Computational biology / plant science / bioinformatics
Alen Zimic / Alen Zimic Sheen
About
I'm an upcoming Computational Biology PhD student at Cornell University, beginning in August 2026 with support from the SUNY Fellowship. I am interested in how computation can help connect plant genes, metabolites, microbes, and environmental stress into clearer biological stories.
I come from Peru, where my first research experiences grew from field-facing questions about agriculture, soil microbes, environmental biotechnology, and public health. That background still shapes how I think about computational biology: useful tools should stay connected to biological systems, local context, and the people who work with them.
At Cornell’s Moghe Lab, I work on data-mining approaches for plant metabolites and gene-function discovery. Before that, I worked across plant-microbe systems, environmental biotechnology, metagenomics, protein modeling, and synthetic biology projects in Peru and at UC Berkeley/USDA.
Experience
Ithaca, NY
Plant Science Department, Cornell University - PI: Gaurav Moghe, PhD
Building computational workflows in the Moghe Lab as part of the C-SPIRIT research team, connecting uncharacterized plant metabolites with genes, tissues, species, and stress-related traits.
Plant Gene Expression Center, UC Berkeley - USDA - PI: Devin Coleman-Derr, PhD
Studied drought-associated plant-microbe interactions in sorghum, connecting greenhouse work, RNA extraction, phenotyping, and Streptomyces genomics.
Bioinformatics and Molecular Biology Laboratory, UPCH - PIs: Mirko Zimic, PhD and Patricia Sheen, PhD
Worked across pathogen bioinformatics, antigen modeling, metagenomics, and molecular biology platforms in a lab spanning health and environmental applications.
Laboratory of Functional Genomics, UPCH - PI: Luis De-Stefano, PhD
Built a field-to-sequencing workflow to study how biofertilizer treatments may shift avocado rhizosphere microbiomes.
Laboratory of Andean-Amazonian Chemistry of Life, UPCH - PI: Denis Castillo, PhD
Developed and analyzed biodegradable hydrogels as a controlled-release approach for agricultural nitrogen management.
Publications
Articles
5 papers
Reviews
2 reviews
Projects
Interactive rotary embeddings teaching demo
A static, dependency-free visual demo for teaching rotary positional embeddings, including real RoPE formulas and cosine-similarity comparisons.
Mentor-mentee collaboration tracker
Built for REU mentoring, this shared workspace helps mentor-mentee teams track notes, tasks, deadlines, and Google Docs/Sheets sync.
Computer vision for saccadic eye movement analysis
A small computer-vision workflow for tracking eye movement responses from video and extracting interpretable motion features.
Sketch feature classification with deep learning embeddings
A machine-learning experiment using learned image embeddings to classify sketch-derived visual features.
A practical AI tools guide for plant scientists
A companion repository for the Plant Cell review, collecting relevant AI tools and learning resources for plant scientists.
Education
Cornell University
Incoming PhD student in Computational Biology at Cornell University, funded by the SUNY Fellowship.
Universidad Peruana Cayetano Heredia, Lima, Peru
Graduated with a GPA of 3.86 and ranked second in order of merit across the Environmental Engineering program.
Recognition
Selected support, awards, presentations, and public science.
Funding & honors
Talks & media
Community
Selected roles in training, synthetic biology, and student leadership.
Notes
A small blog-style space for updates when there is something worth writing down.