoung Lee
    • , Nadia Amrani
    • , Tomás Rodríguez
    • , Sabrina R. T. Koseki
    • , Emma Tysinger
    • , Rui Qing
    • , Shilei Hao
    • , Erik J. Sontheimer
    •  & Joseph Jacobson
  • Brief Communication |

    Luminescence is engineered in whole plants, without an exogenous substrate, using a fungal gene cluster.

    • Tatiana Mitiouchkina
    • , Alexander S. Mishin
    • , Louisa Gonzalez Somermeyer
    • , Nadezhda M. Markina
    • , Tatiana V. Chepurnyh
    • , Elena B. Guglya
    • , Tatiana A. Karataeva
    • , Kseniia A. Palkina
    • , Ekaterina S. Shakhova
    • , Liliia I. Fakhranurova
    • , Sofia V. Chekova
    • , Aleksandra S. Tsarkova
    • , Yaroslav V. Golubev
    • , Vadim V. Negrebetsky
    • , Sergey A. Dolgushin
    • , Pavel V. Shalaev
    • , Dmitry Shlykov
    • , Olesya A. Melnik
    • , Victoria O. Shipunova
    • , Sergey M. Deyev
    • , Andrey I. Bubyrev
    • , Alexander S. Pushin
    • , Vladimir V. Choob
    • , Sergey V. Dolgov
    • , Fyodor A. Kondrashov
    • , Ilia V. Yampolsky
    •  & Karen S. Sarkisyan
  • Brief Communication |

    Prime editors are optimized for use in plants.

    • Qiupeng Lin
    • , Yuan Zong
    • , Chenxiao Xue
    • , Shengxing Wang
    • , Shuai Jin
    • , Zixu Zhu
    • , Yanpeng Wang
    • , Andrew V. Anzalone
    • , Aditya Raguram
    • , Jordan L. Doman
    • , David R. Liu
    •  & Caixia Gao
  • Brief Communication |

    Gene-edited waxy corn lines have higher yields in field trials than hybrids produced by traditional trait introgression.

    • Huirong Gao
    • , Mark J. Gadlage
    • , H. Renee Lafitte
    • , Brian Lenderts
    • , Meizhu Yang
    • , Megan Schroder
    • , Jeffry Farrell
    • , Kay Snopek
    • , Dave Peterson
    • , Lanie Feigenbutz
    • , Spencer Jones
    • , Grace St Clair
    • , Melissa Rahe
    • , Nathalie Sanyour-Doyel
    • , Chenna Peng
    • , Lijuan Wang
    • , Joshua K. Young
    • , Mary Beatty
    • , Brian Dahlke
    • , Jan Hazebroek
    • , Thomas W. Greene
    • , A. Mark Cigan
    • , N. Doane Chilcoat
    •  & R. Bob Meeley
  • Brief Communication
    | Open Access

    Efficient, large-scale genomic analysis is facilitated on the cloud by a computational tool with error-diagnosing and self-healing capabilities.

