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Papers:
Kevrekidis, G. A., Koronaki, E. D., & Kevrekidis, Y. G. (2024). Conformal disentanglement: A neural framework for perspective synthesis and differentiation. arXiv preprint arXiv:2408.15344.
Ehrlich, D. A., Schick-Poland, K., Makkeh, A., Lanfermann, F., Wollstadt, P., & Wibral, M. (2024). Partial information decomposition for continuous variables based on shared exclusions: Analytical formulation and estimation. Physical Review E, 110(1), 014115.
Ponnapalli, S. P., Saunders, M. A., Van Loan, C. F., & Alter, O. (2011). A higher-order generalized singular value decomposition for comparison of global mRNA expression from multiple organisms. PloS one, 6(12), e28072.
Chen H, Chen J, Muir LA, Ronquist S, Meixner W, Ljungman M, Ried T, Smale S, Rajapakse I. "Functional Organization of the Human 4D Nucleome." Proceedings of the National Academy of Sciences 112.26 (2015): 8002-8007. Supporting Information
Lindsly S, Chen C, Liu S, Ronquist S, Dilworth S, Perlman M, Rajapakse I. "4DNvestigator: time series genomic data analysis toolbox." Nucleus, 12:1, 58-64, DOI: 10.1080/19491034.2021.1910437 (2021) .
Rackham, Owen JL, et al. "A predictive computational framework for direct reprogramming between human cell types." Nature genetics 48.3 (2016): 331-335.
Lotfollahi, Mohammad, F. Alexander Wolf, and Fabian J. Thesis. "scGen predicts single-cell perturbation responses." Nature methods 16.8 (2019): 715-721.
Bunne, Charlotte, et al. "Learning single-cell perturbation responses using neural optimal transport." Nature methods 20.11 (2023): 1759-1768.
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