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RA III or Scientist I (AI/ML – Assay Design)

Connexion Systems + Engineering

San Diego, CA

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JOB DETAILS
SALARY
SKILLS
Analysis Skills, Artificial Intelligence (AI), Assay Development, Assays, Automation, Bash Scripting, Benchmarking, Bioinformatics, Biology, Chemistry, Code Reviews, Command Line, Data Analysis, Data Modeling, Data Science, Data Sets, Deep Learning, Genomics, Git, High Throughput, Infectious Diseases, Linux Operating System, Machine Learning, Modeling Languages, Molecular Biology, Operating Systems, Performance Management, Polymerase Chain Reaction (PCR), Predictive Modeling, Process Improvement, Python Programming/Scripting Language, R Programming Language, Scalable System Development, Thermodynamics, Training Data Sets
LOCATION
San Diego, CA
POSTED
20 days ago
Job Title: RA III or Scientist I (AI/ML – Assay Design)
Pay Rate: $60/hr.
Location:  San Diego, CA 92121
Duration: Approved until 7/18/2027

Position Overview:
We are seeking an innovative Bioinformatics Scientist with expertise in AI/ML to build next-generation, high-throughput primer design systems for our 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
  • Build reproducible ML workflows that support end-to-end assay design automation
Model Iteration & Optimization
  • Continuously refine models using newly generated experimental data
  • Implement frameworks for iterative learning, model retraining, and benchmarking
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
Why This Role Is Exciting
You will apply AI/ML to molecular biology to design better assays for women’s health and infectious disease detection.
 

About the Company

C

Connexion Systems + Engineering

Connexion is an award-winning professional staffing firm that strives to be the unrivaled staffing solution for job seekers by expertly connecting talent with opportunity.  Over the last 20 years Connexion has built the most admired team of staffing experts in the industry.  We give back, change lives and offer unconditional support to the candidates we represent.

Put Connexion's 20 years of experience to work for you! Our professionals have unrivaled relationships and contacts with the hiring managers, human resources team and decision makers at the most desirable companies to work for.

Don't let your resume get lost in an inbox, Connexion's recruiting team will advocate on your behalf to get you the job you want

COMPANY SIZE
500 to 999 employees
INDUSTRY
Staffing/Employment Agencies
FOUNDED
1999
WEBSITE
https://www.csetalent.com/

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