Articles

  • Article |

    Nanopore sequencing coupled with a metagenomics framework that effectively removes human DNA from samples enables rapid bacterial LRI diagnosis.

    • Themoula Charalampous
    • , Gemma L. Kay
    • , Hollian Richardson
    • , Alp Aydin
    • , Rossella Baldan
    • , Christopher Jeanes
    • , Duncan Rae
    • , Sara Grundy
    • , Daniel J. Turner
    • , John Wain
    • , Richard M. Leggett
    • , David M. Livermore
    •  & Justin O’Grady
  • Article |

    Combining microfluidics with combinatorial indexing enables rapid mapping of genome accessibility in hundreds of thousands of single cells.

    • Caleb A. Lareau
    • , Fabiana M. Duarte
    • , Jennifer G. Chew
    • , Vinay K. Kartha
    • , Zach D. Burkett
    • , Andrew S. Kohlway
    • , Dmitry Pokholok
    • , Martin J. Aryee
    • , Frank J. Steemers
    • , Ronald Lebofsky
    •  & Jason D. Buenrostro
  • Article |

    CIBERSORTx, a suite of computational tools, enables inference of cell type abundance and cell-type-specific gene expression profiles from bulk RNA profiles.

    • Aaron M. Newman
    • , Chloé B. Steen
    • , Chih Long Liu
    • , Andrew J. Gentles
    • , Aadel A. Chaudhuri
    • , Florian Scherer
    • , Michael S. Khodadoust
    • , Mohammad S. Esfahani
    • , Bogdan A. Luca
    • , David Steiner
    • , Maximilian Diehn
    •  & Ash A. Alizadeh
  • Article |

    Chemical modification of PS-ASO therapeutics reduces binding to cellular proteins and decreases toxic side-effects.

    • Wen Shen
    • , Cheryl L. De Hoyos
    • , Michael T. Migawa
    • , Timothy A. Vickers
    • , Hong Sun
    • , Audrey Low
    • , Thomas A. Bell III
    • , Meghdad Rahdar
    • , Swagatam Mukhopadhyay
    • , Christopher E. Hart
    • , Melanie Bell
    • , Stan Riney
    • , Susan F. Murray
    • , Sarah Greenlee
    • , Rosanne M. Crooke
    • , Xue-hai Liang
    • , Punit P. Seth
    •  & Stanley T. Crooke
  • Article |

    Rice coordinates recruitment of the root microbiota to optimize nitrogen acquisition from soil.

    • Jingying Zhang
    • , Yong-Xin Liu
    • , Na Zhang
    • , Bin Hu
    • , Tao Jin
    • , Haoran Xu
    • , Yuan Qin
    • , Pengxu Yan
    • , Xiaoning Zhang
    • , Xiaoxuan Guo
    • , Jing Hui
    • , Shouyun Cao
    • , Xin Wang
    • , Chao Wang
    • , Hui Wang
    • , Baoyuan Qu
    • , Guangyi Fan
    • , Lixing Yuan
    • , Ruben Garrido-Oter
    • , Chengcai Chu
    •  & Yang Bai
  • Article |

    A new computational method allows key developmental checkpoints and important parameters of population dynamics to be inferred from single-cell RNA-sequencing time series data.

    • David S. Fischer
    • , Anna K. Fiedler
    • , Eric M. Kernfeld
    • , Ryan M. J. Genga
    • , Aimée Bastidas-Ponce
    • , Mostafa Bakhti
    • , Heiko Lickert
    • , Jan Hasenauer
    • , Rene Maehr
    •  & Fabian J. Theis
  • Article |

    A cell-based sensor detects tumors with higher sensitivity than protein and nucleic acid biomarkers.

    • Amin Aalipour
    • , Hui-Yen Chuang
    • , Surya Murty
    • , Aloma L. D’Souza
    • , Seung-min Park
    • , Gunsagar S. Gulati
    • , Chirag B. Patel
    • , Corinne Beinat
    • , Federico Simonetta
    • , Ivana Martinić
    • , Gayatri Gowrishankar
    • , Elise R. Robinson
    • , Eamon Aalipour
    • , Zahra Zhian
    •  & Sanjiv S. Gambhir
  • Article |

    ‘Tubuloids’ grown from human kidney tissue and urine aid the study of BK virus infection, Wilms tumors and cystic fibrosis.

