Bioinformatics Scientist / Senior Bioinformatics Scientist
Yoh, A Day & Zimmermann Company
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Benefits offered by this job
Job summary
Yoh, a Day & Zimmermann company, seeks a Senior Bioinformatics Scientist to lead development, optimization, and validation of computational workflows for a next‑generation oncology diagnostic platform in Sunnyvale, CA.
The role blends bioinformatics, next‑generation sequencing, and statistical modeling with assay development, and requires collaboration with assay science, molecular biology, quality, and regulatory teams; onsite or hybrid, direct-hire, full-time.
Qualifications
- PhD or MS with substantial related industry experience.
- Hands-on experience developing and maintaining NGS bioinformatics pipelines.
- Proficiency in Python and/or R with well-tested code.
- Experience with sequencing QC, alignment, variant/molecular-feature detection, and stats.
- Strong experimental design, evaluation, data quality, and reproducibility.
- Experience in Linux/Unix, Git, and reproducible workflows.
- Ability to troubleshoot complex bioinformatics problems and deliver results.
- Strong communication across scientific and technical teams.
Responsibilities
- Develop, optimize, and maintain end-to-end bioinformatics workflows for cfDNA sequencing assays.
- Process sequencing data across FASTQ, BAM/CRAM, VCF etc.
- Develop quality metrics for sequencing performance and sample-level metrics.
- Detect low-frequency molecular signals in noisy data.
- Apply barcodes, error correction, and background-noise modeling.
- Collaborate with assay scientists to understand variation sources.
- Develop statistical models to distinguish cancer signals from background.
- Evaluate model performance with training and test datasets.
- Assess effects of cfDNA input, depth, quality, and batch effects on performance.
- Design and support bioinformatics verification/validation activities.
- Define QC criteria, acceptance thresholds, and reproducibility requirements.
- Develop modular, version-controlled software (Python/R).
- Implement reproducible workflows (Nextflow/Snakemake/WDL).
- Use tests, containers, logging, and data lineage for reliable releases.
- Investigate pipeline failures and discrepant results.
- Prepare technical documentation for verification and regulatory activities.
- Communicate findings and recommendations to stakeholders.
Skills
Education
Tools
Job description
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 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.
- Experience with cfDNA, ctDNA, liquid biopsy, cancer genomics, or blood‑based molecular diagnostics.
- Familiarity with unique molecular identifiers, molecular barcodes, error‑corrected sequencing, or background‑noise suppression.
- Experience developing or validating computational pipelines for oncology or clinical diagnostic applications.
- Knowledge of analytical validation concepts such as limit of blank, limit of detection, precision, reproducibility, interference, and robustness.
- Experience with statistical classification, predictive modeling, feature selection, and evaluation of clinical biomarkers.
- Experience with Nextflow, Snakemake, WDL, Docker, Apptainer/Singularity, cloud infrastructure, or high‑performance computing.
- Familiarity with regulated software development, design controls, software verification and validation, change control, and traceability.
- Experience integrating computational workflows with LIMS, laboratory automation, or clinical reporting systems.
- Experience supporting clinical studies, regulated product development, or molecular diagnostic commercialization.
- Establish or materially strengthen a reproducible end‑to‑end NGS analysis pipeline.
- Implement documented sequencing‑ and sample‑level quality metrics and failure criteria.
- Improve the reliability of low‑frequency molecular signal detection and classification.
- Establish a bioinformatics verification and analytical‑validation plan with predefined acceptance criteria.
- Demonstrate reproducibility and traceability across representative datasets and software versions.
- Deliver controlled technical documentation, automated testing, and versioned software releases.
- Build productive working relationships across assay development, laboratory automation, clinical, quality, and regulatory functions.
The anticipated base salary range for this position is $175,000–$205,000 annually. Actual compensation will depend on qualifications, relevant experience, technical depth, and the final level of the position.
About Yoh Yoh, a Day & Zimmermann company, is a leading provider of talent and workforce solutions. Yoh connects highly skilled professionals with opportunities across life sciences, technology, engineering, and other specialized industries.
Yoh is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to legally protected characteristics.
$129500.00
We welcome you to be a part of the largest and legendary global staffing companies to meet your career aspirations. Yoh’s network of client companies has been employing professionals like you for over 65 years in the U.S., UK and Canada. Join Yoh’s extensive talent community that will provide you with access to Yoh’s vast network of opportunities and gain access to this exclusive opportunity available to you. Benefit eligibility is in accordance with applicable laws and client requirements. Benefits include:
- Medical, Prescription, Dental & Vision Benefits (for employees working 20+ hours per week)
- Health Savings Account (HSA) (for employees working 20+ hours per week)
- Life & Disability Insurance (for employees working 20+ hours per week)
- MetLife Voluntary Benefits
- Employee Assistance Program (EAP)
- 401K Retirement Savings Plan
- Direct Deposit & weekly epayroll
- Referral Bonus Programs
- Certification and training opportunities
Note: Any pay ranges displayed are estimations. Actual pay is determined by an applicant's experience, technical expertise, and other qualifications as listed in the job description. All qualified applicants are welcome to apply.
Yoh, a Day & Zimmermann company, is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or status as a protected veteran.
Visit https://www.yoh.com/applicants-with-disabilities to contact us if you are an individual with a disability and require accommodation in the application process.
For California applicants, qualified applicants with arrest or conviction records will be considered for employment in accordance with the Los Angeles County Fair Chance Ordinance for Employers and the California Fair Chance Act. All of the material job duties described in this posting are job duties for which a criminal history may have a direct, adverse, and negative relationship potentially resulting in the withdrawal of a conditional offer of employment.
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