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Sebastián Ayala-Ruano
I am a researcher and freelance data scientist with six years of experience in Bioinformatics and Cheminformatics at various laboratories. My current research interests are centered on network science, deep learning, and software development to study complex biological systems. I am an active member of several research, open-science, and software development communities (The Turing Way, Open Life Science, Streamlit Creators, ISCBSC, and The Carpentries) and have led initiatives that advance Bioinformatics in Ecuador and Latin America.
Education
MSc, Systems Biology
Maastricht University (UM)
Maastricht, the Netherlands
2024 - 2022
- Scholarship: UM Holland-High Potential Scholarship (non-EU/EEA students).
- GPA: 8.78/10 (Cum Laude) - highest score in the Systems Biology 2024 class.
- Thesis (MaCSBio thesis award): MicW2Graph - Building a knowledge graph of the wastewater treatment microbiome and its biological context.
B.Eng., Biotechnology
Universidad San Francisco de Quito (USFQ)
Quito, Ecuador
2020 - 2016
- Minor: Software engineering.
- GPA: 3.78/4 (Magna Cum Laude) - second highest score in the College of Biological and Environmental Sciences 2020 class.
Work Experience
Research Assistant
Multi-omics Network Analytics Group - Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
Copenhagen, Denmark
Sep. 2025 - Oct. 2024
- Contributed to the development of Bioinformatics software tools, including VueGen, VueCore, and ACore, a suite of Python packages that automate report generation, visualization, and analytics for multi-omics data.
- Advisor: Alberto Santos Delgado
Research Intern
Multi-omics Network Analytics Group - Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark
Copenhagen, Denmark
May. 2024 - Nov. 2023
- Investigated the wastewater treatment microbiome and developed MicW2Graph, an open-source knowledge graph integrating metagenomic and metatranscriptomic data with their biological context, including biological processes, environmental features, chemical compounds, and additional metadata (More details).
- Advisors: Alberto Santos Delgado, Martina Kutmon
Data Science Consultant
Universidad de Las Américas
Quito, Ecuador
Oct. 2022 - Apr. 2022
- Created a curated database of 50,000 herbarium records from tropical forest species of the Americas using web scraping and the Global Biodiversity Information Facility API.
- Developed machine learning classifiers to predict the phenological stages of forest species from herbarium records, supporting the design of conservation strategies for tropical forests (More details).
Research Assistant
Applied Signal Processing and Machine Learning Research Group - USFQ
Quito, Ecuador
2021
- Created a method based on network science and similarity searching to explore the chemical space of antiparasitic peptides and discover new drugs (More details).
- Advisors: Yovani Marrero-Ponce, Noel Pérez Pérez
Research Intern
Computational and Theoretical Chemistry Group - USFQ
Quito, Ecuador
2020 - 2017
- Studied binding specificity between repressor proteins and a transcriptional factor in the jasmonic acid pathway of Arabidopsis thaliana using molecular dynamics simulations and machine learning algorithms (More details).
- Advisor: Miguel Angel Méndez Silva
Research Intern
Bio-Chemoinformatics Group - Universidad de Las Américas
Quito, Ecuador
2020 - 2018
- Investigated the impact of horizontal gene transfer in the genome of Streptomyces clavuligerus using phylogenetics, and other bioinformatics tools (More details).
- Proposed molecular mimicry between Zika envelope protein and human neuronal proteins through molecular dynamics and protein-protein interaction networks.
- Advisors: Vinicio Armijos, Yunierkis Perez
Research Intern
Tumor Metabolism and Therapeutic Oncology Laboratory - Gwangju Institute of Science and Technology
Gwangju, South Korea
2019
- Performed density functional theory and molecular dynamics simulations to study the effect of a mutation in the ZN domain of the CRBN protein (More details).
- Advisors: Miguel Angel Méndez Silva, Steve K. Cho
Teaching Experience
Bioinformatics Boot Camp Co-organizer and Co-instructor
Virtual
2021
- Designed and taught course materials covering Linux basics, terminal usage, Bash/AWK scripting, and Git/GitHub.
Undergraduate Teaching Assistant
Learning Center - USFQ
Virtual
2020
- Provided online mentorship in Biotechnology, Mathematics, and Engineering subjects to undergraduate students.
Undergraduate Teaching Assistant
General Biology Laboratory - USFQ
Quito, Ecuador
2018 - 2016
- Graded reports, tests, and homework, providing feedback and guidance on course topics.
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. Preprint: doi.org/10.1101/2025.03.05.641152
- 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., Agüero-Chapin G., Antunes A., Aguilar A. (2022). Network Science and Group Fusion Similarity-Based Searching to Explore the Chemical Space of Antiparasitic Peptides. ACS omega, 7 (50), 46012-46036. doi: doi.org/10.1021/acsomega.2c03398. Preprint: doi.org/10.26434/chemrxiv-2021-tgv69-v2.
