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Senior Bioinformaticist

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Rady Children's Hospital-San Diego

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Location:
United States , San Diego

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Contract Type:
Not provided

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Salary:

Not provided

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 productiongrade 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:

  • Helping deploy, maintain, and evolve the bioinformatics framework supporting a high-throughput, ultra-rapid turnaround whole genome sequencing clinical environment
  • Focusing primarily on germline genomics pipelines, population genomics analysis, and the continuous improvement of production-grade bioinformatics workflows
  • Working 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
  • Contributing 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
What we offer:
  • Medical, Dental, Vision, Life, Pet insurance
  • Retirement Plan
  • Tuition Assistance
  • Wellness program

Additional Information:

Job Posted:
May 03, 2026

Employment Type:
Fulltime
Work Type:
Hybrid work
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