In this talk, we discuss the paper "Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage" by Zhiwei Huang, et. al., bioRxiv, 2024. Zoom : https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09 Abstract Cells must adopt flexible regulatory strategies to make decisions regarding their fate, including differentiation, apoptosis, or survival in the face of …

In this talk, we discuss the paper "Achieving Occam’s razor: Deep learning for optimal model reduction" by Botond B. Antal et.al., PLOS Computational Biology, 2024. Abstract  All fields of science depend on mathematical models. Occam’s razor refers to the principle that good models should exclude parameters beyond those minimally required to describe the systems they represent. This …

In this talk we discuss the paper "Mathematical model for the distribution of DNA replication origins" by Alessandro de Moura and Jens Karschau, Physical Review E, 2024. Abstract  DNAreplication in yeast and in many other organisms starts from well-defined locations on the DNA known as replication origins. The spatial distribution of these origins in the genome is particularly …

In this talk, we discuss the paper, “A frequency-amplitude coordinator and its optimal energy consumption for biological oscillators”, by Bo-Wei Qin et. al., Nature Communications, 2021. Zoom : https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09 Abstract  Biorhythm including neuron firing and protein-mRNA interaction are fundamental activities with diffusive effect. Their well-balanced spatiotemporal dynamics are beneficial for healthy sustainability. Therefore, calibrating both anomalous …

In this talk, we discuss the paper : "Noise robustness and metabolic load determine the principles of central dogma regulation" by Teresa W. Lo et al, Sci. Adv, https://doi.org/10.1126/sciadv.ado3095. Zoom: https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09 Abstract The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light …

In this talk, we discuss the paper : "Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment" by Leech et al, nature biotechnology, https://doi.org/10.1371/journal.pcbi.1011879. Zoom: https://us06web.zoom.us/j/99567630778?pwd=N2ZrUWtqZzJ0YURVTzlZT3JJR3FUQT09 Abstract Collective alignment of cell populations is a commonly observed phenomena in biology. An important example …

Abstract: We propose a universal method for data-driven modeling of complex nonlinear dynamics from time-resolved snapshot data without prior knowledge. Complex nonlinear dynamics govern many fields of science and engineering. Data-driven dynamic modeling often assumes a low-dimensional subspace or manifold for the state. We liberate ourselves from this assumption by proposing cluster-based network modeling (CNM) …

In this talk, we discuss the paper "Next generation reservoir computing", by Gauthier, et.al, Nat. Comm., 2021. Abstract : Reservoir computing is a best-in-class machine learning algorithm for processing information generated by dynamical systems using observed time-series data. Importantly, it requires very small training data sets, uses linear optimization, and thus requires minimal computing resources. …