Shen Lab

Publications

  • You, N., Liu, C., Gu, Y., Wang, R., Jia, H., Zhang, T., Jiang, S., Shi, J., Chen, M., Guan, M. X., Sun, S., Pei, S., Liu, Z. *, & Shen, N. * (2024). SpliceTransformer predicts tissue-specific splicing linked to human diseases. Nature Communications
  • Wang, H.*, Jing, H., Yang, J., Liu, C., Hu, L., Tao, G., Zhao, Z.*, & Shen, N.* (2024). Identifying autism spectrum disorder from multi-modal data with privacy-preserving. Npj mental health research,3(1), 15
  • Sun, Y., Xu, L., Li, Y., Jia, S., Wang, G., Cen, X., Xu, Y., Cao, Z., Wang, J., Shen, N., Hu, L., Zhang, J., Mao, J., Xia, H., Liu, Z., & Fu, X. (2024) Mitophagy defect mediates the aging-associated hallmarks in Hutchinson-Gilford progeria syndrome. Aging cell, 4, e14143. Advance online publication.
  • Yuan, X. #, Wang, H. #, Sun, Z. #, Zhou, C., Chu, S. C., Bu, J., Shen, N. (2024) Anchored-fusion enables targeted fusion search in bulk and single-cell RNA sequencing data. Cell reports methods, 4, 100733.
  • Zhang, L. #, Zhao, J. #, Lam, S. M. #, Chen, L. #, Gao, Y. #, Wang, W. #, Xu, Y., Tan, T., Yu, H., Zhang, M., Liao, X., Wu, M., Zhang, T., Huang, J., Li, B., Zhou, Q. D., Shen, N., Lee, H. J., Ye, C., Li, D. *, … Zhang, J. * (2024) Low-input lipidomics reveals lipid metabolism remodelling during early mammalian embryo development. Nature cell biology, 26(2), 278–293.
  • Liu, Y. #, Zhang, T. #, You, N., Wu, S. *, & Shen, N.* (2024). MAGPIE: accurate pathogenic prediction for multiple variant types using machine learning approach. Genome medicine,16(1),3.
  • Zhang, T., Jia, H., Song, T., Lv, L., Gulhan, D. C., Wang, H., Guo, W., Xi, R., Guo, H., & Shen, N. (2023). De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data. Genome medicine, 15(1), 115.
  • Wu, L., Wang, H., Chen, Y., Zhang, X., Zhang, T., Shen, N., Tao, G., Sun, Z., Ding, Y. *, Wang, W. *, & Bu, J. * (2023). Beyond radiologist-level liver lesion detection on multi-phase contrast-enhanced CT images by deep learning. iScience, 26(11), 108183.
  • Lv, L. #, Zhang, T. #, Jia, H., Zhang, Y., Ahsan, A., Zhao, X., Chen, T. *, Shen, Z. *, & 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. Nature communications, 13(1), 1084.
  • Li, J., Cai, Z., Vaites, L. P., Shen, N., Mitchell, D. C., Huttlin, E. L., Paulo, J. A., Harry, B. L. *, & Gygi, S. P. * (2021). Proteome-wide mapping of short-lived proteins in human cells. Molecular cell, 81(22), 4722-4735.e5.
  • 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. N., Cacace, A. M., & Wallace, O. (2020). p38α Regulates Expression of DUX4 in a Model of Facioscapulohumeral Muscular Dystrophy. The Journal of pharmacology and experimental therapeutics, 374(3), 489-498.
  • Shen, N., Zhao, J., Schipper, J. L., Zhang, Y., Bepler, T., Leehr, D., Bradley, J., Horton, J., Lapp, H., & Gordan, R. (2018). Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding. Cell systems, 6(4), 470-483.e8.
  • Sparks, E. E., Drapek, C., Gaudinier, A., Li, S., Ansariola, M., Shen, N., Hennacy, J. H., Zhang, J., Turco, G., Petricka, J. J., Foret, J., Hartemink, A. J., Gordân, R., Megraw, M., Brady, S. M., & 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., Abe, N., Horton, J., Mann, R. S., Bussemaker, H. J., Gordân, R. *, & Rohs, R. * (2015). Quantitative modeling of transcription factor binding specificities using DNA shape. Proceedings of the National Academy of Sciences of the United States of America, 112(15), 4654-4659.
  • Gordân, R., Shen, N., Dror, I., Zhou, T., Horton, J., Rohs, R. *, & Bulyk, 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), 1093-1104.
  • Chen, J., Ma, M., Shen, N., Xi, J. J. *, & 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, M. H., Shen, N., Sobel, R. A., & Mochly-Rosen, D. (2011). Aberrant mitochondrial fission in neurons induced by protein kinase C{delta} 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, 2023. P38 kinase inhibitors reduce dux4 and downstream gene expression for the treatment of fshd. Taiwan TWI793191B.
  • 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. Spain ES2927715T3.
  • 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. US11479770B2.
  • 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. Denmark DK3691620T3.
  • 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. Europe EP3691620B1.
  • 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. China CN111601593B.
  • 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. U.S. US11291659B2.
  • 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. Japan JP7012152B2.
  • 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, 2021. P38 kinase inhibitors reduce dux4 and downstream gene expression for the treatment of fshd. Canada CA3077499C.
  • 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, 2021. P38 kinase inhibitors reduce DUX4 and downstream gene expression for the treatment of FSHD. Australia AU2018346712B2.
  • 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 2023113691A.
  • 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, 2020. Use of p38 inhibitors to reduce expression of dux4. U.S. Patent 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, 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, 2019. 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, 2018. P38 kinase inhibitors reduce dux4 and downstream gene expression for the treatment of fshd. Canadian Intellectual Property Office CA3077499.

    • 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.

    • Contents