Neuroscience · Stanford University
I develop genetic and optical tools to understand how individual neurons contribute to the circuits that shape brain function.
Senior Research Scientist Schnitzer Lab
Explore my research
Schematic illumination
Optogenomics 2.0 validation
Ali Cetin · Unpublished
Actual microscopy. Schematic laser pulses. The animation compresses the interval before EGFP expression.
FiCreV imaging at 1100 nm, neuronal activity imaging at 940 nm, and targeted heart-shaped photoconversion at 920 nm. EGFP expression confirms recombination in the neocortex of Ai140 EGFP reporter mice. Scale bar: 50 µm.
Validation dataset. Wavelength comparisons measure recombination efficiency as a function of distance from the neuron center, with optimal performance at 920 nm. Data represent mean ± SEM (≥8 neurons). The animation illustrates the targeting sequence; the experimental images show the outcome.
Open the full validation figureMolecular tools. Optical precision. Circuit neuroscience.
Stanford, California01 Research
What does a neuron do? Which genes does it express? Where does it connect? I build experimental tools that bring these questions together.
I develop light-inducible recombinases to modify genomes in individual neurons and defined cell populations. RecV established this optogenomic approach; my ongoing TRACE work aims to connect functional imaging with two-photon genetic targeting.
Read the RecV studyI develop viral vectors and tracing methods to identify the connections of defined neuronal populations. At the Allen Institute, I led large-scale workflows for whole-brain monosynaptic input mapping and viral tool development.
Read the visual cortex connectome studyI work to connect neuronal activity with molecular profiles and circuit organization. For the collaborative TRU-FACT study, I contributed genetic barcodes and viral vectors to support the alignment of in vivo imaging with spatial biology.
Read the TRU-FACT preprint02 Publications
Methods and discoveries across optogenomics, viral technology, and neural circuits.
My ORCID recordI also publish as A. Cetin and A. H. Cetin.
TRU-FACT · Connecting functional imaging with spatial biology
26, 350–364 · Cell-class-specific connectivity
598, 159–166 · Cellular architecture and circuit organization
17, 422–429 · Light-controlled genetic access
545, 477–481 · Genetic access to sleep-related circuitry
111, 2150–2159 · Controlled retrograde gene delivery
73, 553–566
71, 617–631
107, 21848–21853
1, 3166–3173
03 About
Neuroscientist & tool builder
I am a Senior Research Scientist in Stanford University’s Department of Biology, working in Mark Schnitzer’s lab, and an Affiliate Assistant Professor at the University of Washington.
My work brings molecular biology, genetics, physiology, and optical imaging together to study defined neurons and their circuits. I develop technologies that give researchers precise access to the cells they want to understand.
Before joining Stanford, I built and directed the Mesoscale Connectomics Pipeline and Viral Vector Core at the Allen Institute for Brain Science. At Stanford, I also served as General Director of the Center for High-Throughput Quantitative Biology (SciQube).
Across these roles, I have paired experimental tool development with research infrastructure, reproducible methods, and scientist training.
My Stanford lab profile2019–present
Senior Research Scientist
General Director, SciQube · 2023–2024
2013–present
Affiliate Assistant Professor
2013–2019
Assistant Investigator
Director, Viral Technology · 2015–2019
2008–2013
Postdoctoral Fellow · Neuroscience
2002–2008
PhD, Neuroscience · 2008
MS, Molecular Biology · 2004
1998–2002
BS, Molecular Biology and Genetics
04 Contact
For research collaborations and conversations about genetic tools, optical methods, and neural circuits, get in touch.
alic@stanford.eduFind me at Stanford
Schnitzer Lab · Department of Biology