Literature DB >> 34061834

Quantifying cell transitions in C. elegans with data-fitted landscape models.

Elena Camacho-Aguilar1,2, Aryeh Warmflash2,3, David A Rand1,4.   

Abstract

Increasing interest has emerged in new mathematical approaches that simplify the study of complex differentiation processes by formalizing Waddington's landscape metaphor. However, a rational method to build these landscape models remains an open problem. Here we study vulval development in C. elegans by developing a framework based on Catastrophe Theory (CT) and approximate Bayesian computation (ABC) to build data-fitted landscape models. We first identify the candidate qualitative landscapes, and then use CT to build the simplest model consistent with the data, which we quantitatively fit using ABC. The resulting model suggests that the underlying mechanism is a quantifiable two-step decision controlled by EGF and Notch-Delta signals, where a non-vulval/vulval decision is followed by a bistable transition to the two vulval states. This new model fits a broad set of data and makes several novel predictions.

Entities:  

Year:  2021        PMID: 34061834     DOI: 10.1371/journal.pcbi.1009034

Source DB:  PubMed          Journal:  PLoS Comput Biol        ISSN: 1553-734X            Impact factor:   4.475


  3 in total

1.  Geometry of gene regulatory dynamics.

Authors:  David A Rand; Archishman Raju; Meritxell Sáez; Francis Corson; Eric D Siggia
Journal:  Proc Natl Acad Sci U S A       Date:  2021-09-21       Impact factor: 12.779

Review 2.  Dynamical landscapes of cell fate decisions.

Authors:  M Sáez; J Briscoe; D A Rand
Journal:  Interface Focus       Date:  2022-06-10       Impact factor: 4.661

3.  Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions.

Authors:  Meritxell Sáez; Robert Blassberg; Elena Camacho-Aguilar; Eric D Siggia; David A Rand; James Briscoe
Journal:  Cell Syst       Date:  2021-09-17       Impact factor: 10.304

  3 in total

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