    • Sergei Yakneen
    • , Sebastian M. Waszak
    • , Sergei Yakneen
    • , Brice Aminou
    • , Javier Bartolome
    • , Keith A. Boroevich
    • , Rich Boyce
    • , Angela N. Brooks
    • , Alex Buchanan
    • , Ivo Buchhalter
    • , Adam P. Butler
    • , Niall J. Byrne
    • , Andy Cafferkey
    • , Peter J. Campbell
    • , Zhaohong Chen
    • , Sunghoon Cho
    • , Wan Choi
    • , Peter Clapham
    • , Brandi N. Davis-Dusenbery
    • , Francisco M. De La Vega
    • , Jonas Demeulemeester
    • , Michelle T. Dow
    • , Lewis Jonathan Dursi
    • , Juergen Eils
    • , Roland Eils
    • , Kyle Ellrott
    • , Claudiu Farcas
    • , Francesco Favero
    • , Nodirjon Fayzullaev
    • , Vincent Ferretti
    • , Paul Flicek
    • , Nuno A. Fonseca
    • , Josep Ll. Gelpi
    • , Gad Getz
    • , Bob Gibson
    • , Robert L. Grossman
    • , Olivier Harismendy
    • , Allison P. Heath
    • , Michael C. Heinold
    • , Julian M. Hess
    • , Oliver Hofmann
    • , Jongwhi H. Hong
    • , Thomas J. Hudson
    • , Barbara Hutter
    • , Carolyn M. Hutter
    • , Daniel Hübschmann
    • , Seiya Imoto
    • , Sinisa Ivkovic
    • , Seung-Hyup Jeon
    • , Wei Jiao
    • , Jongsun Jung
    • , Rolf Kabbe
    • , Andre Kahles
    • , Jules N. A. Kerssemakers
    • , Hyung-Lae Kim
    • , Hyunghwan Kim
    • , Jihoon Kim
    • , Youngwook Kim
    • , Kortine Kleinheinz
    • , Michael Koscher
    • , Antonios Koures
    • , Milena Kovacevic
    • , Chris Lawerenz
    • , Ignaty Leshchiner
    • , Jia Liu
    • , Dimitri Livitz
    • , George L. Mihaiescu
    • , Sanja Mijalkovic
    • , Ana Mijalkovic Lazic
    • , Satoru Miyano
    • , Naoki Miyoshi
    • , Hardeep K. Nahal-Bose
    • , Hidewaki Nakagawa
    • , Mia Nastic
    • , Steven J. Newhouse
    • , Jonathan Nicholson
    • , Brian D. O’Connor
    • , David Ocana
    • , Kazuhiro Ohi
    • , Lucila Ohno-Machado
    • , Larsson Omberg
    • , B. F Francis Ouellette
    • , Nagarajan Paramasivam
    • , Marc D. Perry
    • , Todd D. Pihl
    • , Manuel Prinz
    • , Montserrat Puiggròs
    • , Petar Radovic
    • , Keiran M. Raine
    • , Esther Rheinbay
    • , Mara Rosenberg
    • , Romina Royo
    • , Gunnar Rätsch
    • , Gordon Saksena
    • , Matthias Schlesner
    • , Solomon I. Shorser
    • , Charles Short
    • , Heidi J. Sofia
    • , Jonathan Spring
    • , Lincoln D. Stein
    • , Adam J. Struck
    • , Grace Tiao
    • , Nebojsa Tijanic
    • , David Torrents
    • , Peter Van Loo
    • , Miguel Vazquez
    • , David Vicente
    • , Jeremiah A. Wala
    • , Zhining Wang
    • , Sebastian M. Waszak
    • , Joachim Weischenfeldt
    • , Johannes Werner
    • , Ashley Williams
    • , Youngchoon Woo
    • , Adam J. Wright
    • , Qian Xiang
    • , Liming Yang
    • , Denis Yuen
    • , Christina K. Yung
    • , Junjun Zhang
    • , Jan O. Korbel
    • , Michael Gertz
    •  & Jan O. Korbel
  • Brief Communication |

    A machine learning model allows the identification of new small-molecule kinase inhibitors in days.

    • Alex Zhavoronkov
    • , Yan A. Ivanenkov
    • , Alex Aliper
    • , Mark S. Veselov
    • , Vladimir A. Aladinskiy
    • , Anastasiya V. Aladinskaya
    • , Victor A. Terentiev
    • , Daniil A. Polykovskiy
    • , Maksim D. Kuznetsov
    • , Arip Asadulaev
    • , Yury Volkov
    • , Artem Zholus
    • , Rim R. Shayakhmetov
    • , Alexander Zhebrak
    • , Lidiya I. Minaeva
    • , Bogdan A. Zagribelnyy
    • , Lennart H. Lee
    • , Richard Soll
    • , David Madge
    • , Li Xing
    • , Tao Guo
    •  & Alán Aspuru-Guzik
  • Brief Communication |

    A machine learning model based on data from primary human T cells accurately predicts repair outcomes after CRISPR–Cas9 editing.

    • Ryan T. Leenay
    • , Amirali Aghazadeh
    • , Joseph Hiatt
    • , David Tse
    • , Theodore L. Roth
    • , Ryan Apathy
    • , Eric Shifrut
    • , Judd F. Hultquist
    • , Nevan Krogan
    • , Zhenqin Wu
    • , Giana Cirolia
    • , Hera Canaj
    • , Manuel D. Leonetti
    • , Alexander Marson
    • , Andrew P. May
    •  & James Zou
  • Brief Communication |

    SignalP 5.0 improves proteome-wide detection of signal peptides across all organisms and can distinguish between different types of signal peptides in prokaryotes.

    • José Juan Almagro Armenteros
    • , Konstantinos D. Tsirigos
    • , Casper Kaae Sønderby
    • , Thomas Nordahl Petersen
    • , Ole Winther
    • , Søren Brunak
    • , Gunnar von Heijne
    •  & Henrik Nielsen
  • Brief Communication |

    Precise genome engineering of a handful of genes enables rapid domestication of wild tomato plants.

    • Tingdong Li
    • , Xinping Yang
    • , Yuan Yu
    • , Xiaomin Si
    • , Xiawan Zhai
    • , Huawei Zhang
    • , Wenxia Dong
    • , Caixia Gao
    •  & Cao Xu
  • Brief Communication |

    Diseases caused by different mutations in the two alleles of a gene are treated in mice by Cas-9-induced allelic exchange.

