Scientist I

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

Location: San Diego CA 92121

Duration: 12 Months (Possibilities of extension)

Shift: Standard

Position Overview

We are seeking an innovative Bioinformatics Scientist with expertise in AI/ML to build next-generation high-throughput primer design systems for client diagnostic 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