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Senior Bioinformaticist

United States, San Diego 52.95 - 72.81 USD / Hour · Job Posted July 04, 2026
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Job Description

The Senior Bioinformaticist is a senior-level individual contributor responsible for helping deploy, maintain, and evolve the bioinformatics framework supporting a high-throughput, ultra-rapid turnaround whole genome sequencing clinical environment. This role focuses primarily on germline genomics pipelines, population genomics analysis, and the continuous improvement of production-grade bioinformatics workflows. This position will work as part of a team to build and maintain scalable bioinformatics infrastructure using modern technologies in compute infrastructure, data storage, and genomic analytics, with a strong emphasis on automation, reproducibility, and integration across systems. In addition to maintaining clinical pipelines, this role will contribute to research and innovation initiatives, exploring new computational approaches, emerging genomic technologies, and AI/ML methods applied to genomic data. The environment is highly cross-functional, with strong collaboration across clinicians, bioinformaticians, software engineers, and researchers, as well as partnerships with biotechnology companies, academic institutions, and national or international research programs.

Job Responsibility

  • Help deploy, maintain, and evolve the bioinformatics framework supporting a high-throughput, ultra-rapid turnaround whole genome sequencing clinical environment
  • Focus primarily on germline genomics pipelines, population genomics analysis, and the continuous improvement of production-grade bioinformatics workflows
  • Work as part of a team to build and maintain scalable bioinformatics infrastructure using modern technologies in compute infrastructure, data storage, and genomic analytics, with a strong emphasis on automation, reproducibility, and integration across systems
  • Contribute to research and innovation initiatives, exploring new computational approaches, emerging genomic technologies, and AI/ML methods applied to genomic data

Requirements

  • Master's Degree
  • Area of study in a field related to the position
  • Experience analyzing next-gen sequencing data from raw sequencing output (BCL/FASTQ) through alignment, variant calling, annotation, and prioritization for whole genome or exome sequencing data
  • Experience developing, maintaining, and troubleshooting automated bioinformatics pipelines supporting high-throughput genomic analysis in production or research environments
  • Experience working with and understanding of NGS analysis tools like Dragen, BWA,, GATK, DeepVariant, Samtools, bcftools, Picard, Annovar, VEP, or similar tools
  • Experience with Unix/Linux operating system and software development using any of Ruby, Python, Perl, Bash
  • Experience working with large-scale computational environments, including HPC or distributed compute systems, and workflow orchestration tools (e.g., Nextflow, Snakemake, WDL, Cromwell, or similar frameworks)

Nice to have

  • Ph.D.
  • Experience in CNV and SV detection tools and interpretation of complex genomic variation
  • Previous experience working in a CAP/CLIA environment
  • Previous experience with cloud-based development or analysis and performing benchmarking of bioinformatics tools
  • Experience applying machine learning or AI approaches to genomics, phenomics, or biomedical datasets
  • Experience analyzing multi-omics datasets, including RNA-seq, long-read sequencing, transcriptomics, proteomics, or related genomic technologies

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