Job Description

Compensation: $125,000-$,170,000 per year. You are eligible to a Short-Term Incentive Plan with the target at 7.5% of your annual earnings, terms and conditions apply.

Bioinformatics Scientist III – Remote, USA

As a Bioinformatics Scientist III / Bioinformatics Software Engineer III, you will be responsible for designing, developing, and maintaining bioinformatics algorithms and pipelines to support automated variant interpretation. This position requires expertise in gene-disease ontologies and high-throughput genetic data analysis and offers a unique opportunity to work on innovative bioinformatics tools with a direct impact on clinical applications. You will collaborate with a cross-functional team of bioinformaticians, software engineers, wet lab scientists, and clinicians to drive new products and improvements in diagnostic and research workflows. In addition to writing code and fulfilling needed tickets, the successful candidate will design technical solutions with the bioinformatics and IT operations teams, participate in scrum ceremonies, and work with stakeholders to understand workflows and requests.

Essential Functions

• Algorithm, Pipeline Development, and Analysis: Design, develop, and implement scalable bioinformatics algorithms for variant interpretation and maintain bioinformatics pipelines, ensuring accuracy, efficiency, and integration into clinical workflows. Work with statisticians in validation of new methods, including data collection and analysis algorithms. Develop features/tools assisting clinical and genetic analysis.
• Gene-Disease Ontology Integration: Use expertise in gene-disease ontologies, such as the Human Phenotype Ontology (HPO), to structure and enhance variant impact predictions, aligning algorithms with clinically relevant genotype-phenotype relationships.
• Software Engineering and Custom Development: Develop custom software and features according to specifications and in collaboration with cross-functional teams. Lead end-to-end technical solutions from ideation to release, including time and complexity estimation, testing, and deployment. Drive technical solutions to problems, including end-to-end process flow from ideation to release, and estimating time and complexity. Design and develop custom software according to ticket specifications. Provide clear and consistent feedback on code reviews. Monitor process and log information, troubleshooting issues as needed.
• Collaboration and Stakeholder Engagement: Work with stakeholders, including bioinformatics and IT operations teams, to clarify requirements, design workflows, and understand complex bioinformatics needs. Participate in scrum ceremonies and provide feedback to team members through code reviews and mentorship. Meet with clients, partners, product owners, or other stakeholders to understand and clarify workflows and requirements
• Troubleshooting and Optimization: Monitor processes and troubleshoot issues as they arise, implementing solutions to enhance pipeline reliability. Drive optimizations in data collection, algorithm validation, and the development of tools for clinical and genetic analysis. Highlight blockers or issues arising during development to resolve in a timely manner. Trouble shooting for bioinformatics pipeline and applications for clinical tests
• Documentation and Reporting: Prepare thorough documentation of algorithms, workflows, and methods to ensure reproducibility and support broader team understanding. Support team training and serve as a mentor to junior scientists and engineers.
• Mentorship: Act as a role model for the team, settings standards for excellence and mentoring junior engineers
• Other duties as assigned.

Qualifications

• PhD degree in bioinformatics, computational biology, structural biology, biophysics, biology, computer science, or related discipline and 4+ years post-doctoral research experience or industrial experience
• MS degree in bioinformatics, computational biology, structural biology, biophysics, biology, computer science, or related discipline and 7+ years industrial experience

Preferred

• Technical Expertise: Proficiency with bioinformatics databases (ClinVar, HGMD, OMIM) and programming languages (Python, R, SQL, bash, Perl, C/C++, Java) in Linux/Unix. Skilled in cloud computing (AWS, Azure, Google Cloud), CI/CD (Bamboo, Jenkins), containerization (Docker), and high-performance computing. Strong knowledge of gene-disease ontologies, bioinformatics software.
• Software and Engineering Skills: Experienced in API development, statistical analysis methods, and use of frameworks/tools like PHP, React, Symfony, and Atlassian suite (Jira, Confluence).
• Analytical and Problem-Solving Skills: Advanced analytical skills focused on creating efficient, reproducible bioinformatics solutions for clinical and research applications, with strong statistical analysis expertise.
• Communication and Teamwork: Excellent written and verbal communication skills, with a proven ability to work both independently and collaboratively across teams. Demonstrated leadership in mentoring and setting high performance standards.
• Clinical Genetics and Biology: In-depth knowledge of clinical genetics, mutation analysis, and bioinformatics principles, with experience in gene-disease ontologies and databases (HGVS nomenclatures, ClinVar, HGMD). Proficient in molecular biology, and genomics for automated clinical interpretation.

About Us:

Ambry Genetics Corporation is a CAP-accredited and CLIA-licensed molecular genetics laboratory based in Aliso Viejo, California. We are a genetics-based healthcare company that is dedicated to open scientific exchange so we can work together to understand and treat all human disease faster.

At Ambry, everyone is welcome. A career at Ambry Genetics is a chance to be part of a dynamic company that aims to improve health by understanding the relationships between genetics and human disease. We earned our reputation as industry leaders by responsibly introducing cutting-edge genetic testing solutions and continually sharing what we learn with the global scientific community.

At Ambry you will be learning, challenging yourself, and having fun while collaborating with teammates through the open exchange of ideas. Our outstanding benefits program includes medical, dental, vision, 401k with a 4% employer match, FSA, paid sick leave and generous paid time off (PTO) program. The Company reserves the right to make changes to the 401k plan from time to time. You can learn more about the benefits here. Ambry Genetics is an Equal Opportunity Employer (EOE) and we maintain a drug-free work environment.

The Company believes in second chance employment. Qualified applicants with arrest or conviction history will be considered regardless of their arrest or conviction history, consistent with local laws such as Los Angeles County Fair Chance Ordinance and the California Fair Chance Act. You do not need to disclose your criminal history or participate in a background check until a conditional job offer is made to you. After making a conditional offer and running a background check, if the Company is concerned about conviction that is directly related to the job, you will be given the chance to explain the circumstances surrounding the conviction, provide mitigating evidence, or challenge the accuracy of the background report. For the purpose of the above job description, “Essential Functions” are “Material Job Duties”.

Our salary ranges are determined by role, level, and location. The range displayed on each job posting reflects the minimum and maximum target for new hire salaries for the position across all US locations. Within the range, individual pay is determined by work location and additional factors, including job-related skills, experience, and relevant education or training.

All qualified applicants will receive consideration for employment without regard to race (and traits historically associated with race, including, but not limited to hair texture and protective hairstyles such as braids, locks, and twists), color, creed, religion, sex, sexual orientation, gender identity, gender expression (including transgender status), national origin, ancestry, age, marital status or protected veteran status and will not be discriminated against on the basis of disability, protected medical condition as defined by applicable state or local law, genetic information, or any other characteristic protected by applicable federal, state, or local laws and ordinances. If you have a disability or special need that requires accommodation, please contact us at [email protected]

Ambry does not accept unsolicited resumes from individual recruiters, third party recruiting agencies, outside recruiters or firms without an executed contract in place. We are not responsible for any fees related to resumes that are unsolicited or are received by Ambry. Such resumes will be deemed the sole property of Ambry and will be processed accordingly.

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