    • Dan Wang
    • , Jia Li
    • , Chun-Qing Song
    • , Karen Tran
    • , Haiwei Mou
    • , Pei-Hsuan Wu
    • , Phillip W L Tai
    • , Craig A Mendonca
    • , Lingzhi Ren
    • , Blake Y Wang
    • , Qin Su
    • , Dominic J Gessler
    • , Phillip D Zamore
    • , Wen Xue
    •  & Guangping Gao
  • Brief Communication |

    Neoepitopes derived from intron retention events are processed and presented on MHC I in cancer cell lines.

    • Alicia C Smart
    • , Claire A Margolis
    • , Harold Pimentel
    • , Meng Xiao He
    • , Diana Miao
    • , Dennis Adeegbe
    • , Tim Fugmann
    • , Kwok-Kin Wong
    •  & Eliezer M Van Allen
  • Brief Communication |

    Gene silencing by siRNAs in vivo is reversed using sequence-specific high-affinity oligonucleotides.

    • Ivan Zlatev
    • , Adam Castoreno
    • , Christopher R Brown
    • , June Qin
    • , Scott Waldron
    • , Mark K Schlegel
    • , Rohan Degaonkar
    • , Svetlana Shulga-Morskaya
    • , Huilei Xu
    • , Swati Gupta
    • , Shigeo Matsuda
    • , Akin Akinc
    • , Kallanthottathil G Rajeev
    • , Muthiah Manoharan
    • , Martin A Maier
    •  & Vasant Jadhav
  • Brief Communication |

    Methylation profiling of single cells in high throughput achieves read-alignment rates approaching bulk cell population studies.

    • Ryan M Mulqueen
    • , Dmitry Pokholok
    • , Steven J Norberg
    • , Kristof A Torkenczy
    • , Andrew J Fields
    • , Duanchen Sun
    • , John R Sinnamon
    • , Jay Shendure
    • , Cole Trapnell
    • , Brian J O'Roak
    • , Zheng Xia
    • , Frank J Steemers
    •  & Andrew C Adey
  • Brief Communication |

    A new fusion protein enables precise editing of single bases in A/T-rich regions of the human genome.

    • Xiaosa Li
    • , Ying Wang
    • , Yajing Liu
    • , Bei Yang
    • , Xiao Wang
    • , Jia Wei
    • , Zongyang Lu
    • , Yuxi Zhang
    • , Jing Wu
    • , Xingxu Huang
    • , Li Yang
    •  & Jia Chen
  • Brief Communication
    | Open Access

    Repeat regions in the human Y chromosome centromere are assembled using long-read nanopore sequencing.

    • Miten Jain
    • , Hugh E Olsen
    • , Daniel J Turner
    • , David Stoddart
    • , Kira V Bulazel
    • , Benedict Paten
    • , David Haussler
    • , Huntington F Willard
    • , Mark Akeson
    •  & Karen H Miga
  • Brief Communication |

    Using deep learning to combine target sequence and chromatin accessibility data boosts the accuracy of CRISPR–Cpf1 guide RNA activity

    • Hui Kwon Kim
    • , Seonwoo Min
    • , Myungjae Song
    • , Soobin Jung
    • , Jae Woo Choi
    • , Younggwang Kim
    • , Sangeun Lee
    • , Sungroh Yoon
    •  & Hyongbum (Henry) Kim
  • Brief Communication |

    Libraries of natively paired human VH:VL chains enable screening of the human B-cell repertoire in yeast.

    • Bo Wang
    • , Brandon J DeKosky
    • , Morgan R Timm
    • , Jiwon Lee
    • , Erica Normandin
    • , John Misasi
    • , Rui Kong
    • , Jonathan R McDaniel
    • , George Delidakis
    • , Kendra E Leigh
    • , Thomas Niezold
    • , Chang W Choi
    • , Elise G Viox
    • , Ahmed Fahad
    • , Alberto Cagigi
    • , Aurélie Ploquin
    • , Kwanyee Leung
    • , Eun Sung Yang
    • , Wing-Pui Kong
    • , William N Voss
    • , Aaron G Schmidt
    • , M Anthony Moody
    • , David R Ambrozak
    • , Amy R Henry
    • , Farida Laboune
    • , Julie E Ledgerwood
    • , Barney S Graham
    • , Mark Connors
    • , Daniel C Douek
    • , Nancy J Sullivan
    • , Andrew D Ellington
    • , John R Mascola
    •  & George Georgiou
  • Brief Communication |

    Labeling of cell-type-specific proteomes in the brains of live mice is enabled by an orthogonal-amino-acid approach.

