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Deep Learning

  • 1.
    Pereira T, Tabris N, Matsliah A, Turner D, Li J, Ravindranath S, Papadoyannis E, Normand E, Deutsch D, Wang Y, McKenzie-Smith G, Mitelut C, Castro M, D’Uva J, Kislin M, Sanes D, Kocher S, Wang S, Falkner A, Shaevitz J, Murthy M. SLEAP: A deep learning system for multi-animal pose tracking. Nat Methods. 2022;19(4):486–495. PMCID: PMC9007740
    Reference Link
  • 1.
    Li V, Zhang Z, Troyanskaya O. CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. Bioinformatics. 2021;37(Suppl_1):i342-i348. PMCID: PMC8275342
    Reference Link
  • 1.
    Cofer E, Raimundo J, Tadych A, Yamazaki Y, Wong A, Theesfeld C, Levine M, Troyanskaya O. Modeling transcriptional regulation of model species with deep learning. Genome Res. 2021;31(6):1097–1105. PMCID: PMC8168591
    Reference Link
  • 1.
    Park C, Zhou J, Wong A, Chen K, Theesfeld C, Darnell R, Troyanskaya O. Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk. Nat Genet. 2021;53(2):166–173. PMCID: PMC7886016
    Reference Link
  • 1.
    Zhou J, Park C, Theesfeld C, Wong A, Yuan Y, Scheckel C, Fak J, Funk J, Yao K, Tajima Y, Packer A, Darnell R, Troyanskaya O. Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. Nat Genet. 2019;51(6):973–980. PMCID: PMC6758908
    Reference Link
  • 1.
    Chen K, Cofer E, Zhou J, Troyanskaya O. Selene: a PyTorch-based deep learning library for sequence data. Nat Methods. 2019;16(4):315–318. PMCID: PMC7148117
    Reference Link
  • 1.
    Pereira T, Aldarondo D, Willmore L, Kislin M, Wang S, Murthy M, Shaevitz J. Fast animal pose estimation using deep neural networks. Nat Methods. 2019;16(1):117–125. PMCID: PMC6899221
    Reference Link
  • 1.
    Zhou J, Theesfeld C, Yao K, Chen K, Wong A, Troyanskaya O. Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nat Genet. 2018;50(8):1171–1179. PMCID: PMC6094955
    Reference Link

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