Stéphane Boutet, Ph.D.

Biotechnology R&D leader · Single-cell genomics · AI-driven biology

I'm a biologist who has spent more than 20 years turning new science into products people use. I've done it in single-cell genomics at 10x Genomics, AI-driven cell analysis at Deepcell, and large-scale sequencing for the Virtual Cell initiative at Arc Institute.

What I enjoy most is building the team, the assay and the product together, and getting all three from concept to launch.

Where biology, technology and product meet

My career started at the bench, studying muscle stem cells at Stanford. It has since moved toward building the platforms and teams that let other scientists do their best work.

Build & scale R&D teams

I've grown and led organizations of up to 13 people across three functions, managed budgets of $2–5M, and run more than 30 external collaborations with academic and industry partners.

Take science to product

I've owned products end to end: prototyping, specs, manufacturing, validation and launch. That includes 6 single-cell launches at 10x Genomics and the REM-I reagent kit at Deepcell.

Bridge biology and AI

I've built ground truth, training data and biological validation for more than 8 AI models, from a cell-morphology foundation model to cancer classifiers for liquid biopsy.

From the bench to product launch

2025 – 2026

Arc Institute

Senior Director, Genomics Platform

Scaled sequencing to ~3 trillion reads per month across Ultima, Illumina and 10x platforms, powering the Virtual Cell and Alzheimer's Disease initiatives, which include some of the largest single-cell Perturb-seq screens in the field.
Cut sequencing turnaround from 15 days to 5 by redesigning operational workflows.
Managed a $3M+ annual budget, $4M+ of sequencing infrastructure and a team spanning development and production sequencing.

2022 – 2024

Deepcell

Senior Director (2023–24) · Director (2022–23), Applications & Assay Development

Built and led a 13-person biology department (3 teams, 2 R&D lab functions) reporting to the CEO.
Developed ground truth, training data and validation for 8 AI models, including the Human Foundation Model, liquid biopsy, melanoma and lung-cancer detection, and CRISPR morphology screening.
Owned the REM-I reagent kit from prototype to commercial launch, delivered on schedule with >95% first-pass manufacturing yield.
Managed 16 external collaborations that led to the first 3 instrument sales ($1.5M), and filed 4 patent applications.

2021

ImpriMed

Director, Biosciences

Directed an A2LA-accredited diagnostic lab that delivered AI-driven drug-response predictions for 300 patient samples a month at >90% on-time.
Designed genomic biomarker programs that improved AI prediction accuracy by 30%.

2016 – 2021

10x Genomics

Staff Scientist, Sample Preparation Lead (2019–21) · Applications Lead (2016–19)

Led product validation and scientific content for 6 single-cell launches (3′ v2/v3, 5′, ATAC, CNV, V(D)J, Feature Barcoding), products that generated $200M+ in first-year revenue.
Invented the lipid-tagged barcoding concept that became the 3′ CellPlex Kit, and took it from proof of concept through internal validation.
Conceived the Chromium Nuclei Isolation Kit (500 units sold in year one) and built clinical-trial workflows that enabled 3 CRO contracts.
Invited speaker at ASHG 2017 and Keystone. Author of 8 application notes and 2 white papers.

2013 – 2016

Fluidigm

Collaboration Manager / Scientist

Initiated 6 collaborations to develop new single-cell applications (scDNA-seq, scRRBS-seq, imaging + scRNA-seq).
Ran customer test sites for 3 products, and the feedback loop cut post-launch customer issues by 30%.

2010 – 2013

Palo Alto VA Health Care System

Stem Cell Core Director, then Consulting Professor. Built the single-cell qPCR and RNA-seq workflow at the heart of the lab's regenerative-medicine program.

1997 – 2009

Stanford University

Doctoral research, postdoc and Instructor. Discovered how Pax3 is regulated by monoubiquitin-mediated degradation in muscle stem cells, published in Cell (2007).

Education & expertise

Education

Ph.D., Biology of AgingParis, France, with research conducted at Stanford University
D.E.A. (Diploma of Advanced Studies), Biology of AgingDenis Diderot University, Paris
M.Sc., Molecular & Cellular BiologyClaude Bernard University & École Normale Supérieure de Lyon

Expertise

Single-cell genomics scRNA / ATAC / DNA-seq · V(D)J Spatial transcriptomics AI/ML for cell biology Liquid biopsy Immuno-oncology Stem-cell biology Sequencing operations

10x Chromium Illumina NovaSeq X Ultima UG100 ISO 13485 · A2LA Python · R · SwiftUI