Hi, I'm Erik Serrano

Computational biologist | Software developer

Welcome to my personal website. Explore my work and get in touch!

About Me

Profile picture

I'm a fifth-year PhD student in Computational Bioscience at the University of Colorado Anschutz Medical Campus. My research centers on developing reproducible software for processing and analyzing image-based profiles, enabling large-scale and interpretable insights into cellular morphology. I have a strong background in software development, data analysis, and computational biology, and I’m passionate about creating open, collaborative tools that promote reproducible science. I’m preparing to defend my dissertation in the spring and am currently seeking post-graduation opportunities that combine computational biology, open science, and data-driven discovery.

Outside of research, I love hiking, learning new languages, reading, and dancing.

Get In Touch

I'm always open to new opportunities and collaborations. Feel free to reach out if you'd like to connect!

erik.serrano{at}cuanschutz.edu

Education

University of Colorado, Anschutz Medical Campus

Aurora, Colorado

PhD. Computational Bioscience

September 2021 - May 2026

University of California, Northridge

Northridge, California

B.S in Biology; Minor in Chemistry

September 2017 - May 2020

Los Angeles Valley College

Valley Glen, California

AS in Health Sciences

December 2012 - May 2017

Software contributions

Here is a collection of open-source software tools I have developed or contributed to, designed to advance image-based profiling and biological data analysis.

pycytominer

Efficient processing of high-dimensional readouts from high-throughput cell experiments.

Copairs-mAP

A versatile information retrieval framework for evaluating profile strength and similarity.

CytoTable

Scalable data harmonization for single-cell image-based profiling.

Buscar

Framework that leverages single-cell image-based profiles to identify hits in high-content drug screens.

Publications

Progress and new challenges in image-based profiling

Serrano, E., Peters, J., Wagner, J., Graham, R. E., Chen, Z., Feng, B., Miranda, G., Kalinin, A. A., Vulliard, L., Tomkinson, J., Mattson, C., Lippincott, M. J., Kang, Z., Sitani, D., Bunten, D., Seal, S., Carragher, N. O., Carpenter, A. E., Singh, S., … Way, G. P. (2025). In arXiv [q-bio.QM]. arXiv.

Reproducible image-based profiling with Pycytominer

Serrano, E., Chandrasekaran, S. N., Bunten, D., Brewer, K. I., Tomkinson, J., Kern, R., Bornholdt, M., Fleming, S. J., Pei, R., Arevalo, J., Tsang, H., Rubinetti, V., Tromans-Coia, C., Becker, T., Weisbart, E., Bunne, C., Kalinin, A. A., Senft, R., Taylor, S. J., … Way, G. P. (2025). Nature Methods, 22(4), 677–680.

A versatile information retrieval framework for evaluating profile strength and similarity

Kalinin, A. A., Arevalo, J., Serrano, E., Vulliard, L., Tsang, H., Bornholdt, M., Muñoz, A. F., Sivagurunathan, S., Rajwa, B., Carpenter, A. E., Way, G. P., & Singh, S. (2025). Nature Communications, 16(1), 5181.

Scalable data harmonization for single-cell image-based profiling with CytoTable

Bunten, D., Tomkinson, J., Serrano, E., Lippincott, M. J., Brewer, K. I., Rubinetti, V., Alquaddoomi, F., & Way, G. P. (2025). In bioRxiv.

Systemic HER3 ligand-mimicking nanobioparticles enter the brain and reduce intracranial tumour growth

Alonso-Valenteen, F., Mikhael, S., Wang, H., Sims, J., Taguiam, M., Teh, J., Sances, S., Wong, M., Miao, T., Srinivas, D., Gonzalez-Almeyda, N., Cho, R. H., Sanchez, R., Nguyenle, K., Serrano, E., Ondatje, B., Benhaghnazar, R. L., Gray, H. B., Gross, Z., … Medina-Kauwe, L. K. (2025). Nature Nanotechnology, 20(5), 683–696.

Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs

Abrol, R., Serrano, E., & Santiago, L. J. (2022). Advances in Protein Chemistry and Structural Biology, 128, 325–359.

Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain dependent

Luna, E., Parkar, S. G., Kirmiz, N., Hartel, S., Hearn, E., Hossine, M., Kurdian, A., Mendoza, C., Orr, K., Padilla, L., Ramirez, K., Salcedo, P., Serrano, E., Choudhury, B., Paulchakrabarti, M., Parker, C. T., Huynh, S., Cooper, K., & Flores, G. E. (2022). Applied and Environmental Microbiology, 88(1), e0148721.

Skills

Languages

Fluent in English, Spanish, and intermediate in Portuguese (BR)

Programming Languages (Expert)

  • Python
  • Rust
  • R

Software & Technical Skills

  • Version Control: Git, GitHub
  • DevOps & CI/CD: GitHub Actions, Docker
  • Data Analysis & Scientific Computing: Pandas/Polars, NumPy, SciPy, scikit-learn, PyTorch
  • Workflow Managers: Snakemake, Nextflow
  • Data Visualization: ggplot, seaborn, matplotlib, plotly