Genomics Data Scientist – New Grad

Genomics Data Scientist – New Grad – Illumina

Illumina (NASDAQ: ILMN) is the world's leading provider of DNA sequencing technology — responsible for 90% of all genome sequencing performed worldwide. Illumina's NovaSeq X and NextSeq platforms have democratized genomic sequencing, reducing the cost of sequencing a human genome from $1 billion in 2001 to under $200 today. Illumina's sequencing instruments and reagents power genomic medicine at 1,000+ hospitals, university research centers, and population genomics programs worldwide — enabling newborn screening, cancer liquid biopsy, and infectious disease surveillance. We are hiring New Grad Genomics Data Scientists in San Diego to build the bioinformatics algorithms and data science tools powering the next generation of genomic medicine.

Responsibilities

• Develop and optimize next-generation sequencing (NGS) analysis algorithms — implementing FASTQ quality control, read alignment, variant calling, and copy number analysis pipelines
• Build machine learning models improving Illumina's base-calling accuracy — applying deep learning (CNNs, transformers) to improve variant detection sensitivity and specificity
• Develop liquid biopsy bioinformatics — implementing cell-free DNA (cfDNA) fragment analysis, methylation sequencing, and copy number variant (CNV) detection for cancer early detection
• Analyze whole-genome sequencing (WGS) and whole-exome sequencing (WES) data for population genomics programs supporting Illumina's clinical sequencing customers
• Build data validation pipelines for Illumina's clinical sequencing assays (TSO 500, TruSight Oncology) ensuring analytical accuracy for regulatory CE-IVD and FDA submissions
• Develop benchmarking datasets comparing Illumina's sequencing accuracy against Oxford Nanopore and PacBio long-read sequencing platforms

Requirements

• Bachelor's or Master's degree in Bioinformatics, Genomics, Computer Science, or Bioengineering
• Python and R proficiency for genomics data analysis (BioConductor, biopython, pysam)
• Understanding of next-generation sequencing: library preparation, base-calling, alignment, and variant calling
• Familiarity with standard bioinformatics tools: BWA, GATK, SAMtools, bcftools
• Deep learning experience (PyTorch, TensorFlow) for sequence analysis is a strong plus

Benefits

• Competitive salary with Illumina RSU equity and annual incentive
• Work on the genomics technology sequencing the human genome to cure disease
• Comprehensive medical, dental, and vision benefits
• 401(k) with Illumina matching
• San Diego campus — excellent weather, beaches, and one of the world's top biotech ecosystems