Bioinformatics Scientist I

FULGENT THERAPEUTICS LLC•El Monte, CA

1d•$90,000 - $120,000•Onsite

About The 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.

Requirements

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.

Nice To Haves

Familiarity with workflow management systems (e.g., Nextflow, WDL, or Snakemake) preferred.
Experience in team software development and integration projects is a plus.

Responsibilities

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.
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.
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.
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.