César Nieto, & Sayeh Rezaee. Simulator and Inference script for the article "Dynamical Inference of Cell Size Regulation Parameters":
This is a repository for simulation cell size dynamics. We also perform Parameter inference using Maximum Likelikood Estimation methods.
https://doi.org/10.5281/zenodo.17730929
Juan Sebastian, H., & Nieto, C. (2026). Example of the simulation algorithm for the article "Intrinsic limits of timekeeping precision in gene regulatory cascades".
This is a repository for simulation of gene expression in regulatory cascades.
Nieto, C., Zhang, Z., & Zabaikina, I. (2024). Dataset an codes for the article "Stochastic Gene Expression in Proliferating Cells: Differing Noise intensity in Single-Cell and Population Perspectives".
This is a repository for simulation of gene expression in proliferating cell colonies.
https://doi.org/10.5281/zenodo.14503484
Cesar, N. (2024). Dataset for the article: Unique growth and morphology properties of Clade 5 Clostridioides difficile strains revealed by single-cell time-lapse microscopy.
This is a repository with images and data showing the proliferation of c difficile cells. We perfrom cell segmentation and tracking techniques with analysis of cell dimensions.
https://doi.org/10.5281/zenodo.13352469
Cesar, N. (2024). Simulator for the article: "A generalized adder mechanism for cell size homeostasis: Implications for stochastic dynamics of clonal proliferation".
This is a repository for simulation of cell division and proliferation dynamis using as size-based division strategy. It can be used to simulate a wide range of cells from bacteria to human cells.
https://doi.org/10.5281/zenodo.13251255
Nieto, C. (2024). Data set and data processing software of: Bacterial cell size modulation along the growth curve across nutrient conditions
In this repository we implement image processing algorithms for studying cells size of bacteria in contiuosly changing environments.
https://doi.org/10.5281/zenodo.13208281
Cesar Nieto, C. N. (2023). Data Analysis for: Coupling Cell Size Regulation and Proliferation Dynamics for C. glutamicum Reveals Cell Division Based on Surface Area
This is a repository we analyze cell dimensions and proliferation trends of C glutamicum bacteria. We study the number of cells in the colony over time.
https://doi.org/10.5281/zenodo.10433707
Camilo Blanco, & Cesar Nieto. (2023). SystemsBiologyUniandes/PyEcoLib: V2.0.3 (V2.0.3).
In this repositoy we implement a library for imulation of cell proliferation and cell size regulation for bacteria growing exponential
https://doi.org/10.5281/zenodo.4579183