Staff Bioinformatics Software Engineer

Responsibilities

• Lead the design and development of new features and enhancements for Cooper Bioinformatics products and applications, as well as new products and initiatives to meet the evolving needs of our business.
• Play a pivotal role as a Bioinformatics Software Development subject matter expert, demonstrating deep expertise in analyzing and interpreting biological data using statistical and computational techniques.
• Collaborate with biologists to design experiments and analyze data outcomes
• Drive the evolution of software development practices, including identifying opportunities for automation, efficiency, and innovation.
• Mentor and guide junior engineers, fostering their growth and development.
• Collaborate with the team to set the direction of future development within current and future CSI projects, contributing to architectural decisions and technical strategy.

Qualifications

• Extensive experience in NGS algorithms and analysis pipeline development, including data workflows, processing pipelines, and bioinformatics file formats (FASTQ, SAM/BAM, VCF).
• Strong experience in the design and optimization of targeted NGS panels, genome assemblies, and statistical modeling.
• Extensive experience in high-level scripting languages used in bioinformatics, such as R or Python, with a proven track record of delivering complex, high-quality software solutions.
• Extensive experience with the Linux operating system and its terminal commands.
• Knowledge of Bash scripting is a strong plus.
• Extensive knowledge of common bioinformatics toolkits, including Bowtie 2, BWA, GATK, SAMtools, and FastQC.
• Strong understanding of AWS cloud solutions, including S3, RDS, and EC2.
• Familiarity with pipeline development tools such as Snakemake and Nextflow.
• Strong experience with Git version control and software development best practices, including writing clean, maintainable code and designing modular, reusable components.
• Familiarity with unit testing and test-driven development (TDD) methodologies to ensure high code quality and reliability.
• Familiarity with containerization technologies such as Docker, as well as package management tools like Conda.
• Knowledge of statistical methods such as Hidden Markov Models, along with a strong foundation in linear algebra, is a strong plus.
• Familiarity with modern GPU-accelerated frameworks, such as NVIDIA Parabricks, is a strong plus.
• Outcome-focused mindset with strong process discipline and a commitment to timely project delivery.
• Strong interpersonal and communication skills, with the ability to collaborate effectively and mentor team members.
• Strong commitment to continuous learning and staying current with emerging technologies

Benefits

• Outstanding total compensation plan
• Medical coverage
• 401(k)
• Paid time off for vacation, personal, sick and holidays
• Multiple other perks and benefits