    • Frans Schutgens
    • , Maarten B Rookmaaker
    • , Thanasis Margaritis
    • , Anne Rios
    • , Carola Ammerlaan
    • , Jitske Jansen
    • , Linda Gijzen
    • , Marianne Vormann
    • , Annelotte Vonk
    • , Marco Viveen
    • , Fjodor Yousef Yengej
    • , Sepide Derakhshan
    • , Karin M. de Winter-de Groot
    • , Benedetta Artegiani
    • , Ruben van Boxtel
    • , Edwin Cuppen
    • , Antoni P. A. Hendrickx
    • , Marry M. van den Heuvel-Eibrink
    • , Ellen Heitzer
    • , Henriette Lanz
    • , Jeffrey Beekman
    • , Jean-Luc Murk
    • , Rosalinde Masereeuw
    • , Frank Holstege
    • , Jarno Drost
    • , Marianne C Verhaar
    •  & Hans Clevers
  • Article |

    A sensitive method to analyze metagenomes, CATCH, enables detection and characterization of diverse viral sequences, including the 356 viruses known to infect humans.

    • Hayden C. Metsky
    • , Katherine J. Siddle
    • , Adrianne Gladden-Young
    • , James Qu
    • , David K. Yang
    • , Patrick Brehio
    • , Andrew Goldfarb
    • , Anne Piantadosi
    • , Shirlee Wohl
    • , Amber Carter
    • , Aaron E. Lin
    • , Kayla G. Barnes
    • , Damien C. Tully
    • , Bjӧrn Corleis
    • , Scott Hennigan
    • , Giselle Barbosa-Lima
    • , Yasmine R. Vieira
    • , Lauren M. Paul
    • , Amanda L. Tan
    • , Kimberly F. Garcia
    • , Leda A. Parham
    • , Ikponmwosa Odia
    • , Philomena Eromon
    • , Onikepe A. Folarin
    • , Augustine Goba
    • , Etienne Simon-Lorière
    • , Lisa Hensley
    • , Angel Balmaseda
    • , Eva Harris
    • , Douglas S. Kwon
    • , Todd M. Allen
    • , Jonathan A. Runstadler
    • , Sandra Smole
    • , Fernando A. Bozza
    • , Thiago M. L. Souza
    • , Sharon Isern
    • , Scott F. Michael
    • , Ivette Lorenzana
    • , Lee Gehrke
    • , Irene Bosch
    • , Gregory Ebel
    • , Donald S. Grant
    • , Christian T. Happi
    • , Daniel J. Park
    • , Andreas Gnirke
    • , Pardis C. Sabeti
    •  & Christian B. Matranga
  • Article |

    RNA-binding proteins can be identified and quantified in any organism using a simple method that combines UV cross-linking and phase separation.

    • Rayner M. L. Queiroz
    • , Tom Smith
    • , Eneko Villanueva
    • , Maria Marti-Solano
    • , Mie Monti
    • , Mariavittoria Pizzinga
    • , Dan-Mircea Mirea
    • , Manasa Ramakrishna
    • , Robert F. Harvey
    • , Veronica Dezi
    • , Gavin H. Thomas
    • , Anne E. Willis
    •  & Kathryn S. Lilley
  • Article |

    Neoantigen prediction from clinical samples is improved using a neural network model trained on a large HLA peptide and genomic tumor dataset.

    • Brendan Bulik-Sullivan
    • , Jennifer Busby
    • , Christine D Palmer
    • , Matthew J Davis
    • , Tyler Murphy
    • , Andrew Clark
    • , Michele Busby
    • , Fujiko Duke
    • , Aaron Yang
    • , Lauren Young
    • , Noelle C Ojo
    • , Kamilah Caldwell
    • , Jesse Abhyankar
    • , Thomas Boucher
    • , Meghan G Hart
    • , Vladimir Makarov
    • , Vincent Thomas De Montpreville
    • , Olaf Mercier
    • , Timothy A Chan
    • , Giorgio Scagliotti
    • , Paolo Bironzo
    • , Silvia Novello
    • , Niki Karachaliou
    • , Rafael Rosell
    • , Ian Anderson
    • , Nashat Gabrail
    • , John Hrom
    • , Chainarong Limvarapuss
    • , Karin Choquette
    • , Alexander Spira
    • , Raphael Rousseau
    • , Cynthia Voong
    • , Naiyer A Rizvi
    • , Elie Fadel
    • , Mark Frattini
    • , Karin Jooss
    • , Mojca Skoberne
    • , Joshua Francis
    •  & Roman Yelensky
  • Article |

    Controlled tissue fixation with polyepoxides protects protein fluorescence, antigenicity, nucleic acids and tissue architecture.