    • Toke P Krogager
    • , Russell J Ernst
    • , Thomas S Elliott
    • , Laura Calo
    • , Václav Beránek
    • , Ernesto Ciabatti
    • , Maria Grazia Spillantini
    • , Marco Tripodi
    • , Michael H Hastings
    •  & Jason W Chin
  • Brief Communication |

    High-throughput quantification of protein and gene expression in single cells is achieved using DNA-barcoded antibodies.

    • Vanessa M Peterson
    • , Kelvin Xi Zhang
    • , Namit Kumar
    • , Jerelyn Wong
    • , Lixia Li
    • , Douglas C Wilson
    • , Renee Moore
    • , Terrill K McClanahan
    • , Svetlana Sadekova
    •  & Joel A Klappenbach
  • Brief Communication |

    Targeted editing of single base pairs is achieved in monocot rice and dicot tomato using Target-AID (Cas9 activation-induced cytidine deaminase fusion).

    • Zenpei Shimatani
    • , Sachiko Kashojiya
    • , Mariko Takayama
    • , Rie Terada
    • , Takayuki Arazoe
    • , Hisaki Ishii
    • , Hiroshi Teramura
    • , Tsuyoshi Yamamoto
    • , Hiroki Komatsu
    • , Kenji Miura
    • , Hiroshi Ezura
    • , Keiji Nishida
    • , Tohru Ariizumi
    •  & Akihiko Kondo
  • Brief Communication |

    The most effective shRNAs to silence a gene are calculated by a machine learning algorithm.

    • Raphael Pelossof
    • , Lauren Fairchild
    • , Chun-Hao Huang
    • , Christian Widmer
    • , Vipin T Sreedharan
    • , Nishi Sinha
    • , Dan-Yu Lai
    • , Yuanzhe Guan
    • , Prem K Premsrirut
    • , Darjus F Tschaharganeh
    • , Thomas Hoffmann
    • , Vishal Thapar
    • , Qing Xiang
    • , Ralph J Garippa
    • , Gunnar Rätsch
    • , Johannes Zuber
    • , Scott W Lowe
    • , Christina S Leslie
    •  & Christof Fellmann
  • Brief Communication |

    Mice with targeted point mutations are generated efficiently using Cas9–cytidine deaminase fusions.

    • Kyoungmi Kim
    • , Seuk-Min Ryu
    • , Sang-Tae Kim
    • , Gayoung Baek
    • , Daesik Kim
    • , Kayeong Lim
    • , Eugene Chung
    • , Sunghyun Kim
    •  & Jin-Soo Kim
  • Brief Communication |

    Multiplexed genome editing is simplified by harnessing the ability of Cpf1 to process its own pre-crRNA.

    • Bernd Zetsche
    • , Matthias Heidenreich
    • , Prarthana Mohanraju
    • , Iana Fedorova
    • , Jeroen Kneppers
    • , Ellen M DeGennaro
    • , Nerges Winblad
    • , Sourav R Choudhury
    • , Omar O Abudayyeh
    • , Jonathan S Gootenberg
    • , Wen Y Wu
    • , David A Scott
    • , Konstantin Severinov
    • , John van der Oost
    •  & Feng Zhang
  • Brief Communication |

    The small RNA transcriptome is sequenced in single cells, facilitating study of microRNAs and other small RNAs.

    • Omid R Faridani
    • , Ilgar Abdullayev
    • , Michael Hagemann-Jensen
    • , John P Schell
    • , Fredrik Lanner
    •  & Rickard Sandberg
  • Brief Communication |

    Softening in tomatoes is uncoupled from ripening by silencing a pectate lyase, thereby identifying a route to engineering (or breeding) tomatoes with better shelf life and flavor.

    • Selman Uluisik
    • , Natalie H Chapman
    • , Rebecca Smith
    • , Mervin Poole
    • , Gary Adams
    • , Richard B Gillis
    • , Tabot M D Besong
    • , Judith Sheldon
    • , Suzy Stiegelmeyer
    • , Laura Perez
    • , Nurul Samsulrizal
    • , Duoduo Wang
    • , Ian D Fisk
    • , Ni Yang
    • , Charles Baxter
    • , Daniel Rickett
    • , Rupert Fray
    • , Barbara Blanco-Ulate
    • , Ann L T Powell
    • , Stephen E Harding
    • , Jim Craigon
    • , Jocelyn K C Rose
    • , Eric A Fich
    • , Li Sun
    • , David S Domozych
    • , Paul D Fraser
    • , Gregory A Tucker
    • , Don Grierson
    •  & Graham B Seymour