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Bioinformatics and Complex Networks group

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The Bioinformatics and Complex Networks group at Cinvestav Irapuato brings together research and training in biology, computation, mathematics, and data-driven approaches to complex systems.

This site serves as a common entry point for the group's academic activities, events, and community initiatives.

B&CN Retreat

The annual retreat brings together students, researchers, and collaborators for scientific exchange, short talks, and community activities.

WABio

The Workshop of Algorithms in Bioinformatics focuses on algorithmic, mathematical, and computational approaches to bioinformatics.

Lab members

  • Postdoctoral researcher Elizabeth Cadenas-Castrejon
  • PhD student José Antonio Ramírez-Rafael
  • PhD student Manuel Barrios-Izás
  • PhD student Luis Felipe Hernández-Ramírez
  • PhD student Brenda Fernanda Noguez-Ruiz
  • PhD student Randy Brandon Gallegos-Rodríguez
  • PhD student Astou Diop
  • Undergrad student David Azael Nava Santana
  • Undergrad Student Elena Altair Pozas-Ramírez
  • PhD internship student Aminat Shokunbi

Publications

Aviña-Padilla, K., Ramírez-Rafael, J. A., Herrera-Oropeza, G. E., Muley, V. Y., Valdivia, D. I., Díaz-Valenzuela, E., García-García, A., Varela-Echavarría, A., & Hernández-Rosales, M. (2021). Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role. Frontiers in Genetics, 12. https://doi.org/10.3389/fgene.2021.654256

Aviña-Padilla, K., Zambada-Moreno, O., Jimenez-Limas, M. A., Hammond, R. W., & Hernández-Rosales, M. (2023). Dynamic co-expression modular network analysis of bHLH transcription factors regulation in the potato spindle tuber viroid-tomato pathosystem. https://doi.org/10.1101/2023.11.10.566618

Diop, I. M., Cruz-Bonilla, E., Wolff, C., Cherifi, H., & Hernández-Rosales, M. (2026). Multiscale mobility: How the COVID-19 pandemic reshaped Mexico’s intermunicipal connectivity. PLOS Complex Systems, 3(1), e0000086. https://doi.org/10.1371/journal.pcsy.0000086

Hellmuth, M., Korchmaros, A., Ramírez-Rafael, J. A., Schmidt, B., Stadler, P. F., & Thekkumpadan Puthiyaveedu, S. (2024). Partial Fitch Graphs: Characterization, Satisfiability and Complexity∗. https://doi.org/10.1101/2024.04.30.591842

Miranda-Rodríguez, J. R., Okendo, J., Gutiérrez-Sarmiento, W., Ber, T., Pasulka, J., Nemesh, K., Torrado-Tapias, A., Ortiz-Ávila, E., Ramírez-Sánchez, O., Lozano-Flores, C., Hernández-Ramírez, L. F., Hernández-Rosales, M., Svoboda, P., Burgess, S. M., & Varela-Echavarría, A. (2025). The chromosome-level genome assembly of the slug Deroceras laeve facilitates its use as a comparative model of regeneration. G3: Genes, Genomes, Genetics, 15(10). https://doi.org/10.1093/g3journal/jkaf164

Ramírez-Rafael, J. A., Korchmaros, A., Aviña-Padilla, K., López-Sánchez, A., Martinez-Medina, G., Hernández-Álvarez, A. J., Hellmuth, M., Stadler, P. F., & Hernández-Rosales, M. (2025). REvolutionH-tl: A Fast and Robust Tool for Decoding Evolutionary Gene Histories. https://doi.org/10.1101/2025.04.03.646975

Sánchez, A. L., Ramírez-Rafael, J. A., Flores-Lamas, A., Hernández-Rosales, M., & Lafond, M. (2025). The path-label reconciliation (PLR) dissimilarity measure for gene trees. Algorithms for Molecular Biology, 20(1), 16. https://doi.org/10.1186/s13015-025-00284-8