Single-molecule
gene expression
How is translation regulated in living cells? I study molecular dynamics through live-cell imaging and quantitative analysis of individual RNA and protein signals.
Translation dynamicsComputational biology & biophysics
Luis Aguilera, PhD
Connecting single molecules to predictive biology.
I combine single-molecule imaging, stochastic models, and open-source software to understand how cells regulate gene expression.
Research Associate
Biochemistry & Molecular Genetics
University of Colorado Anschutz Medical Campus
From observation to understanding
Making molecular dynamics measurable.Live-cell single-molecule tracking · MicroLive
01 / Research
Measuring molecules.
Understanding mechanisms.
My work connects experimental observations with computational models: extracting reliable measurements, testing biological mechanisms, and designing more informative experiments.
Single-molecule
Predictive models
& experiment design
What can a measurement tell us about a mechanism? I use stochastic models, simulation, and inference to connect gene expression dynamics with testable predictions.
Computational frameworkAccessible tools
for quantitative biology
How can complex data become useful biological measurements? I build open-source workflows for microscopy analysis, molecular tracking, and computational experimentation.
Research software02 / Scholarship
Selected publications
8 selected works
-
2026
UTag, a cysteine-free thermostable tagging system for tracking single mRNA translation live
-
2026
MicroLive: An Image Processing Toolkit for Quantifying Live-cell Single-Molecule Microscopy
-
2025
Methods in quantitative biology—from analysis of single-cell microscopy images to inference of predictive models for stochastic gene expression
-
2024
Sequential design of single-cell experiments to identify discrete stochastic models for gene expression
-
2023
Using mechanistic models and machine learning to design single-color multiplexed nascent chain tracking experiments
-
2020
Quantifying the dynamics of IRES and cap translation with single-molecule resolution in live cells
-
2019
Computational design and interpretation of single-RNA translation experiments
-
2019
Live-cell single RNA imaging reveals bursts of translational frameshifting
Selected work, listed by year. Preprints are identified separately; author names follow the original publications.
03 / Open science
Software for discovery
Reusable tools that connect imaging, simulation, and biological interpretation. Source code and practical examples are openly available.
From microscopy images to quantitative measurements.
Featured research software
MicroLive
A toolkit for quantifying live-cell single-molecule microscopy. An integrated graphical interface brings together cell segmentation, particle tracking, spot quantification, and analysis of translation dynamics.
Published in Bioinformatics Advances, 2026
Image analysis
FISH Processing
Automated cell segmentation, spot detection, and transcript quantification in fluorescence in situ hybridization images.
Simulation & design
rSNAPed
Simulated single-molecule gene expression experiments for testing analysis pipelines and exploring experimental designs.
Bioinformatics
NGS Biomarker
Discovery Toolkit
Workflows for somatic variant detection, digital PCR primer design, and simulation of rare mutation detection in circulating tumor DNA.
Beyond the lab Creative computing & exploration
6EQUJ5
A Python terminal game inspired by the 1977 Wow! signal, combining science fiction, radio astronomy, and AI-driven dialogue.
Explore the project Watch trailer04 / Teaching & mentorship
Opening doors to
quantitative biology.
I am committed to making computational biology accessible to students from diverse backgrounds through hands-on learning and inclusive mentorship.
My background spans Mexico, Germany, and the United States, shaping how I approach interdisciplinary research and education.
Co-founder & lead organizer
UQ-Bio Summer School
The Undergraduate Quantitative Biology Summer School (2020–2024) introduced students to computational modeling, microscopy analysis, and stochastic gene expression through practical Python-based learning. Recorded tutorials and learning materials remain available.
- Image processing & microscopy analysis
- Stochastic models of gene expression
- Data-driven inference & experiment design
05 / Background
At the intersection of
biology and computation.
I am a computational biologist and Research Associate in the Department of Biochemistry and Molecular Genetics at the University of Colorado Anschutz Medical Campus. My background in biomedical engineering and physics informs my work across molecular imaging, mathematical modeling, and scientific software.
I am interested in academic opportunities that bring together research in gene expression, the development of quantitative methods, and the training of the next generation of scientists.
Google Scholar GitHub06 / CV & contact
Let’s move the
science forward.
For academic opportunities, research collaborations, or speaking invitations, please connect with me on LinkedIn.
My curriculum vitae is available on request.
Connect on LinkedIn