    • Young-Gyun Park
    • , Chang Ho Sohn
    • , Ritchie Chen
    • , Margaret McCue
    • , Dae Hee Yun
    • , Gabrielle T Drummond
    • , Taeyun Ku
    • , Nicholas B Evans
    • , Hayeon Caitlyn Oak
    • , Wendy Trieu
    • , Heejin Choi
    • , Xin Jin
    • , Varoth Lilascharoen
    • , Ji Wang
    • , Matthias C Truttmann
    • , Helena W Qi
    • , Hidde L Ploegh
    • , Todd R Golub
    • , Shih-Chi Chen
    • , Matthew P Frosch
    • , Heather J Kulik
    • , Byung Kook Lim
    •  & Kwanghun Chung
  • Article |

    Analysis of more than a billion repair outcomes yields an algorithm that predicts Cas9-induced mutations.

    • Felicity Allen
    • , Luca Crepaldi
    • , Clara Alsinet
    • , Alexander J. Strong
    • , Vitalii Kleshchevnikov
    • , Pietro De Angeli
    • , Petra Páleníková
    • , Anton Khodak
    • , Vladimir Kiselev
    • , Michael Kosicki
    • , Andrew R. Bassett
    • , Heather Harding
    • , Yaron Galanty
    • , Francisco Muñoz-Martínez
    • , Emmanouil Metzakopian
    • , Stephen P. Jackson
    •  & Leopold Parts
  • Article |

    Preeclampsia, a hypertension condition with no approved therapies, is treated in monkeys by gene silencing in the placenta.

    • Anton A Turanov
    • , Agnes Lo
    • , Matthew R Hassler
    • , Angela Makris
    • , Ami Ashar-Patel
    • , Julia F Alterman
    • , Andrew H Coles
    • , Reka A Haraszti
    • , Loic Roux
    • , Bruno M D C Godinho
    • , Dimas Echeverria
    • , Suzanne Pears
    • , Jim Iliopoulos
    • , Renuka Shanmugalingam
    • , Robert Ogle
    • , Zsuzsanna K Zsengeller
    • , Annemarie Hennessy
    • , S Ananth Karumanchi
    • , Melissa J Moore
    •  & Anastasia Khvorova
  • Article |

    Trio binning assembles both haplotypes of a genome by combining long-read sequence data with short-read data from both parents.

    • Sergey Koren
    • , Arang Rhie
    • , Brian P Walenz
    • , Alexander T Dilthey
    • , Derek M Bickhart
    • , Sarah B Kingan
    • , Stefan Hiendleder
    • , John L Williams
    • , Timothy P L Smith
    •  & Adam M Phillippy
  • Article |

    Tomato rhizosphere microbiome alterations that contribute to bacterial wilt resistance are detected using metagenomics.

    • Min-Jung Kwak
    • , Hyun Gi Kong
    • , Kihyuck Choi
    • , Soon-Kyeong Kwon
    • , Ju Yeon Song
    • , Jidam Lee
    • , Pyeong An Lee
    • , Soo Yeon Choi
    • , Minseok Seo
    • , Hyoung Ju Lee
    • , Eun Joo Jung
    • , Hyein Park
    • , Nazish Roy
    • , Heebal Kim
    • , Myeong Min Lee
    • , Edward M Rubin
    • , Seon-Woo Lee
    •  & Jihyun F Kim
  • Article |

    A wild tomato species is domesticated by targeted CRISPR–Cas9 editing of just six genes.

    • Agustin Zsögön
    • , Tomáš Čermák
    • , Emmanuel Rezende Naves
    • , Marcela Morato Notini
    • , Kai H Edel
    • , Stefan Weinl
    • , Luciano Freschi
    • , Daniel F Voytas
    • , Jörg Kudla
    •  & Lázaro Eustáquio Pereira Peres
  • Article |

    The expression profile and tissue coordinates of liver endothelial cells are determined using a paired-cell sequencing approach that extracts spatial information from attached hepatocytes.

    • Keren Bahar Halpern
    • , Rom Shenhav
    • , Hassan Massalha
    • , Beata Toth
    • , Adi Egozi
    • , Efi E Massasa
    • , Chiara Medgalia
    • , Eyal David
    • , Amir Giladi
    • , Andreas E Moor
    • , Ziv Porat
    • , Ido Amit
    •  & Shalev Itzkovitz
  • Article |

    Three linked microfluidic chips model transport across the blood–brain barrier.

    • Ben M Maoz
    • , Anna Herland
    • , Edward A FitzGerald
    • , Thomas Grevesse
    • , Charles Vidoudez
    • , Alan R Pacheco
    • , Sean P Sheehy
    • , Tae-Eun Park
    • , Stephanie Dauth
    • , Robert Mannix
    • , Nikita Budnik
    • , Kevin Shores
    • , Alexander Cho
    • , Janna C Nawroth
    • , Daniel Segrè
    • , Bogdan Budnik
    • , Donald E Ingber
    •  & Kevin Kit Parker
  • Article |

    Synthetic probiotic for a human metabolic disease is taken through a drug development pathway to enable translation into clinic trials.