- Oña-Chuquimarca, S., Ayala-Ruano, S., Goossens, Pauwels, L., Goossens, A., Leon-Reyes, A., & Méndez, M. A (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 included in the Frontiers in Plant Science 2020 highlights e-book. 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., Carrascal, D., Sánchez-Luquez, K., & Puche-Quiñonez, R. (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., Cuesta-Astroz, Y., Parra, G (2020). 4th ISCB Latin American Student Council Symposium: a virtual and inclusive experience during COVID19 times. F1000Research, 9. doi: 10.12688/f1000research.28330.1.
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
Selected presentations
- VueGen: Automating the creation of scientific reports. (2025). Oral presentation. Bioinformatics Open Source Conference (BOSC) - ISMB/ECCB 2025.
- MicW2Graph: Building a knowledge graph of the wastewater treatment microbiome and its biological context. (2025). Oral presentation. Conference on Complex Systems 2025.
- Contributing Guidelines and Codes of Conduct for Open Projects. (2022). Expert talk. 6th cohort of Open Life Science.
- Exploring the chemical space of antiparasitic peptides and discovery of new leads using network science and similarity searching. (2022). Oral presentation. International Society for Computational Biology Student Council Webinar series.
- HerrCompBioinfo: An open-source educational resource of computational tools for Bioinformatics enthusiasts written in Spanish. (2022). Oral presentation. 4th cohort of Open Life Science Graduation.
- The molecular basis of JAZ-MYC coupling, a protein-protein interface essential for plant response to stressors. (2021). Oral presentation. 6th Brazilian Student Council Symposium: Omics and Data Science.
- In silico detection of horizontal gene transfer in Streptomyces clavuligerus. (2020). Oral presentation. International Society for Computational Biology Student Council Webinar series.
- Structural changes due to a mutation in Cereblon might be a cause for intellectual disability. (2019). Poster presentation). Global Intern Program - Gwangju Institute of Science and Technology.
Honors and Awards
MaCSBio Thesis Award
Maastricht University
Maatricht, the Netherlands
2024
- Recognizes one MSc System Biology thesis based on scientific merit, thesis quality, and academic performance.
Visit Grant
Copenhagen, Denmark
2024
- Covered travel and accommodation expenses for MSc thesis internship.
Cum Laude Graduation Distinction
Maastricht University
Maatricht, the Netherlands
2024 - 2022
- Awarded to students with a GPA ≥ 8/10.
UM Holland-High Potential Scholarship
Maastricht University
Maatricht, the Netherlands
2022
- Full scholarship covering tuition and stipend support for highly talented non-EU students admitted to a master’s program.
Best oral presentation award
6th Brazilian Student Council Symposium: Omics and Data Science
Virtual
2021
“For More Data on Labor Informality” Innovation Challenge Award
Datalat, PNUD Ecuador, UN Women Ecuador, and the International Labour Organization
Virtual
2021
- Selected among 39 proposals from 80 interdisciplinary teams to design a technological solution for collecting labor informality data in Ecuador (More details).
Chancellor’s Honor List and Magna Cum Laude Graduation Distinction
Universidad San Francisco de Quito
Quito, Ecuador
2020 - 2016
- Recognized students with a GPA ≥ 3.7/4.
Third HPC Summer School Colombia: Bio and Data Science scholarship
CyberColombia
Virtual
2020
- Covered registration expenses for the event.
2nd RSG-Colombia Symposium travel award
RSG Colombia
Ibagué, Colombia
2019
- Covered travel expenses to attend the event.
Global Intern Program Scholarship
Gwangju Institute of Science and Technology
Gwangju, South Korea
2019
- Covered accommodation and stipend for an 8-week research internship with training and mentoring.
Leadership and Service
Streamlit Creators Program
Virtual
Current - 2022
- Developed multiple web applications using the Streamlit Python package and became part of the creators community.
Open Life Science (OLS) program
Virtual
Current - 2021
- Led the HerrCompBioinfo project during the 4th cohort, creating an open-source educational resource of computational tools for Bioinformatics enthusiasts written in Spanish.
- Mentored a team in the 5th cohort to create a computer vision tool for improving cancer diagnosis in Cameroon.
- Delivered a talk about contributing guidelines and codes of conduct for open projects in the 6th cohort.
Regional Student Group (RSG) Ecuador
International Society for Computational Biology Student Council
Virtual
2023 - 2020
- Co-founder, built a community of Bioinformatics students and researchers in Ecuador.
- Co-chair of the 1st Ecuadorian-Venezuelan Symposium of Young Bioinformatics Researchers.
- Fellowship committee chair, 17th Student Council Symposium.
- Contributed to the program and fellowships committees of the 4th ISCB Latin American Student Council Symposium.
Saturdays.AI Quito 2021
Virtual
2021
- Led a project developing a maize disease detector based on convolutional neural networks.
Note: I have developed additional personal projects related to Data Science, Machine Learning, and Bioinformatics.