Bioinformatics Scientist I

Fulgent Therapeutics LLC; El Monte (CA); On-site; USD 90,000 - 120,000; Full time

Job summary

Fulgent Therapeutics LLC is seeking an Experienced Bioinformatics Scientist to design and improve computational pipelines for high-throughput NGS data, focusing on tumor and tumor-normal analyses within a collaborative Somatic/Oncology team.

You will refine methodologies, manage data processing, visualization, storage, and contribute to clinical oncology reports while ensuring data integrity and adherence to best practices.

Qualifications

• Ph.D. or M.S. with 3+ years in related field.
• 1-3 years experience in cancer genomics or somatic variant analysis preferred.
• Experience with multiple NGS data types and somatic variant callers.
• Strong hands-on skills in bioinformatics databases and programming (Python, R).
• Enjoys collaboration in a multi-disciplinary software development environment.

Responsibilities

• Design and improve computational pipelines for high-throughput NGS data analysis.
• Oversee pipeline development, validation, and integration with software teams.
• Review client projects and implement customizations for oncology reports.
• Maintain data sources like COSMIC, OncoKB, CIViC, and ClinVar; write SOPs.

Skills

Python

R

Nextflow

Team collaboration

Education

Ph.D. in Bioinformatics/Biostatistics or related field

M.S. in related field with 3+ years of experience

Tools

Mutect2

Strelka2

VarDict

COSMIC

OncoKB

CIViC

Nextflow

WDL

Snakemake

Job description

Job Level: Experienced

Job Location: FLGT 4399 BLDG 2 - El Monte, CA 91731

Position Type: Full Time

Education Level: Graduate Degree

Salary Range: $90,000.00 - $120,000.00 Salary/year

Job Category: Biotech

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.

QualificationsKnowledge/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

Please note that Fulgent (and its affiliated companies, including Inform Diagnostics and CSI Laboratories) does not accept unsolicited information and/or resumes from search firms or agencies for our job postings. Search firms or agencies without an applicable contract and/or express approval to recruit for the role in question — that choose to submit a resume or client information to our career page or to any employee of Fulgent — will not be eligible for payment of any fee(s), and any associated shared data will become the property of Fulgent.