Publications

Peer reviewed journal articles

  • Ayala-Ruano, S., Webel, H., & Santos, A. (2025). VueGen: Automating the generation of scientific reports. Bioinformatics Advances, vbaf149. doi: doi.org/10.1093/bioadv/vbaf149.

  • Ordoñez, J., Tovar, C., Walker, B., Wheeler, J., Ayala-Ruano, S., Aguirre-Carvajal, K., McMahon S., & Cuesta, F. (2025). Phenological patterns of tropical mountain forest trees across the neotropics: evidence from herbarium specimens. Proc. R. Soc. B, 292 (2041), 20242748. doi: doi.org/10.1098/rspb.2024.2748

  • Aguilera-Mendoza, L., Ayala-Ruano, S.^, Martinez-Rios, F., Chavez, E., García-Jacas, C. R., Brizuela, C. A., & Marrero-Ponce, Y. (2023). StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks. Bioinformatics, 39 (8), btad506. doi: doi.org/10.1093/bioinformatics/btad506

  • Ayala-Ruano S., Marrero-Ponce Y., Aguilera‑Mendoza L., Pérez N., et al. (2022). Exploring the Chemical Space of Antiparasitic Peptides and Discovery of New Promising Leads through a Novel Approach based on Network Science and Similarity Searching. ACS omega. doi: doi.org/10.1021/acsomega.2c03398.

  • Oña-Chuquimarca, S., Ayala-Ruano, S., Goossens, Pauwels, L., et al. (2020). The molecular basis of JAZ-MYC coupling, a protein-protein interface essential for plant response to stressors. Frontiers in Plant Science, 11, 1139. doi: 10.3389/fpls.2020.01139.

    • This article was chosen to feature in the Frontiers in Plant Science 2020 highlights e-book collection. doi: 10.3389/978-2-88966-723-9

  • Ayala‐Ruano, S., Santander‐Gordón, D., Tejera, E., Perez‐Castillo, Y., & Armijos-Jaramillo, V. (2019). A putative antimicrobial peptide from Hymenoptera in the megaplasmid pSCL4 of Streptomyces clavuligerus ATCC 27064 reveals a singular case of horizontal gene transfer with potential applications. Ecology and Evolution, 9 (5), 2602-2614. doi: 10.1002/ece3.4924.

Editorial journal articles

  • Osorio-Mogollon C, Grentzinger V, Olguin-Orellana GJ, Ayala-Ruano S., et al. (2023). ISCB Student Council Symposium 2021, a virtual global venue: challenges and lessons learned. F1000Research, 12(50). doi: 10.12688/f1000research.129945.1

  • Ayala-Ruano S.^, Hernandez, F., Ortega, A., Infante, D., et al. (2022). Highlights of the 1st Ecuadorian-Venezuelan Symposium of Young Researchers in Bioinformatics (1SEVJIB). F1000Research, 11(1086), 1086. doi: 10.12688/f1000research.125381.1.

  • Castillo-Vilcahuaman, C., Valdivia C., Osorio-Mogollón C., Silva-Andrade, C., Puche, R., Ayala‐Ruano, S., et al. (2020). 4th ISCB Latin American Student Council Symposium: a virtual and inclusive experience during COVID19 times. F1000Research, 9. doi: 10.12688/f1000research.28330.1.

Preprints

  • Vidal E., Phanthanourak, A.L., Gharib, A., Webel, H., Assis, J., Ayala-Ruano, S., Cunha, A.F., & Santos, A. (2025). ABaCo: Addressing Heterogeneity Challenges in Metagenomic Data Integration with Adversarial Generative Models. bioRxiv. doi: https://doi.org/10.1101/2025.09.22.677692.

Others

  • Ayala-Ruano, S.^, & Zurita, J. (2021). HerrCompBioinfo: un recurso educativo de código abierto de herramientas computacionales para entusiastas de la Bioinformática. doi: doi.org/10.5281/zenodo.5748335

^co-first author