Computational/Systems Biology

Computational/Systems Biology This page aims to serve as a place for sharing the theoretical side of the Computational and Systems Biology field in a mathematical modeling-oriented fashion.

We would like to complement the bottom-up with the top-down approach.

How Cells Control Their Size and Impact Population GrowthRecent studies examining how cells change size over time have u...
01/04/2025

How Cells Control Their Size and Impact Population Growth

Recent studies examining how cells change size over time have uncovered fascinating patterns across many different organisms. One key discovery is the "adder" principle, where cells add a consistent amount of size between birth and division, regardless of how big they were at birth.

Our research provides a deeper understanding of this adder mechanism, showing it works with any pattern of cell growth—not just the commonly assumed exponential growth. The main requirement is surprisingly simple: the molecules that trigger cell division must be produced at a rate that matches the cell's growth rate, accumulating until they reach a specific threshold that signals division.

This discovery has important implications for how groups of cells derived from a single ancestor (clones) grow over time. When cells grow exponentially with the adder mechanism, initial differences between clonal populations eventually disappear—clone sizes become more uniform over time. However, with several non-exponential growth patterns, these differences between clones actually increase over time and stabilize at a higher level of variation.

These findings help explain the connection between how individual cells regulate their size and how entire populations of related cells grow. This provides insight into why we see such wide variations in clone sizes in labeled human cell lines used in research.

I am so happy to share with you guys my most recent article in Biophysical Journal! I have been working for almost ten years culminating with a project like this! It explores a simple model explaining how cell division is related to colony expansion. Check it out https://lnkd.in/eeHxWfhZ

🎉 More than 38K downloads and counting! 📈 Over 500+ per month and 100+ per week! 🚀Explore our library PyEcoLib and repro...
30/09/2024

🎉 More than 38K downloads and counting! 📈 Over 500+ per month and 100+ per week! 🚀

Explore our library PyEcoLib and reproduce all our research on cell size dynamics. Whether you’re in biology, computational modeling, or data science, PyEcoLib provides all the tools you need to dive into cutting-edge research.

Check it out and start exploring today! 🔬📊

View download stats for the Pyecolib python package. Download stats are updated daily

Previous models of cell size homeostasis primarily assume exponential growth, limiting their applicability to non-expone...
27/09/2024

Previous models of cell size homeostasis primarily assume exponential growth, limiting their applicability to non-exponential cases observed in some cell types. By reformulating the problem, this study identifies a key mechanism—cell cycle regulators produced at a rate proportional to growth—that leads to adder behavior independent of growth laws. This generalized model not only accounts for cell size control across different organisms but also explains the stochastic dynamics of clonal populations, offering insights into the broad variability observed in clonal sizes, particularly in cancer and microbial colonies.

Measurements of cell size dynamics have revealed phenomenological principles by which individual cells control their size across diverse organisms. One of the emerging paradigms of cell size homeostasis is the adder , where the cell cycle duration is established such that the cell size increase from...

08/06/2024

For the first time, we have exact simple formulas for stationary size statistics from single-cell size trajectories. It is mind-blowing how an intricate stochastic hybrid system turns into such a neat description of cell size statistics. This work offers new insights into cell size regulation, impacting both biological and agricultural systems. Dive into the details in the latest paper.

This contribution explores mechanisms that regulate the dynamics of single-cell size, maintaining equilibrium around a target set point. Using the formalism of

30/05/2024

We explore how E. coli cells regulate their size under adverse conditions, using models beyond the "adder". Experimental data from microfluidic studies identified division size functions based on birth size. Although no single function explains all experiments, this insight reveals the cells' adaptive capacity. The findings show that while E. coli cells typically follow the adder model in optimal conditions, they adjust their division strategy under stress, with larger cells better explained by reversible steps in cell cycle progression and smaller cells by target size models.

Our new collaboration presents a significant advancement in understanding cell growth and division. For the first time, ...
22/12/2023

Our new collaboration presents a significant advancement in understanding cell growth and division. For the first time, it provides closed-form expressions for the mean size and noise in fluctuations within biologically relevant regimes. This breakthrough allows for a deeper comprehension of cell size homeostasis, particularly in the context of adder-based size control in bacteria and its extensions to multi-stage models with size-dependent transitions.

In this contribution, we use the framework of discrete-event dynamical systems to model a fundamental aspect of life - the proliferation of cells. This process starts with a newborn cell, whose size (as quantified by its volume or mass) increases exponentially over time. At a prescribed time during....

13/11/2023

An international research team led by James Umen, PhD, member, Donald Danforth Plant Science Center has made an unexpected discovery of a biased counting mechanism used by the single-celled green alga Chlamydomonas to control cell division.

https://www.mdpi.com/2076-2607/11/7/1748
06/07/2023

https://www.mdpi.com/2076-2607/11/7/1748

Inoculation with phosphate-solubilizing bacteria (PSB) and the application of phosphorus (P) sources can improve soil P availability, enhancing the sustainability and efficiency of agricultural systems. The implementation of this technology in perennial grasses, such as Kikuyu grass, for cattle feed...

24/05/2023

1 Electrical Engineering, University of Delaware, 139 The Green, Newark, DE 19716, Newark, Delaware, 19716-5600, UNITED STATES

08/05/2023

Understanding how size homeostasis emerges from stochastic individual cell behaviors within a population remains a challenge in biology. The unicellular green a

13/02/2023

Check out our new book in progress. We are trying to describe my passion — cell growth and proliferation dynamics — through mathematical…

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