Principal Research Scientist, Cell Biology & Single-Cell Genomics

Onyx Bio•Berkeley, CA

9d•$150,000 - $180,000

About The Position

Onyx is pioneering a virtual immune system, accelerating the development of safer and more effective precision medicines. We capture rich, longitudinal multi-omics data in clinical settings to deeply understand the progression of autoimmune diseases. As our biorepository expands, we apply advanced AI to high-quality immune data, leveraging robust cell-based workflows to discover new strategies for treatment and prevention. Join us to help build the technical foundation that enables our AI-powered insights into immune-related diseases. We’re looking for a Principal Scientist who will own cell biology and single-cell genomics at Onyx—from the moment a sample collection happens to the point where sequencing-ready libraries are handed off for computational analysis. You’ll own the cell biology and single-cell genomics side of the lab: collection, fixation, isolation, processing, and library generation. You will design the sample collection strategy, build the biobanking workflows for cell-based assays, establish and validate single-cell and multi-omics protocols, and drive the technical decisions that determine the quality ceiling of our genomics data. You’ll report directly to the CTO and operate as the scientific authority on everything cell-side. The right person for this role has the scientific judgment to make hard technical calls independently, the hands to do the bench work themselves, and the rigor to build systems that scale. They should have a healthy appetite to work on "impossible" things.

Requirements

PhD in cell biology, immunology, molecular biology, or a related field with 5+ years of post-doctoral hands-on bench experience; or Master’s with 8+ years equivalent
Deep, demonstrated expertise with single-cell RNA-seq: you’ve personally run 10x Chromium (or comparable) workflows end-to-end, troubleshot failures, and improved data quality over time
Proven ability to isolate high-quality, viable cells from whole blood (PBMCs, leukocytes, enriched subsets) at a level where you can explain the tradeoffs of every step in your protocol
Track record in clinical sample collection, biobanking, or GLP/GCLP-regulated environments
Experience designing or significantly improving multi-step protocols—not just following them
Strong first-principles scientific reasoning: you can evaluate a new method, identify its failure modes, and decide whether to adopt, adapt, or reject it
Exceptional documentation habits; you write SOPs that other people can actually follow

Nice To Haves

Experience with NGS library preparation and sequencing QC beyond single-cell (e.g., bulk RNA-seq, targeted panels)
Hands-on experience designing and validating internal controls or spike-in standards for genomics assays
Familiarity with cell-based multi-omics workflows: CITE-seq, ATAC-seq, or spatial transcriptomics
Basic bioinformatics fluency—you can look at a UMAP, interpret QC metrics from Cell Ranger, and have a productive conversation with a computational biologist
Knowledge of autoimmune disease biology and immune cell phenotyping
Experience with automated liquid handling (Hamilton, Beckman, OpenTrons) or lab robotics
Familiarity with Benchling, LIMS, and IATA/DOT shipping regulations for biological materials
Prior experience at an early-stage startup or in a role where you built something from scratch

Responsibilities

Architect and validate the blood collection and cell processing pipeline: kit design, fixation strategy, cold chain logistics, receiving, and cryopreservation
Establish and maintain SOPs for clinical sample handling that meet or exceed GLP/GCLP standards
Own chain-of-custody and traceability for cell-based samples; ensure every specimen has complete, standardized metadata from draw to sequencing
Evaluate and qualify novel collection chemistries (e.g., chemical fixatives for ambient-temperature stabilization) and make build-vs-buy decisions on collection kit components
Lead all wet-lab processing: PBMC isolation, viable cell enrichment, counting, QC, and preparation for downstream assays
Execute and continuously optimize 10x Genomics single-cell RNA-seq workflows (GEX, BCR, TCR) from sample prep through library generation
Design and implement internal controls, spike-ins, and reference standards to quantify and correct technical variability across batches
Expand the platform to additional cell-based modalities (CITE-seq, ATAC-seq, spatial transcriptomics) as the science demands
Troubleshoot aggressively—when something doesn’t work, you dig into root causes rather than re-running the same protocol
Analyze sample and library QC metrics systematically; identify failure modes, quantify batch effects, and drive continuous workflow improvement
Maintain rigorous experimental documentation in Benchling; establish tracking and annotation standards for the team
Contribute to internal scientific strategy discussions and present findings to leadership, collaborators, and partners
As the lab team grows, help hire and mentor junior scientists and technicians; set the bar for experimental rigor from day one