    • Vincent M Isabella
    • , Binh N Ha
    • , Mary Joan Castillo
    • , David J Lubkowicz
    • , Sarah E Rowe
    • , Yves A Millet
    • , Cami L Anderson
    • , Ning Li
    • , Adam B Fisher
    • , Kip A West
    • , Philippa J Reeder
    • , Munira M Momin
    • , Christopher G Bergeron
    • , Sarah E Guilmain
    • , Paul F Miller
    • , Caroline B Kurtz
    •  & Dean Falb
  • Article |

    Anti-PD-1 secreted by CAR-T cells remains localized to the tumor and improves therapeutic outcome in mice.

    • Sarwish Rafiq
    • , Oladapo O Yeku
    • , Hollie J Jackson
    • , Terence J Purdon
    • , Dayenne G van Leeuwen
    • , Dylan J Drakes
    • , Mei Song
    • , Matthew M Miele
    • , Zhuoning Li
    • , Pei Wang
    • , Su Yan
    • , Jingyi Xiang
    • , Xiaojing Ma
    • , Venkatraman E Seshan
    • , Ronald C Hendrickson
    • , Cheng Liu
    •  & Renier J Brentjens
  • Article |

    Rapid, multiplex identification of pathogens and disease-associated mutations is possible with a new semiconductor biochip.

    • Arjang Hassibi
    • , Arun Manickam
    • , Rituraj Singh
    • , Sara Bolouki
    • , Ruma Sinha
    • , Kshama B Jirage
    • , Mark W McDermott
    • , Babak Hassibi
    • , Haris Vikalo
    • , Gelareh Mazarei
    • , Lei Pei
    • , Luc Bousse
    • , Mark Miller
    • , Mehrdad Heshami
    • , Michael P Savage
    • , Michael T Taylor
    • , Nader Gamini
    • , Nicholas Wood
    • , Pallavi Mantina
    • , Patrick Grogan
    • , Peter Kuimelis
    • , Piyush Savalia
    • , Scott Conradson
    • , Yuan Li
    • , Rich B Meyer
    • , Edmond Ku
    • , Jessica Ebert
    • , Benjamin A Pinsky
    • , Gregory Dolganov
    • , Tran Van
    • , Kirsten A Johnson
    • , Pejman Naraghi-Arani
    • , Robert G Kuimelis
    •  & Gary Schoolnik
  • Article |

    Systematic evaluation of library preparation methods for small RNA-seq identifies reproducible and accurate methods.

    • Maria D Giraldez
    • , Ryan M Spengler
    • , Alton Etheridge
    • , Paula M Godoy
    • , Andrea J Barczak
    • , Srimeenakshi Srinivasan
    • , Peter L De Hoff
    • , Kahraman Tanriverdi
    • , Amanda Courtright
    • , Shulin Lu
    • , Joseph Khoory
    • , Renee Rubio
    • , David Baxter
    • , Tom A P Driedonks
    • , Henk P J Buermans
    • , Esther N M Nolte-'t Hoen
    • , Hui Jiang
    • , Kai Wang
    • , Ionita Ghiran
    • , Yaoyu E Wang
    • , Kendall Van Keuren-Jensen
    • , Jane E Freedman
    • , Prescott G Woodruff
    • , Louise C Laurent
    • , David J Erle
    • , David J Galas
    •  & Muneesh Tewari
  • Article |

    Cardiomyocyte transplantation after heart attack improves contractile function in monkeys.

    • Yen-Wen Liu
    • , Billy Chen
    • , Xiulan Yang
    • , James A Fugate
    • , Faith A Kalucki
    • , Akiko Futakuchi-Tsuchida
    • , Larry Couture
    • , Keith W Vogel
    • , Clifford A Astley
    • , Audrey Baldessari
    • , Jason Ogle
    • , Creighton W Don
    • , Zachary L Steinberg
    • , Stephen P Seslar
    • , Stephanie A Tuck
    • , Hiroshi Tsuchida
    • , Anna V Naumova
    • , Sarah K Dupras
    • , Milly S Lyu
    • , James Lee
    • , Dale W Hailey
    • , Hans Reinecke
    • , Lil Pabon
    • , Benjamin H Fryer
    • , W Robb MacLellan
    • , R Scott Thies
    •  & Charles E Murry