SENIOR BIOINFORMATICS SCIENTIST (SOUTH SAN FRANCISCO, CA)

Cedent Consulting Inc.; San Francisco (CA); On-site; USD 90,000 - 150,000; Full time

Job summary

An innovative firm is seeking a Senior Bioinformatics Scientist to drive advancements in synthetic biology. This role combines computational and molecular biology, focusing on developing DNA sequence analysis pipelines and predictive models. You will collaborate with scientists and engineers, applying machine learning to enhance DNA synthesis efficiency. The ideal candidate will have a strong background in bioinformatics, experience with sequencing technologies, and proficiency in Python and machine learning frameworks. Join a dynamic team dedicated to pioneering solutions in synthetic biology and making a significant impact in the field.

Qualifications

• 6-8 years of industry experience in Bioinformatics or a related field.
• Hands-on experience with ONT, Illumina, or PacBio sequencing technologies.

Responsibilities

• Develop bioinformatics methods for DNA assembly and synthetic biology workflows.
• Collaborate with teams to troubleshoot molecular biology processes.

Skills

Python

Machine Learning

Bioinformatics

Statistical Analysis

Data Visualization

Education

Bachelor's/Master's in Bioinformatics or related field

Ph.D. in Bioinformatics or related field

Tools

Nextflow

Scikit-learn

TensorFlow

R

SQL

Job description

Senior Bioinformatics Scientist (South San Francisco, CA)

We are seeking a highly motivated and innovative Senior / Staff Bioinformatics Scientist to join our R&D team focused on synthetic biology product development. In this role, you will work at the intersection of computational and molecular biology , developing advanced DNA sequence analysis pipelines, gene design algorithms, and predictive models to optimize DNA synthesis and assembly.

You will collaborate with molecular biologists, product teams, and manufacturing engineers to refine our core synthetic biology platform, troubleshoot assembly challenges , and improve DNA synthesis efficiency . This position emphasizes predictive modeling, algorithm development, and data-driven approaches to enhance synthetic biology workflows.

Key Responsibilities

• Synthetic Biology & DNA Assembly
• Develop bioinformatics methods supporting DNA assembly strategies and synthetic biology workflows .
• Apply machine learning and predictive modeling to improve DNA assembly success rates and optimize synthesis parameters.
• Collaborate with wet-lab scientists to analyze and troubleshoot molecular biology processes.
• Develop bioinformatics approaches for diagnosing and resolving complex DNA synthesis and assembly issues.
• Build and maintain NGS analysis pipelines (e.g., Nextflow) to support quality control and performance tracking of synthetic biology products.
• Leverage Oxford Nanopore Technologies (ONT), Illumina, or PacBio sequencing to analyze and optimize synthesis workflows.
• Develop predictive models to identify challenging sequences and recommend optimizations to improve synthesis efficiency.
• Ensure pipeline accuracy, reproducibility, and scalability in research environments.
• Data Analysis & Insights
• Apply advanced statistical and machine learning methods to evaluate improvements in synthetic biology product iterations .
• Use Python, R, and visualization tools to generate actionable insights and present findings to stakeholders.
• Design and implement novel bioinformatics algorithms for sequence analysis and synthetic biology applications .
• Cross-Functional Collaboration
• Partner with R&D, manufacturing, and product development teams to troubleshoot assay issues and implement data-driven solutions .
• Support the broader Bioinformatics team by integrating synthetic biology workflows with existing genomic data processing pipelines.
• Assist with customer-facing analyses related to synthetic biology assay performance.

Required Qualifications

• Educational Background & Experience :
• Bachelor’s / Master’s degree with 6–8 years of industry experience , or a Ph.D. with 3+ years of industry experience in Bioinformatics, Molecular Biology, Biochemistry, Genetics, Genomics, Computational Biology, or a related field .
• Experience with ONT, Illumina, or PacBio sequencing technologies .
• Proficiency in workflow management tools (Nextflow, Snakemake).
• Hands-on experience designing predictive models for sequence design & synthetic biology applications .
• Technical Skills :
• Expertise in Python (Pandas, NumPy, SciPy) and visualization libraries (Matplotlib, Seaborn, Plotly).
• Experience with machine learning frameworks (scikit-learn, TensorFlow, PyTorch) applied to biological sequence data.
• Familiarity with R, SQL, or other statistical tools .
• Molecular Biology & Synthetic Biology Knowledge :
• Understanding of DNA assembly, cloning techniques, and molecular biology workflows .
• Ability to interpret experimental data and provide feedback on laboratory procedures.

Preferred Qualifications

• Experience developing design algorithms for synthetic biology applications.
• Familiarity with deep learning approaches for biological sequence analysis.
• Exposure to high-throughput experimental design and laboratory automation.
• Hands-on experience with gene synthesis and synthetic biology assay development .

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