Experiments, code, and light.

Biochemist working at the intersection of protein science and data analysis. I design assays, optimize workflows, and use computational tools to make sense of the results.

Assay development Python & R Data visualization
Jason Hernandez portrait

Good experiments are designed for analysis from the start. Clean plate maps, systematic controls, and reproducible workflows turn noise into signal.

Science

Projects combining protein biochemistry, assay development, and computational analysis.

Scientific work overview
Structure-Guided Design

Peptide-protein interaction optimization

Led computational-experimental optimization of protein-binding peptides, achieving 6-fold affinity improvement. Used structure predictions to guide design and fluorescence-based assays for validation.

Built SAR datasets across 20+ variants using multiple biophysical techniques. Published in Structure (2025).

AlphaFold Binding assays SAR analysis
High-Throughput Screening

Assay development for multi-protein systems

Developed 384-well fluorescence assay for bacterial chaperone complex. Executed pilot screen of 1,857 compounds using automated liquid handling, delivering 253 validated hits.

Built Python pipelines for quality control and hit analysis. Manuscript submitted to Chemical Biology & Drug Design.

384-well HTS Automation Data pipelines
Protein Characterization

Validating computationally designed proteins

Characterized binding and stability of de novo designed protein mimics in collaboration with computational design groups. Bridged structural predictions with experimental validation.

Documented protocols and optimization logic in detail. Published in Cell Chemical Biology (2025).

Biophysical assays Collaboration Documentation

Code & Notebooks

Analysis workflows for exploring data, fitting models, and quality control.

Code and computational work

Approach: Code should make experimental logic visible and workflows reproducible. Each notebook tells a story: what was measured, how it was analyzed, and whether results make sense.

Jupyter Notebook

Binding curve analysis

Import tabular data, clean outliers, fit dose-response curves, validate assumptions. Includes diagnostic plots and goodness-of-fit checks.

Python scipy pandas
R Markdown

Screening QC and diagnostics

Automated quality control for 384-well screens. Computes plate statistics, flags suspect wells, generates heatmaps for batch processing.

R ggplot2 QC metrics
Python Pipeline

SAR visualization

Generate publication-quality SAR figures. Integrates chemical structure rendering with activity data plotting.

RDKit Matplotlib Visualization

Photography

Visual documentation from the lab, travel, and everyday moments.

Street Photography
"No Kings Day" Demonstration
Golden Gate Bridge
Most Destroyed Bridge in Media.
Portrait photography
People and Memories

More photos on Instagram (@hsphoto70)

Blog

Writing about science, career transitions, and computational approaches to biology.

Writing and blog

Heat Shock Pineapple

I write on Substack about the intersection of experimental science and data analysis, navigating career transitions in biotech, and lessons learned from building reproducible workflows. Topics range from assay troubleshooting to job market realities.

Read on Substack →

About

Background, approach, and what I'm looking for.

About Jason

Background

Biochemist with experience in protein assay development and computational analysis. I work at the intersection of wet lab and data science—designing experiments that produce clean, analyzable datasets.

My approach: build workflows that produce model-ready data from the start. Think about analysis during experimental design. Choose controls that test assumptions. Document like someone else will need to reproduce it.

Currently

Looking for roles combining protein biochemistry, data analysis, and scientific communication. Geographically focused on Southern California (LA/OC, San Diego), with secondary interest in Seattle/Portland.

I also write about science and career development on my Substack.