Bioinformatics RA III or Scientist ; AI​/ML Assay Design

Position: Bioinformatics RA III or Scientist I (AI/ML   Assay Design)
$50/hr - $60/hr

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

Position Overview
We are seeking an innovative Bioinformatics Scientist with expertise in AI/ML to build next-generation, high-throughput primer design systems for
*** s 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, Tensor Flow, 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, Num Py, Sci Py, pipeline development
Machine Learning:
PyTorch, Tensor Flow, 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.