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.
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portfolio
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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talks
teaching
Genetics
Undergraduate course, Autonomous University of Mexico City (UACM), College of Sciences and Humanities, 2021
This course provides a comprehensive foundation in genetic principles, covering molecular, classical, and population genetics within the context of health and biological sciences.
Cell Biology
Undergraduate course, Autonomous University of Mexico City (UACM), College of Sciences and Humanities, 2022
This course explores the fundamental unit of life, focusing on the structural and functional organization of prokaryotic and eukaryotic cells, as well as the molecular mechanisms governing cellular homeostasis.
Biostatistics
Undergraduate course, Autonomous University of Mexico City (UACM) Cuautepec, College of Sciences and Humanities, 2024
This course focuses on analytical tools for biological and health sciences.