Senior Bioinformatics Scientist – Oncology Diagnostics (Hybrid)

Yoh; Sunnyvale (CA); Hybrid; USD 175,000 - 205,000; Full time

Benefits offered by this job

Medical, Prescription, Dental & Vision

Health Savings Account

Life & Disability Insurance

401K Retirement Savings Plan

Direct Deposit & weekly epayroll

Referral Bonus Programs

Certification and training

Job summary

Yoh is partnering with a privately held molecular diagnostics company to hire a Senior Bioinformatics Scientist focused on oncology. The role leads development, optimization, and validation of computational workflows for a next-generation oncology diagnostic platform, interfacing with assay development, laboratory automation, biostatistics, and regulatory teams.

The position demands expertise in NGS analysis, statistical modeling, and reproducible software, with strong coding in Python/R and

Qualifications

• Ph.D. in Bioinformatics, Computational Biology, Genomics, Biostatistics, Computer Science, or related field, or an MS with substantial industry experience.
• Hands-on experience developing and maintaining NGS bioinformatics pipelines.
• Strong proficiency in Python, R, or both, including reusable and well-tested analytical code.
• Experience with sequencing quality control, alignment, variant or molecular-feature detection, and statistical analysis.
• Strong understanding of experimental design, model evaluation, data quality, and analytical reproducibility.
• Experience working in Linux/Unix environments with Git and reproducible computational workflows.
• Ability to independently troubleshoot complex bioinformatics problems and drive technical deliverables.
• Strong communication skills and experience working across scientific and technical disciplines.

Responsibilities

• 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.

Skills

Statistical modeling

Experimental design

Cross-functional communication

Troubleshooting bioinformatics

Independent work

Education

Ph.D. in Bioinformatics / related field

M.S. with substantial industry experience

Tools

Python

R

Linux/Unix

Git

Nextflow

Snakemake

Docker

Apptainer/Singularity

Job description

Yoh is partnering with a privately held molecular diagnostics company to hire a Senior Bioinformatics Scientist focused on oncology. The role leads development, optimization, and validation of computational workflows for a next-generation oncology diagnostic platform, interfacing with assay development, laboratory automation, biostatistics, and regulatory teams.

The position demands expertise in NGS analysis, statistical modeling, and reproducible software, with strong coding in Python/R and