Latest Research

  • Brief Communication |

    CRISPR-based single-cell pooled screens that use linked barcodes suffer from lost sensitivity due to lentiviral template switching. The barcode-free CROP-seq design circumvents this problem.

    • Andrew J Hill
    • , José L McFaline-Figueroa
    • , Lea M Starita
    • , Molly J Gasperini
    • , Kenneth A Matreyek
    • , Jonathan Packer
    • , Dana Jackson
    • , Jay Shendure
    •  & Cole Trapnell
  • Brief Communication |

    The iSAFE software accurately identifies the favored mutation within a positive selective sweep region of the genome.

    • Ali Akbari
    • , Joseph J Vitti
    • , Arya Iranmehr
    • , Mehrdad Bakhtiari
    • , Pardis C Sabeti
    • , Siavash Mirarab
    •  & Vineet Bafna
  • Article |

    Labeling newly transcribed RNA with 5-ethynyluridine and adding biotin via click chemistry allows the analysis of the proteome bound to the various RNA species, including nascent RNA.

    • Xichen Bao
    • , Xiangpeng Guo
    • , Menghui Yin
    • , Muqddas Tariq
    • , Yiwei Lai
    • , Shahzina Kanwal
    • , Jiajian Zhou
    • , Na Li
    • , Yuan Lv
    • , Carlos Pulido-Quetglas
    • , Xiwei Wang
    • , Lu Ji
    • , Muhammad J Khan
    • , Xihua Zhu
    • , Zhiwei Luo
    • , Changwei Shao
    • , Do-Hwan Lim
    • , Xiao Liu
    • , Nan Li
    • , Wei Wang
    • , Minghui He
    • , Yu-Lin Liu
    • , Carl Ward
    • , Tong Wang
    • , Gong Zhang
    • , Dongye Wang
    • , Jianhua Yang
    • , Yiwen Chen
    • , Chaolin Zhang
    • , Ralf Jauch
    • , Yun-Gui Yang
    • , Yangming Wang
    • , Baoming Qin
    • , Minna-Liisa Anko
    • , Andrew P Hutchins
    • , Hao Sun
    • , Huating Wang
    • , Xiang-Dong Fu
    • , Biliang Zhang
    •  & Miguel A Esteban
  • Article |

    RaPID uses biotin ligases BirA* and the faster acting BASU to label proteins in the proximity of an RNA motif of interest in living cells.

    • Muthukumar Ramanathan
    • , Karim Majzoub
    • , Deepti S Rao
    • , Poornima H Neela
    • , Brian J Zarnegar
    • , Smarajit Mondal
    • , Julien G Roth
    • , Hui Gai
    • , Joanna R Kovalski
    • , Zurab Siprashvili
    • , Theo D Palmer
    • , Jan E Carette
    •  & Paul A Khavari
  • Perspective |

    This Perspective reviews nanoscopy via stimulated emission depletion (STED), focusing on challenges for biologists and how technical advances are helping to meet these challenges.

    • Giuseppe Vicidomini
    • , Paolo Bianchini
    •  & Alberto Diaspro
  • Article |

    Direct sequencing of RNA molecules in real time using nanopores allows for the detection of splice variants and hold promises for profiling RNA modifications.

    • Daniel R Garalde
    • , Elizabeth A Snell
    • , Daniel Jachimowicz
    • , Botond Sipos
    • , Joseph H Lloyd
    • , Mark Bruce
    • , Nadia Pantic
    • , Tigist Admassu
    • , Phillip James
    • , Anthony Warland
    • , Michael Jordan
    • , Jonah Ciccone
    • , Sabrina Serra
    • , Jemma Keenan
    • , Samuel Martin
    • , Luke McNeill
    • , E Jayne Wallace
    • , Lakmal Jayasinghe
    • , Chris Wright
    • , Javier Blasco
    • , Stephen Young
    • , Denise Brocklebank
    • , Sissel Juul
    • , James Clarke
    • , Andrew J Heron
    •  & Daniel J Turner
  • Brief Communication |

    3DNetMod identifies nested topologically associating domains (TADs) and subTADs from Hi-C data.

    • Heidi K Norton
    • , Daniel J Emerson
    • , Harvey Huang
    • , Jesi Kim
    • , Katelyn R Titus
    • , Shi Gu
    • , Danielle S Bassett
    •  & Jennifer E Phillips-Cremins
  • Brief Communication |

    GIGGLE is a genome interval search engine that enables extremely fast queries of genome features from thousands of genome annotation sets.

    • Ryan M Layer
    • , Brent S Pedersen
    • , Tonya DiSera
    • , Gabor T Marth
    • , Jason Gertz
    •  & Aaron R Quinlan
  • Resource |

    Based on machine learning-predicted interaction interfaces, this resource enables interpretation of genomic variants and disease mutations in light of the protein-protein interactome.

