Senior Bioinformatics Scientist

The Position:

We are seeking an experienced and motivated Bioinformatics Scientist to join our Bioinformatics and Data Science Team focused on developing regulated diagnostics products. The ideal candidate will bring deep expertise in NGS technologies with a strong understanding of regulatory environments including CAP/CLIA and IVD product development. The successful candidate will play a crucial role in designing, developing, and optimizing our next generation of genomic assays. This position requires a unique blend of expertise in bioinformatics, extensive experience in assay optimization, analytical validation, strong skills in analytical pipeline development, automation and optimization, a deep understanding of molecular biology, and a passion for transforming complex biological data into actionable insights.

KEY RESPONSIBILITIES:

• Lead bioinformatics design, development and validation efforts in assay development for new and on-market products. As part of project core teams, this individual must be responsible for coordinating planning, execution, and delivery within timelines and budget constraints.
• Apply leading edge knowledge in bioinformatics, genomics, and assay technologies, to contribute to development of company's concepts and principles and to achieve assay development objectives in creative and effective ways.
• Drive development study design and all analysis for assay development effort in collaboration with cross-functional teams.
• Develop statistical and machine learning techniques to comprehensively evaluate assay performance and create optimization strategies.
• Communicate analysis results, methodologies, and scientific findings to internal teams, external collaborators, and stakeholders.
• Develop scalable, production-grade workflows for high-throughput NGS data analysis using AWS and containerized environments.
• Facilitate successful production pipeline deployment by working closely with infrastructure and engineering teams
• Ensure compliance with regulatory standards (CAP/CLIA, FDA, IVDR) throughout the bioinformatics development lifecycle, including rigorous testing and documentation.
• Contribute to regulatory submissions and audits by providing technical documentation and validation reports.
• Provide scientific guidance and mentorship to junior bioinformatics team members.

Who You Are:

REQUIRED EXPERIENCE:

• PhD or MS in bioinformatics, computational biology, or an adjacent data science field, such as biostatistics, statistics or computer science.
• Proven experience - A minimum of 6 -7 years of experience in bioinformatics analysis, algorithm development, and pipeline implementation.
• Thorough understanding of NGS technologies and various methods for library preparation (WGS, enrichment, RNA-Seq, methylation, etc.).
• Proficiency in quantitative transcriptomics from NGS or expression microarray data in human disease/biology specifically, such as differential expression, dimension reduction, expression-based classifier development, RNA-based signatures, cell type deconvolution.
• Proficiency in machine learning, development of novel bioinformatics methodologies, and algorithms development, including benchmarking of computational methods.
• Proven experience developing and deploying bioinformatics workflows in AWS (e.g., EC2, S3, Step Functions, Batch, Lambda, etc.).
• Strong proficiency in Python, including experience with testing frameworks and SDLC best practices.
• Close collaboration with Quality and Regulatory Affairs team on assay and analysis pipeline development and verification.
• Demonstrated record of technical and scientific leadership, ownership, and independent work.

RELEVANT EXPERIENCE (preferred but not required):

• Track record of working with wet lab scientists on iterative experiment design, execution, analysis, and interpretation as a tightly integrated team.
• Proficiency in genomics, sequence analysis, and secondary analysis, such as variant calling (e.g., SNVs/MNVs/indels, CNV, structural variants), NGS QC, splicing, circular nucleic acids.
• Strong understanding of germline and somatic mutation processes leading to complex variation and genome-wide biomarkers with potential clinical utility, such as TMB, mutational signatures, LOH.
• Working knowledge of R.
• Experience with relational and non-relational database technologies is a plus.
• Excellent communicator about complex technical topics in an interdisciplinary setting, especially by using data visualizations and diagrams.
• Excellent technical problem solving and troubleshooting skills.

CULTURAL FIT:

• Passion for Innovation: You are deeply curious and driven to explore uncharted territories in genomics. Your passion for discovery motivates you to use novel analytical approaches to bring new insights to assay optimization and evaluation.
• Collaborative Spirit: You thrive in a collaborative environment, bringing a positive, can-do attitude to interdisciplinary projects. You are skilled at communicating complex ideas to non-experts and active listening, fostering an inclusive atmosphere that values each team member's contribution. You are receptive to feedback and motivated to better serve the team’s needs.
• Adaptability: In our fast-paced industry, change is constant. You are agile and flexible, ready to pivot strategies in response to new data or technologies. Your resilience and open-mindedness help our team navigate the uncertainties inherent in groundbreaking research.

#LI-Hybrid, or #LI-Remote

For candidates based in our San Diego office, the salary range is $160,000 - $180,000.

For candidates based in our South San Francisco office, the salary range is $175,000 - $189,000. 

For candidates working remote (US), the salary range is $150,000 - $168,000. 

• Highlight any prior work with CAP/CLIA or FDA‑regulated diagnostics in your resume; concrete examples of compliance activities stand out.
• Include a short portfolio link that showcases a reproducible NGS pipeline you built, preferably containerized and deployed on AWS.
• Prepare to discuss specific statistical or machine‑learning models you used to assess assay performance; be ready to walk through the rationale and results.
• Practice explaining complex bioinformatics concepts in plain language; interviewers will assess your ability to communicate with cross‑functional teams.
• Research Veracyte’s current assay portfolio and be ready to suggest one realistic improvement or new feature based on your expertise.
• When negotiating, emphasize the value of your regulatory experience and any mentorship responsibilities you’ll assume.
• Watch for vague statements about “flexible hours” without clear remote‑work policies; ask about core collaboration windows and equipment support.