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Aarón Castillo Jiménez PhD | Systems biologist

Academic website of Dr. Aarón Castillo Jiménez, Researcher in Systems biology.

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Posts

Future Blog Post

less than 1 minute read

Published: January 01, 2199

This post will show up by default. To disable scheduling of future posts, edit config.yml and set future: false.

Blog Post number 4

less than 1 minute read

Published: August 14, 2015

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 3

less than 1 minute read

Published: August 14, 2014

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 2

less than 1 minute read

Published: August 14, 2013

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 1

less than 1 minute read

Published: August 14, 2012

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

portfolio

Meta-GRN: Diffusion-Coupled Model of Root Epidermis

A computational framework in Python to simulate the emergence of spatial patterns in Arabidopsis root through the coupling of gene regulatory networks and molecular diffusion.

Automated 3D Segmentation of the Root Meristem

A high-throughput pipeline utilizing Convolutional Neural Networks (PlantSeg & Cellpose) for characterizing cell geometry and cycle dynamics.

publications

A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle

Published in PLOS Computational Biology, 2015

This research proposes a Boolean gene regulatory network (GRN) that recovers the robust cyclic behavior of key molecular components in the Arabidopsis thaliana cell cycle.

Recommended citation: Ortiz-Gutiérrez, E., García-Cruz, K., Azpeitia, E., Castillo, A., Sánchez, M. D. L. P., & Álvarez-Buylla, E. R. (2015). A dynamic gene regulatory network model that recovers the cyclic behavior of Arabidopsis thaliana cell cycle. PLoS computational biology, 11(9), e1004486.
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Multi-level gene regulatory network models to understand complex mechanisms underlying plant development

Published in Current Opinion in Plant Biology, 2020

This review discusses the integration of gene regulatory networks with physicochemical fields through multi-level modeling to understand plant morphogenesis.

Recommended citation: García-Gómez, M. L., Castillo-Jiménez, A., Martínez-García, J. C., & Alvarez-Buylla, E. R. (2020). Multi-level gene regulatory network models to understand complex mechanisms underlying plant development. Current Opinion in Plant Biology, 57, 171-179.
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Stochastic Turing patterns of trichomes in Arabidopsis leaves

Published in Proceedings of the National Academy of Sciences (PNAS), 2023

This paper combines statistical characterization and theoretical modeling to show that trichome patterns in Arabidopsis are driven by demographic noise, manifesting as stochastic Turing patterns.

Recommended citation: Di Patti, F., Ugartechea Chirino, Y., Arbel-Goren, R., Sharon, T., Castillo, A., Alvarez–Buylla, E., ... & Stavans, J. (2023). Stochastic Turing patterns of trichomes in Arabidopsis leaves. Proceedings of the National Academy of Sciences, 120(42), e2309616120.
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Extended discrete gene regulatory network model for the Arabidopsis thaliana root-hair cell fate

Published in bioRxiv, 2023

This work presents an updated and expanded discrete model of the gene regulatory network governing root-hair cell fate, incorporating additional regulatory nodes and hormonal signaling pathways.

Recommended citation: Castillo-Jiménez, A., Garay-Arroyo, A., de La Paz Sánchez, M., García-Ponce, B., Martínez-García, J. C., & Álvarez-Buylla, E. R. (2023). Extended discrete gene regulatory network model for the Arabidopsis thaliana root-hair cell fate. bioRxiv, 2023-11.
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Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback

Published in npj Systems Biology and Applications, 2025

This paper introduces a diffusion-coupled meta-GRN model to explain how spatial cellular patterns emerge from the feedback between genetic networks and molecular diffusion.

Recommended citation: Castillo-Jiménez, A., Garay-Arroyo, A., Sánchez, M. D. L. P., Martínez-García, J. C., & Álvarez-Buylla, E. R. (2025). Cellular patterns in Arabidopsis root epidermis emerge from gene regulatory network and diffusion dynamical feedback. npj Systems Biology and Applications, 11(1), 107.
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