Staff Bioinformatics Software Engineer

CooperCompanies•Houston, TX

8h•Onsite

About The Position

The Cooper Surgical R&D Software team within Cooper Surgical is dedicated to developing and maintaining cutting-edge software solutions. We are expanding our team to provide digital capabilities for the Life Sciences product portfolio. As a Staff Bioinformatics Software Engineer on the CSI Software R&D team, you will lead the charge in the design, development and maintenance, and innovation of digital solutions that underpin the Life Science products, with a focus on high throughput next generation sequencing data and analysis platform that powers CooperSurgical’s genetic testing product offerings, along with steering new initiatives and pioneering state-of-the-art software solutions, providing guidance and expertise. This role will report to the Head of Software Development and have a dotted line reporting to the Head of Life Sciences. As a Staff Bioinformatics Software Engineer on the Cooper Surgical R&D Software Development team, you will assume a technical leadership role in designing, developing, maintaining, enhancing, and supporting internal-facing software products. This position will require a high level of technical expertise, with a focus on designing and delivering advanced Bioinformatics solutions, statistical modeling, and next generation sequencing algorithm and analysis pipelines for detection and interpretation of complex genomic features. You will collaborate closely with a multidisciplinary team of bench scientists with expertise in molecular and cellular biology as well as Operations and Quality teams and be responsible for the evolution of existing offerings and leading the development of new software products and services, while also specializing in key areas.

Requirements

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
Minimum of 7 years of relevant experience, with track record of increase in responsibilities and leadership within the software development field.
Minimum bachelor’s degree in computer science, bioinformatics, data science, mathematics, statistics or related field.

Nice To Haves

Knowledge of Bash scripting is a strong plus.
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.
Master’s or Ph.D. degree preferred.

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
Work on algorithm development for sequence analysis, gene prediction, and other applications
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.