Shen Lab

Preprint

  • Tianyun Zhang, Ning Shen. Detecting expressed cancer somatic mutations from single-cell RNA sequencing data. biorxiv

    • Publications

  • Lv, L., Zhang, T.Y., Jia, H.Y., Zhang, Y.Y., Ahsan, A., Zhao, X.Y., Chen, T., Shen, Z.Q., Shen, N.(2022). Temporally integrated transcriptome analysis reveals ASFV pathology and host response dynamics. Frontiers in Immunology. 13:995998
  • Jin, Z., Huang, W., Shen, N., Li, J., Wang, X., Dong, J., Park, P.J., Xi, R. (2022). Single-cell gene fusion detection by scFusion. Nat Commun, 13(1084).
  • Li, J., Cai, Z., Vaites, L. P., Shen, N., Mitchell, D. C., Huttlin, E. L., ... & Gygi, S. P. (2021). Proteome-wide mapping of short-lived proteins in human cells. Molecular Cell, 81(22), 4722-4735.
  • Rojas, L.A., Valentine, E., Accorsi, A., Maglio, J., Shen, N., Robertson, A., Kazmirski, S., Rahl, P., Tawil, R., Cadavid, D., Thompson, L.A., Ronco, L., Chang, A., Cacace, A., and Wallace, O., 2020. P38α Regulates Expression of DUX4 in Facioscapulohumeral Muscular Dystrophy. Journal of Pharmacology and Experimental Therapeutics. 119.264689
  • Shen, N., Zhao, J., Schipper, J.L., Zhang, Y., Bepler, T., Leehr, D., Bradley, J., Horton, J., Lapp, H. and Gordan, R., 2018. Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding. Cell systems, 6(4), pp.470-483
  • Sparks, E.E., Drapek, C.E., Gaudinier, A., Li, S., Ansariola, M., Shen, N., Matsumoto, N., Turco, G., Qiu, Y., Petricka, J.J., Foret, J., Chen, M., Gordân, R., Megraw, M. and Brady, S., Benfey, P.N., 2016. Establishment of expression in the SHORTROOT-SCARECROW transcriptional cascade through opposing activities of both activators and repressors. Developmental Cell 39(5):585-596
  • Zhou, T.*, Shen, N.*, Yang, L., Horton, J., Bussemaker, H., Gordân, R.+ and Rohs, R+., 2015. Quantitative modeling of transcription factor binding specificities using DNA shape. Proceedings of the National Academy of Science 112(15); 4654-4659
  • Gordân, R., Shen, N., Dror, I., Zhou, T., Horton, J., Rohs, R. and Bulky, M.L., 2013. Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Reports 3(4):1093-104
  • Chen, J., Ma, M., Shen, N., Xi, J. and Tian, W., 2013. Integration of cancer gene co-expression network and metabolic network to uncover potential cancer drug targets. Journal of Proteome Research 12(6): 2354-2364
  • Qi, X., Disatnik, MH., Shen, N., Sobel, RA. and Mochly-Rosen, D., 2011. Aberrant Mitochondrial Fission in Neurons Induced by Delta Protein Kinase C under Oxidative Stress Conditions, in Vivo. Molecular Biology of the Cell 22(2):256-265

