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2024

Systems biology: 105. Wu, Z., Shen, S., Mizikovsky, D., Cao, Y., Naval-Sanchez, M., Tan, S., Alvarez, Y., Sun, Y., Chen, X., Zhao, Q., Kim, D., Yang, P., Hill, T., Jones. A., Fairlie, D., Pébay, A., Hewitt, A., Tam, P., White, M., Nefzger, C., Palpant, N. (2024) Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm. Developmental Cell, 59, https://doi.org/10.1016/j.devcel.2024.01.019 [Full Text] Methodology and tools: 104. Chen, C.✢, Kim, H.✢† & Yang, P.† (2024) Evaluating spatially variable gene detection methods for spatial transcriptomics data. Genome Biology, 25, 18. [Full Text] [Repo]
Zero Carbon World

Systems biology: 103. Kim, H., O'Hara-Wright, M., Kim, D., Loi, T., Lim, B., Jamieson, R., Gonzalez-Cordero, A.† & Yang, P.† (2023) Comprehensive characterization of fetal and mature retinal cell identity to assess the fidelity of retinal organoids. Stem Cell Reports, 18(1), 175-189. [Full Text] [Eikon Shiny Web Server] 102. Kim, D., Tran, A., Kim, H., Lin, Y., Yang, J.† & Yang, P.† (2023) Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data. npj Systems Biology and Applications, 9, 51. [Full Text] 101. Ting, T., Coleman, P., Kim, H., Zhao, Y., Mulangala, J., Cheng, N., Li, W., Gunatilake, D., Johnstone, D., Loo, L., Neely, G., Yang, P., Götz, J., Vadas, M & Gamble, J. (2023) Vascular senescence and leak are features of the early breakdown of the blood–brain barrier in Alzheimer’s disease models. GeroScience, 45(6), 3307-3331. [Full Text]
2022

Systems biology: 89. Kim, H., Li, P., Kim, T., Oldfield, A., Zheng, X. † & Yang, P.† (2022) Integrative Analysis Reveals Histone Demethylase LSD1 Promotes RNA Polymerase II Pausing. iScience, 25(10), 105049. [Full Text] 88. Blazev, R., Carl, C., Ng, Y., Molendijk, J., Voldstedlund, C., Zhao, Y., Xiao, D., Kueh, A., Miotto, P., Haynes, V., Hardee, J., Chung, J., McNamara, J., Qian, H., Gregorevic, P., Oakhill, J., Herold, M., Jensen, T., Lisowski, L., Lynch, G., Dodd, G., Watt, M., Yang, P., Kiens, B., Richter, E., Parker, B. (2022) Phosphoproteomics of three exercise modalities identifies canonical signaling and C18ORF25 as an AMPK substrate regulating skeletal muscle function. Cell Metabolism, 34(10), 1561-1577. [Full Text] 87. Xiao, D., Caldow, M., Kim, H., Blazev, R., Koopman, R., Manandi, D., Parker, B. † & Yang, P.† (2022) Time-resolved phosphoproteome and proteome analysis reveals kinase signalling on master transcription factors during myogenesis. iScience, 25(6), 104489. [Full Text]