Bioinformatics Scientist

Job Title: Bioinformatics Scientist/ Bioinformatics Research Associate Location: Genetic Center Drive, San Diego, CA 92121 Duration: 12 Months contract Job Summary: We are seeking an innovative Bioinformatics Scientist with expertise in AI/ML to build next-generation, high-throughput primer design systems for diagnostic platforms. In this role, you will combine molecular biology, machine learning, and data engineering to develop intelligent pipelines that translate experimental data into improved assay performance. You will build models that learn from large-scale PCR and sequencing datasets, enabling data-driven optimization of assay design. This role is ideal for someone excited about applying modern ML and AI techniques—including deep learning and emerging language model approaches—to real-world diagnostic challenges. Key Responsibilities: • Experimental Data Analysis: Develop scalable pipelines to process and analyze high-throughput PCR and NGS datasets Transform raw experimental outputs into structured datasets for modeling Engineer biologically meaningful features (e.g., sequence composition, thermodynamics, secondary structure) • Machine Learning Development: Design, train, and deploy models to predict primer efficiency, specificity, and robustness Integrate sequence-derived features, thermodynamic calculations, and experimental outcomes • AI-Driven Applications: Develop AI-powered tools to support primer design, assay optimization, and data interpretation Apply LLM-based methods for sequence annotation, workflow automation, and design recommendations Contribute to reusable internal platforms enabling AI-assisted assay development at scale Required Qualifications Education: • Ph.D. (0–2 years), M.S. (2–4 years), or B.S. (3–5+ years) in Bioinformatics, Computational Biology, Data Science, Molecular Biology, or a related field. • Bioinformatics: Strong foundation in sequence analysis, primer design, and computational biology workflows • Programming & Data Analysis: Proficiency in Python, with experience in statistical analysis and experimental data interpretation • Machine Learning: Hands-on experience developing ML or deep learning models using frameworks such as PyTorch, TensorFlow, or scikit-learn Preferred Qualifications: • Experience with sequence-based modeling or genomic data analysis • Experience developing or maintaining reproducible bioinformatics workflows (e.g., Nextflow, Bash) • Experience working in Linux command-line and shared server environments • Experience using Git (e.g., pull requests, code review, issue tracking) • Understanding of PCR chemistry and assay design principles Technical Skills: • Programming: Python (required), R, Git • Bioinformatics Tools: Primer3, BLAST, Biopython • Data & Engineering: Pandas, NumPy, SciPy, pipeline development • Machine Learning: PyTorch, TensorFlow, scikit-learn, XGBoost, LightGBM • AI/Automation: LLMs, workflow automation tools, AI-assisted development • Operating Systems: Linux command-line environments, Linux-based servers, shared computational infrastructure