Research Engineer · Computational Physiologist

Alex Gonzalez, PhD

Rigorous inference from noisy biological data: large-scale wearables, medical devices, and human neuroscience, at the intersection of domain science and machine learning.

Portrait of Alex Gonzalez
// signal in, structure out
01 / About

Signal, not noise

I'm currently at the Wu Tsai Human Performance Alliance at Stanford, where I build individual-level models of physiological adaptation from longitudinal wearable and training data, and lead a cohort-scale study on menstrual cycle physiology and sleep. I also manage the Alliance's external partnerships, run the Agility Projects program ($1M in annual funding), and keep track of its research portfolio across Stanford.

I studied electrical engineering at the University of Puerto Rico at Mayagüez, then at Stanford, where I completed my PhD with support from NSF, Sloan, and NIH fellowships. My background also includes postdoctoral work on hippocampal and parahippocampal circuits in rodents, supported by an NIH NRSA fellowship and funded in part by the Simons Foundation, and signal processing consulting for FDA-regulated cardiac devices.

First principles, sound methods, the right tool for the problem.

02 / Research Areas

What I work on

Performance

Physiological adaptation & performance

Modeling training responses, injury risk, and recovery from longitudinal wearable data; investigating injury mechanisms in elite athletes from biomechanics and historical load data.

Physiology

Menstrual cycle biology

Cohort-scale normative physiology, sleep, and cycle variability from wearable biometrics (npj Digital Medicine, 2026).

Neuroscience

Neural coding & memory

How hippocampal and parahippocampal circuits represent space and experience.

03 / Technical Expertise

Toolbox

Causal inference

Wearable data is observational, unbalanced, and missing nights. Natural experiments, state-space models, and double-robust ML pull causal answers out of it anyway.

Example: sleep-phase natural experiment

ML for biology

Off-the-shelf architectures rarely match biological questions. I design encoder models and custom architectures where the hypothesis is built into the model itself.

Example: eLife 2024 · encoder-decoder notebook

Signal processing

Biological signals bury structure under artifact. Adaptive filtering, multi-band decomposition, and real-time event detection, from EEG-fMRI to an FDA-regulated wearable defibrillator.

Example: EEG-fMRI preprocessing code

Decoding

What does a population of neurons know, and when? Representational similarity analyses and population-level decoders, from single units to intracranial EEG.

Example: PNAS 2015 · eLife 2024

Agentic AI

AI agents are only as rigorous as the structure around them. I build ADR-governed research repos with codified assumption surfacing and parallel subagent review.

04 / Open Science

Reproducible by design

I try to make my research auditable end to end: not just sharing code, but sharing it in a form where every figure and statistic can be traced back to the data.

npj Digital Medicine, 2026

Fully reproducible analysis, from raw biometrics to published figures

The menstrual cycle paper ships with dedicated figure-generation code, every statistic worked through in Jupyter notebooks, and the API built to generate those figures and statistics, alongside a companion website. Browse the repo, or see an example notebook: the sleep-phase natural experiment.

Open code

Open code for key papers

Analysis and behavioral control code for the eLife navigation work (TMA, TreeMaze), and MATLAB source for the PNAS ECoG analyses (repo).

Open education

Neuromatch Academy

Contributor to Neuromatch's open, global computational neuroscience school: leadership roles, conflict-resolution ombuds team, and mentoring dozens of students.

05 / Publications

Publications

Wearables & Digital Health
The menstrual cycle through the lens of a wearable device: insights into physiology, sleep, and cycle variabilitySelected
Gonzalez, A., O'Day, J.J., Johnson, S.C., Kim, J., Jasinski, S.R., Holmes, K.E., Delp, S.L., Hicks, J.L.
npj Digital Medicine, 2026
Memory & Navigation
Structured navigation in a goal-directed task reveals flexible spatial coding
Fisher, T., Sosa, M., Gonzalez, A., Cheng, X., Giocomo, L.
Under review, 2026
Hippocampal patterns and associative memory: Distinct intracranial EEG temporal encoding patterns support memory
Xue, A.M., Hsu, S., LaRocque, K.F., Raccah, O., Gonzalez, A., Parvizi, J., Wagner, A.D.
bioRxiv, 2026
Parahippocampal neurons encode task-relevant information for goal-directed navigation
Gonzalez, A., Giocomo, L.
eLife, 2024
From Rats to Humans: how novel behavioral paradigms and reinforcement learning can bridge the gap in translation
Gonzalez, A., Giocomo, L.
Lab Animal, 2022
Electrocorticography reveals the temporal dynamics of posterior parietal cortical activity during recognition memory decisions
Gonzalez, A., et al.
Proceedings of the National Academy of Sciences, 2015
Neurotechnology & Bioengineering
NeuroRoots, a bio-inspired seamless brain-machine interface for long-term recording in delicate brain regions
Ferro, M.D., Proctor, C.M., Gonzalez, A., et al.
AIP Advances, 2024
Integrated strain array for cellular mechanobiology studies
Simmons, C.S., Sim, J.Y., Baechtold, P., Gonzalez, A., et al.
Journal of Micromechanics and Microengineering, 2011
Teaching & Open Education
Neuromatch Academy: a 3-week, online summer school in computational neuroscience
't Hart, B.M., et al.
Journal of Open Source Education, 2022
Teaching Digital Signal Processing with Stanford's Lab-in-a-Box
Mujica, F.A., Esposito, W.J., Gonzalez, A., et al.
IEEE Signal Processing Education, 2015
06 / Awards

Honors & Fellowships

NIH Ruth L. Kirschstein National Research Service Award (NRSA F32)
Stanford DARE Fellowship (Diversifying Academia, Recruiting Excellence)
NIH Biotechnology Training Grant
Alfred P. Sloan PhD Graduate Fellowship
NSF Graduate Research Fellowship
07 / Off the clock

Meanwhile

While my Claude Code sessions run, you might find me on a run of my own, cycling up the Santa Cruz Mountains, homebrewing beer, making pizza, or chasing two little ones.