    • Michael J Meyer
    • , Juan Felipe Beltrán
    • , Siqi Liang
    • , Robert Fragoza
    • , Aaron Rumack
    • , Jin Liang
    • , Xiaomu Wei
    •  & Haiyuan Yu
  • Article |

    Proximity-based labeling represents a useful approach for mapping protein environment, but current methods for this are limited to application to cell lines. This approach is now extended to primary human tissues with a method that uses antibodies to guide proximity labeling.

    • Daniel Z Bar
    • , Kathleen Atkatsh
    • , Urraca Tavarez
    • , Michael R Erdos
    • , Yosef Gruenbaum
    •  & Francis S Collins
  • Article |

    Mouse tumor organoids are characterized as a model to study tumor biology and drug resistance.

    • Alexandra A Duarte
    • , Ewa Gogola
    • , Norman Sachs
    • , Marco Barazas
    • , Stefano Annunziato
    • , Julian R de Ruiter
    • , Arno Velds
    • , Sohvi Blatter
    • , Julia M Houthuijzen
    • , Marieke van de Ven
    • , Hans Clevers
    • , Piet Borst
    • , Jos Jonkers
    •  & Sven Rottenberg
  • Article |

    Using the ORI of plasmids used in enhancer assays as the sole core promoter and inhibiting the interferon I response triggered by plasmid transfection greatly reduces false positive and negative results in single-candidate and massively parallel enhancer assays and enables genome-wide enhancer screens.

    • Felix Muerdter
    • , Łukasz M Boryń
    • , Ashley R Woodfin
    • , Christoph Neumayr
    • , Martina Rath
    • , Muhammad A Zabidi
    • , Michaela Pagani
    • , Vanja Haberle
    • , Tomáš Kazmar
    • , Rui R Catarino
    • , Katharina Schernhuber
    • , Cosmas D Arnold
    •  & Alexander Stark
  • Brief Communication |

    Molecular force microscopy employs a combination of fluorescence polarization microscopy and molecular tension sensors to determine the orientation of cellular forces. The technology is demonstrated for integrin-mediated forces in platelets and fibroblasts.

    • Joshua M Brockman
    • , Aaron T Blanchard
    • , Victor Pui-Yan Ma
    • , Wallace D Derricotte
    • , Yun Zhang
    • , Meredith E Fay
    • , Wilbur A Lam
    • , Francesco A Evangelista
    • , Alexa L Mattheyses
    •  & Khalid Salaita
  • Article |

    NetSig is a network-based statistic that identifies cancer driver genes with high accuracy and can be combined with gene-based statistical tests; results are validated with a large-scale in vivo tumorigenesis assay.

    • Heiko Horn
    • , Michael S Lawrence
    • , Candace R Chouinard
    • , Yashaswi Shrestha
    • , Jessica Xin Hu
    • , Elizabeth Worstell
    • , Emily Shea
    • , Nina Ilic
    • , Eejung Kim
    • , Atanas Kamburov
    • , Alireza Kashani
    • , William C Hahn
    • , Joshua D Campbell
    • , Jesse S Boehm
    • , Gad Getz
    •  & Kasper Lage
  • Brief Communication |

    Designer cells executing rationally assembled genetic programs that can process input signals with programmable logic are combined in a 3D cell culture that performs three-input, two-output full-adder computations.

    • David Ausländer
    • , Simon Ausländer
    • , Xavier Pierrat
    • , Leon Hellmann
    • , Leila Rachid
    •  & Martin Fussenegger
  • Brief Communication |

    An integrated cheminformatics workflow aids the functional and structural annotation of unknown metabolites found across multiple biological systems.

    • Zijuan Lai
    • , Hiroshi Tsugawa
    • , Gert Wohlgemuth
    • , Sajjan Mehta
    • , Matthew Mueller
    • , Yuxuan Zheng
    • , Atsushi Ogiwara
    • , John Meissen
    • , Megan Showalter
    • , Kohei Takeuchi
    • , Tobias Kind
    • , Peter Beal
    • , Masanori Arita
    •  & Oliver Fiehn
  • Article |

    The window for high-resolution imaging of the lung (WHRIL) enables longitudinal imaging of the same region of murine lung tissue over a period of weeks, and this enables the visualization of spontaneous cancer metastasis from the earliest stages.

    • David Entenberg
    • , Sonia Voiculescu
    • , Peng Guo
    • , Lucia Borriello
    • , Yarong Wang
    • , George S Karagiannis
    • , Joan Jones
    • , Francis Baccay
    • , Maja Oktay
    •  & John Condeelis