We will discuss about “Multiparameter persistent homology landscapes identify immune cell spatial patterns in tumors”, Vipond, Oliver, et al, Proceedings of the National Academy of Sciences 118.41 (2021): e2102166118. Abstract Highly resolved spatial data of complex systems encode rich and nonlinear information. Quantification of heterogeneous and noisy data—often with outliers, artifacts, and mislabeled points—such as …

We will discuss about "Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators”, Karapetyan, Sargis, and Nicolas E. Buchler,Physical Review E 92.6 (2015): 062712. Abstract Genetic oscillators, such as circadian clocks, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest …

We will discuss about “Optimal control of aging in complex networks”, Sun, Eric D., Thomas CT Michaels, and L. Mahadevan, Proceedings of the National Academy of Sciences 117.34 (2020): 20404-20410. Abstract Many complex systems experience damage accumulation, which leads to aging, manifest as an increasing probability of system collapse with time. This naturally raises the question …

We will discuss about “Analytical time-dependent distributions for gene expression models with complex promoter switching mechanisms”,Jia, Chen, and Youming Li, BioRxiv (2022). Abstract Classical gene expression models assume exponential switching time distributions between the active and inactive promoter states. However, recent experiments have shown that many genes in mammalian cells may produce non-exponential switching time …

We will discuss about “Bayesian Physics Informed Neural Networks for real-world nonlinear dynamical systems”, Linka, Kevin, et al., Computer Methods in Applied Mechanics and Engineering Volume 402, 1 December 2022, 115346 Abstract Understanding real-world dynamical phenomena remains a challenging task. Across various scientific disciplines, machine learning has advanced as the go-to technology to analyze nonlinear dynamical …

We will discuss about “Topological Data Analysis in Time Series: Temporal Filtration and Application to Single-Cell Genomics" , Lin, Baihan., arXiv preprint arXiv:2204.14048 (2022). Abstract The absence of a conventional association between the cell-cell cohabitation and its emergent dynamics into cliques during development has hindered our understanding of how cell populations proliferate, differentiate, and compete, i.e. …