Bioinformatics Scientist​/Senior Bioinformatics Scientist

Location: Sunnyvale, California

Work Arrangement: Onsite or hybrid, based on business requirements

Employment Type: Direct Hire, Full-Time

Salary Range: $175,000–$205,000 annually

Yoh is partnering with a privately held molecular diagnostics company developing blood-based technologies for earlier cancer detection. We are seeking a Senior Bioinformatics Scientist to take a leading, hands‑on role in the development, optimization, and validation of computational workflows supporting a next‑generation oncology diagnostic platform.

This position sits at the intersection of bioinformatics, next-generation sequencing, statistical modeling, and molecular assay development. The successful candidate will transform sequencing data into reliable analytical outputs, improve the detection of low-frequency molecular signals, and help establish a reproducible, scalable, and validation‑ready bioinformatics workflow.

This is an opportunity for an experienced bioinformatics scientist to have meaningful technical ownership within a growing, cross‑functional organization. The role will work closely with assay development, molecular biology, laboratory automation, biostatistics, quality, clinical, and regulatory partners.

• Develop, optimize, and maintain end‑to‑end bioinformatics workflows for targeted, cell‑free DNA sequencing assays.
• Process and analyze sequencing data across FASTQ, BAM/CRAM, VCF, and assay‑specific intermediate formats.
• Develop and monitor quality metrics related to sequencing performance, mapping, coverage, library complexity, molecular error rates, contamination, and sample‑level performance.
• Develop or optimize methods for detecting low‑frequency molecular signals in noisy sequencing data.
• Apply molecular barcodes, error‑correction, background‑noise modeling, or related approaches appropriate to the assay.
• Partner with assay scientists to understand biological, technical, and pre‑analytical sources of variation.
• Develop and evaluate statistical models or classification methods used to distinguish cancer‑associated signals from non‑cancer background.
• Assess model performance using appropriate training, tuning, cross‑validation, and independent test datasets.
• Evaluate the effects of cfDNA input, sequencing depth, sample quality, batch effects, and other technical variables on assay performance.
• Design and support bioinformatics verification and analytical validation activities.
• Define computational quality‑control criteria, acceptance thresholds, failure conditions, and reproducibility requirements.
• Develop modular, maintainable, version‑controlled software using Python, R, or other appropriate languages.
• Implement reproducible workflows using Nextflow, Snakemake, WDL, or a comparable workflow‑management framework.
• Use automated testing, containers, execution logging, data lineage, and version tracking to support reliable software releases.
• Investigate pipeline failures, discrepant results, unexpected performance, and potential sources of false‑positive or false‑negative calls.
• Prepare clear technical documentation supporting software verification, analytical validation, design controls, and future regulatory activities.
• Communicate findings and technical recommendations to both computational and non‑computational stakeholders.

• Ph.D. in Bioinformatics, Computational Biology, Genomics, Biostatistics, Computer Science, or a related discipline, or an M.S. with substantial relevant industry experience.
• Hands‑on experience developing and maintaining NGS bioinformatics pipelines.
• Strong proficiency in Python, R, or both, including development of reusable and well‑tested analytical code.
• Experience with sequencing quality…