Deep-learning augmented RNA-seq analysis of transcript splicing

Latest Research

  • Brief Communication |

    DARTS first uses public domain data to train a deep neural network to predict differential alternative splicing; the predictions are then combined with observed RNA-seq data in a Bayesian framework to infer changes in alternative splicing between biological samples.

    • Zijun Zhang
    • , Zhicheng Pan
    • , Yi Ying
    • , Zhijie Xie
    • , Samir Adhikari
    • , John Phillips
    • , Russ P. Carstens
    • , Douglas L. Black
    • , Yingnian Wu
    •  & Yi Xing
  • Brief Communication |

    SNAC-tags allow for versatile sequence-specific cleavage of soluble and membrane proteins with Ni2+ under biocompatible conditions, bypassing enzymatic cleavage and enabling cleavage in situations where commonly used enzymes fail.

    • Bobo Dang
    • , Marco Mravic
    • , Hailin Hu
    • , Nathan Schmidt
    • , Bruk Mensa
    •  & William F. DeGrado
  • 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
  • Brief Communication |

    The solid media portable cell killing assay uses metabolism-sensitive staining to illuminate the killing of antibiotic-tolerant bacteria under resource-depleted conditions, thereby enabling multiplex, genome-scale analyses for the identification of target strains.

    • Jonathan M. Stokes
    • , Arnaud Gutierrez
    • , Allison J. Lopatkin
    • , Ian W. Andrews
    • , Shawn French
    • , Ivan Matic
    • , Eric D. Brown
    •  & James J. Collins

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