Publications

Articles

Tip

See my google scholar for a full list of publications.

  1. Amstalden, M. K., Olayo-Alarcon, R., … & Brochado A. R. (2026). Large-scale screen reveals extensive regulation of intrinsic antibiotic resistance and virulence by human-targeted drugs in Salmonella Typhimurium. biorxiv.

  2. Olayo-Alarcon, R., Pugno, D., Müller, C.L. (2025) Protein Content-Based Microbial Representations Improve Predictions of Antimicrobial Activity. Proceedings of the 34th International Conference on Artificial Neural Networks (ICANN 2025). Workshop on AI in Drug Discovery. https://doi.org/10.1007/978-3-032-04552-2.

  3. Olayo-Alarcon, R., Amstalden, M. K., Zannoni, A., Bajramovic, M., Sharma, C. M., Brochado, A. R., … & Müller, C. L. (2025). Pre-trained molecular representations enable antimicrobial discovery. Nature Communications, 16(1), 3420.

  4. Feldl, M.*, Olayo-Alarcon, R.*, Amstalden, M. K., Zannoni, A., Peschel, S., Sharma, C. M., … & Müller, C. L. (2025). Statistical end-to-end analysis of large-scale microbial growth data with DGrowthR. bioRxiv, 2025-03. *co-first authors.

  5. Binsfeld, C., Olayo-Alarcon, R., Wartel, M., Stadler, M., Mueller, C., & Brochado, A. R. (2024). Systematic screen uncovers regulator contributions to chemical cues in Escherichia coli. PLoS biology, 23(7), e3003260.

  6. Ostner, J., Kirk, T., Olayo-Alarcon, R., Thöming, J. G., Rosenthal, A. Z., Häussler, S., & Müller, C. L. (2024). BacSC: A general workflow for bacterial single-cell RNA sequencing data analysis. bioRxiv.

  7. Stadler, M., Olayo-Alarcon, R., Bien, J., & Müller, C. L. (2024). Predictive modeling of microbial data with interaction effects. bioRxiv.

  8. Dietl, A., Ralser, A., Taxauer, K., Dregelies, T., Sterlacci, W., Stadler, M., Olayo-Alarcon, R., … & Mejias Luque, R. (2024). RNF43 is a gatekeeper for colitis-associated cancer. bioRxiv, 2024-01. [Preprint] Available at: https://www.biorxiv.org/content/10.1101/2024.01.30.577936v1.abstract.

  9. Soto, L.M*, Olayo-Alarcon, R.*. et al. (2019) “GeDex: A consensus gene-disease event extraction system based on frequency patterns and supervised learning,” bioRxiv [Preprint]. Available at: https://doi.org/10.1101/839704.

Posters

1. MolE: Pre-trained molecular representations can aid antimicrobial discovery.

Roberto Olayo-Alarcon*, Martin K. Amstalden, Annamaria Zannoni, et al. (2023)

Presented at ISMB/ECCB 2023

PDF version here.

2. StressRegNet: Molecular representations decipher stress response in gut pathogens

Roberto Olayo-Alarcon*, Martin K. Amstalden, Annamaria Zannoni, et al. (2022)

Presented at Keystone Symposia - Novel Approaches Against Emerging Antimicrobial Resistance.

AWAREDED KEYSTONE SYMPOSIA SCHOLARSHIP.

PDF version here.

3. Cheminformatics deciphers stress response and virulence pathways in infection

Roberto Olayo-Alarcon*, Christoph Binsfeld, Ana Rita Brochado, Christian L. Müller. (2022)

Presented at DAGStat 2022 - Hamburg

PDF version here.

4. RNF43 in colitis associated cancer.

Alisa Dietl*, Mara Stadler, Roberto Olayo-Alarcon, et al. (2022)

Presented at Digestive Disease Week - 2022

5. Glucose starvation in Huh7 cells triggers a transcriptional memory.

Jessica A. Pellegrino*, Saulius Lukauskas, Roberto Olayo-Alarcon, et al. (2019).

Presented at CSH meeting: mechanisms of metabolic signaling

Other

Bachelor’s Thesis

Roberto Olayo Alarcón (2020) Differential Activity of Transcriptional Regulatory Elements During Glucose Starvation. Research Report to obtain the degree of B.Sc. in Genomic Sciences. Universidad Nacional Autónoma de México.

Full thesis here.