Bioinformatics Scientist I

Fulgent Genetics; El Monte (CA); On-site; USD 120,000 - 160,000; Full time

Job summary

Fulgent Therapeutics LLC in California seeks a Bioinformatics Scientist to design and optimize computational pipelines for high-throughput tumor and tumor-normal NGS data analysis. You will refine methods, ensure data quality, and support cancer genomic testing with cross-functional teams.

The role focuses on somatic variant calling, annotation, and integration with clinical oncology reports, requiring strong programming in Python/R and experience with workflow systems.

Qualifications

• Ph.D. in Bioinformatics, Biostatistics, or a related field; or M.S. in a related field with 3+ years of relevant experience.
• 1-3 years of experience in a related scientific discipline, with experience in cancer genomics or somatic variant analysis strongly preferred.
• Experience analyzing multiple types of next-generation sequencing (NGS) data, including somatic variant calling tools and cancer genomics annotation databases.

Responsibilities

• Design, implement and improve computational pipelines for tumor and tumor-normal NGS analysis.
• Oversee pipeline development, validation, and integration with software teams.
• Review and support clinical oncology reporting workflows and data quality.
• Maintain up-to-date knowledge of somatic variant annotation resources and best practices.

Skills

Bioinformatics

Statistics

Teamwork

Communication

Problem solving

Education

Ph.D. in Bioinformatics

M.S. in related field with 3+ years

Tools

Mutect2

Strelka2

VarDict

COSMIC

OncoKB

CIViC

Nextflow

Snakemake

Job description

About Us

Founded in 2011, Fulgent has evolved into a premier, full-service genomic testing company built around a foundational technology platform.

Through our diverse testing menu, Fulgent is focused on transforming patient care in oncology, anatomic pathology, infectious and rare diseases, and reproductive health. We believe that by providing a wide range of effective, flexible testing options in conjunction with best-in-class service and support, we can redefine the way medicine is managed for patients and clinicians alike.

Since integrating with our therapeutic development business, Fulgent is also developing drug candidates for treating a broad range of cancers using a novel nanoencapsulation and targeted therapy platform. By merging our fields of expertise, we aim to become a fully integrated precision medicine company.

Summary of Position

As a Bioinformatics Scientist, you will collaborate in cross-functional teams to design, implement and continually improve advanced computational pipelines for high-throughput analysis of multiple types of NGS data. You will refine methodologies for data analysis, processing, visualization and storage. You will strive to maximize efficiency, quality, reliability and customer usability and satisfaction. This role sits within the Somatic/Oncology bioinformatics team, with a primary focus on tumor and tumor-normal NGS analysis pipelines supporting cancer genomic testing.

Key Job Elements

Research and Development

• Investigate and compare available algorithms, methods and data sources, including somatic variant calling, annotation, and filtering strategies (SNVs, indels, CNVs, gene fusions) in tumor and tumor-normal samples.
• Make recommendations for pipeline component improvements, or new pipelines.
• Write SOPs for new or updated pipeline components, or new pipelines.
• Write specifications for implementation by software developers.
• Oversee pipeline development and integration.

Production and Customer Support

• Investigate and resolve analysis and pipeline production issues.
• Review client projects for compatibility with current pipelines, make recommendations and implement customizations as needed.
• Oversee sequencing service projects, including variant classification and interpretation workflows that feed into clinical oncology reports, ensuring timely processing, quality results and client satisfaction.
• Support software and LIMS developers in automation efforts.
• Perform specialized analyses as needed for specific projects, keep up-to-date with current best practices and emerging methods, and treat data with a high level of integrity and ethics.

Data Maintenance

• Investigate available annotation and reference data sources, including cancer-specific knowledgebases such as COSMIC, OncoKB, CIViC, and ClinVar for somatic variant annotation.
• Validate and deploy/update selected data sources.
• Write reports detailing validation/update methodology and results.
• Write SOPs for updating existing or new data sources.

Validation

• Develop appropriate procedures for testing and validation of new or updated pipelines or pipeline components.
• Document and maintain data used for testing and validation.
• Write validation reports detailing validation methodology and results.

Qualifications

Knowledge/Experience

• Ph.D. in Bioinformatics, Biostatistics, or a related field; or M.S. in a related field with 3+ years of relevant experience.
• 1-3 years of experience in a related scientific discipline, with experience in cancer genomics or somatic variant analysis strongly preferred.
• Experience analyzing multiple types of next-generation sequencing (NGS) data, including somatic variant calling tools (e.g., Mutect2, Strelka2, VarDict) and cancer genomics annotation databases (e.g., COSMIC, OncoKB, CIViC), and facility with statistics for big data analysis and multi-omics data integration.
• Strong hands‑on skills in bioinformatics databases, bioinformatics tools and relevant programming languages (e.g., Python, R), with familiarity with workflow management systems (e.g., Nextflow, WDL, or Snakemake) preferred.
• Must enjoy working in a multi‑disciplinary, collaborative environment; ability to troubleshoot both individually and as part of a team; excellent oral and written communication skills; and experience in team software development and integration projects is a plus.

Supervisory Responsibilities

• No

Reports To

• Director of Bioinformatics

Environment

Fulgent Therapeutics LLC is an Equal Employment Opportunity Employer.

The work environment characteristics described here are representative of those an employee encounters while performing the essential functions of this job. Reasonable accommodations may be made to enable qualified individuals with disabilities to perform the essential functions of the position.

For California residents, please see the link below to access our CCPA Privacy Notice.

CCPA Privacy Notice for California Residents

https://tinyurl.com/FulgentCCPA