    • Patents

  • Cacace, A.M., SOTO, L.G.A.R., Thompson III, L.A., Wallace, O.B., Ronco, L.V., Shen, N., Robertson, A.S. and Chang, A.N., Fulcrum Therapeutics Inc, 2020. P38 kinase inhibitors reduce DUX4 and downstream gene expression for the treatment of FSHD. U.S. Patent 10,537,560.
  • Cacace, A.M., SOTO, L.G.A.R., Thompson III, L.A., Wallace, O.B., Ronco, L.V., Shen, N., Robertson, A.S. and Chang, A.N., Fulcrum Therapeutics Inc, 2020. P38 kinase inhibitors reduce DUX4 and downstream gene expression for the treatment of FSHD. Israel Patent Offiece IL273589.
  • Cacace, A.M., SOTO, L.G.A.R., Thompson III, L.A., Wallace, O.B., Ronco, L.V., Shen, N., Robertson, A.S. and Chang, A.N., Fulcrum Therapeutics Inc, 2019. P38 kinase inhibitors reduce DUX4 and downstream gene expression for the treatment of FSHD. U.S. Patent 10342786.
  • Cacace, A.M., SOTO, L.G.A.R., Thompson III, L.A., Wallace, O.B., Ronco, L.V., Shen, N., Robertson, A.S. and Chang, A.N., Fulcrum Therapeutics Inc, 2019. P38 kinase inhibitors reduce dux4 and downstream gene expression for the treatment of fshd. Japanese Patent Application 7012152.
  • Cacace, A.M., SOTO, L.G.A.R., Thompson III, L.A., Wallace, O.B., Ronco, L.V., Shen, N., Robertson, A.S. and Chang, A.N., Fulcrum Therapeutics Inc, 2018. P38 kinase inhibitors reduce dux4 and downstream gene expression for the treatment of fshd. Canadian Intellectual Property Office CA3077499.
  • Cacace, A.M., SOTO, L.G.A.R., Thompson III, L.A., Wallace, O.B., Ronco, L.V., Shen, N., Robertson, A.S. and Chang, A.N., Fulcrum Therapeutics Inc, 2022. Use of p38 inhibitors to reduce expression of dux4. U.S. Patent Application 11479770B2.
  • Cacace, A.M., SOTO, L.G.A.R., Thompson III, L.A., Wallace, O.B., Ronco, L.V., Shen, N., Robertson, A.S. and Chang, A.N., Fulcrum Therapeutics Inc, 2022. P38 kinase inhibitors reduce dux4 and downstream gene expression for the treatment of fshd. European Patent Office 3691620T3.
  • Cacace, A.M., SOTO, L.G.A.R., Thompson III, L.A., Wallace, O.B., Ronco, L.V., Shen, N., Robertson, A.S. and Chang, A.N., Fulcrum Therapeutics Inc, 2023. P38 kinase inhibitors reduce dux4 and downstream gene expression for the treatment of fshd. Japanese Patent Application 2023081029A.

    • Conference Proceedings

  • Ronco, L., Wagner, K., Cadavid, D., Chang, A., Mellion, M., Robertson, A., Raines, S., Chadchankar, J., Rojas, A., Shieh, P., Shen, N., Statland, J., Tapscott, S., Tawil, R., Engelen, B., Wang, L., Johnson, N., Wallace, O., 2020, A biomarker of DUX4 activity to evaluate losmapimod treatment effect in FSHD phase 2 trials. Neuromuscular Disorders, 30, p.S113
  • Ronco, L., Cadavid, D., Chang, A., Mellion, M., Rojas, A., Shen, N., Tawil, R., Tapscott, S., Wang, L. and Wallace, O., 2019. P. 47Design of a biomarker of DUX4 activity to evaluate losmapimod treatment effect in FSHD Phase 2 trials. Neuromuscular Disorders, 29, pp.S54-S55.
  • Wallace, O., Accorsi, A., Barnes, R., Cacace, A., Cadavid, D., Chang, A., Eyerman, D., Gould, R., Kazmirski, S., Maglio, J., Mellion, M., Rahl, P., Rojas, L., Ronco, L., Shen, N., Thompson, L., and Valentine, E., 2019. P. 43Targeting DUX4 expression, the root cause of FSHD: identification of a drug target and development candidate. Neuromuscular Disorders, 29, pp.S53-S54.
  • Mellion, M., Valentine, E., Accorsi, A., Maglio, J., Shen, N., Robertson, A., Barnes, R., Kazmirski, S., Chang, A., Eyerman, D. and Thompson, L., 2019. FTX-1821 for Treatment of FSHD at its Root Cause: Results of a Clinical Trial in a Dish Neurology 92 S23. 006.
  • Leehr, D., Bradley, J., Gordan, R., Shen, N. and Lapp, H., 2018. iMADS: A sustainable software collaboration for predicting transcription factor binding specificity. F1000Research, 7.
  • Rojas, L., Accorsi, A., Shen, N., Maglio, J., Chang, A., Rahl, P. and Cacace, A., 2017. Pharmacologic modulation of DUX4-dependent phenotypes in FSHD. Neuromuscular Disorders, 27, p.S200.