Principal Bioinformatics Scientist

Job Summary: 

Baylor Genetics is seeking an accomplished Principal Bioinformatics Scientist to join the Bioinformatics R&D and Data Science organization. This individual will serve as a senior technical expert and key individual contributor responsible for developing, optimizing, and maintaining the computational methods and pipelines that power Baylor Genetics’ genomic testing and interpretation platforms. 

The Principal Bioinformatics Scientist will drive research and development efforts across secondary and tertiary analysis, variant interpretation, and computational genomics, while also providing technical expertise and production support for Baylor Genetics’ operational bioinformatics systems. The ideal candidate combines deep expertise in genomics, bioinformatics, and computational modeling with strong practical skills in data science, pipeline development, and system optimization in a clinical genomics environment. 

This role bridges R&D innovation and production support, ensuring that novel research solutions are validated, robust, and seamlessly integrated into clinical operations under CLIA, CAP, and other regulatory standards. 

QUALIFICATIONS: 

Education: 

• Master’s or higher degree (PhD preferred) in Bioinformatics, Computational Biology, Genomics, Computer Science, or a related quantitative field. 

Experience: 

• 6+ years of professional experience in bioinformatics, computational genomics, or computational biology, including extensive hands-on work with large-scale NGS datasets. 

• Proven experience developing and maintaining bioinformatics pipelines in both R&D and production settings. 

• Strong record of integrating computational, statistical, and/or machine learning methods into genomics applications. 

• Experience working in a clinical genomics or regulated diagnostic environment strongly preferred. 

• Demonstrated success collaborating with clinical or laboratory teams to troubleshoot and improve production systems. 

• Proficiency in Python and R; familiarity with one or more compiled languages (C/C++, Java, or similar). 

• Strong experience with NGS data formats and tools. 

• Expertise with workflow orchestration frameworks (Nextflow, Snakemake, Cromwell). 

• Deep knowledge of genomic databases. 

• Familiarity with cloud computing (Azure, AWS, GCP), containerization (Docker/Kubernetes), and version control (Git). 

• Background in statistical modeling, data analysis, and machine learning frameworks (e.g., Scikit-learn, TensorFlow, PyTorch) preferred. 

• Knowledge of multi-omics data integration and data visualization methods a plus. 

• Core Competencies: 

• Strong scientific reasoning and analytical problem-solving abilities. 

• Hands-on approach to both R&D innovation and operational troubleshooting. 

• Ability to collaborate effectively with multidisciplinary teams. 

• Excellent written and verbal communication skills. 

• Commitment to quality, compliance, and scientific excellence in a clinical setting. 

DUTIES AND RESPONSIBILITIES: 

• Scientific and Technical Contribution: 

• Design, develop, and optimize computational workflows and pipelines for secondar and tertiary genomic analyses. 

• Implement reproducible and scalable bioinformatics workflows using Nextflow, Snakemake, or similar orchestration frameworks. 

• Develop, evaluate, and apply algorithms and statistical or machine learning models for variant detection, classification, and genotype–phenotype correlation. 

• Integrate multi-omics, phenotypic, and clinical datasets to enhance analytical accuracy and interpretability. 

• Translate R&D innovations into production-ready tools that improve diagnostic accuracy, speed, and reproducibility. 

System Support and Clinical Collaboration: 

• Provide ongoing support and maintenance for bioinformatics systems and pipelines, ensuring operational stability, accuracy, and efficiency. 

• Actively collaborate with clinical and laboratory teams to investigate and resolve pipeline bugs, data inconsistencies, and performance issues. 

• Participate in root-cause analyses and implement sustainable solutions to ensure reliable clinical operations. 

• Work closely with clinical stakeholders to define, design, and deploy enhancements and new system capabilities based on user feedback and evolving clinical requirements. 

• Ensure all production updates and improvements comply with regulatory and quality standards (CLIA, CAP, etc.) and are appropriately documented and validated. 

• Clinical R&D and Validation: 

• Support the design and validation of new computational tools and pipelines according to clinical genomic standards and regulatory requirements. 

• Conduct analytical validation, benchmarking, and verification of newly developed algorithms and workflows. 

• Collaborate with quality, laboratory, and clinical teams to ensure smooth transition of tools from R&D to production. 

• Research and Development Innovation: 

• Lead exploratory projects to develop and assess novel computational or statistical methods for variant classification, annotation, and interpretation. 

• Perform benchmarking studies to evaluate emerging algorithms, annotation resources, and data integration approaches. 

• Contribute to internal documentation, publications, and presentations highlighting R&D advancements. 

• Collaboration and Mentorship: 

• Collaborate closely with data scientists, software engineers, and clinical scientists on cross-functional R&D and production initiatives. 

• Provide technical mentorship and peer review for bioinformatics scientists and analysts. 

• Promote best practices in scientific computing, code reproducibility, and analytical rigor. 

• Operational Excellence: 

• Maintain clear, version-controlled documentation of all analytical pipelines and validation processes. 

• Contribute to continuous improvement of computational infrastructure, software practices, and data management. 

• Stay current with evolving trends, standards, and technologies in computational genomics and clinical bioinformatics. 

WHY JOIN BAYLOR GENETICS 

At Baylor Genetics, you’ll join a world-class team dedicated to transforming patient care through genomic innovation. As a Principal Bioinformatics Scientist, you’ll directly contribute to advancing Baylor Genetics’ bioinformatics ecosystem; developing, validating, and supporting analytical systems that empower precision medicine. 

You will collaborate with leading scientists, engineers, and clinicians to ensure that cutting-edge research is translated into reliable, high-impact clinical solutions that improve lives through genomic insight. 

PHYSICAL DEMANDS AND WORK ENVIRONMENT: 

• Frequently required to sit 

• Frequently required to stand 

• Frequently required to utilize hand and finger dexterity 

• Frequently required to talk or hear 

• Frequently required to utilize visual acuity to operate equipment, read technical information, and/or use a keyboard 

• Occasionally exposed to bloodborne and airborne pathogens or infectious materials 

EEO Statement: 

Baylor Genetics is an equal-opportunity employer dedicated to building an inclusive and diverse workforce. We do not discriminate based on race, religion, color, national origin, sex, sexual orientation, age, gender identity, veteran status, disability, genetic information, pregnancy, childbirth, or related medical conditions, or any other status protected under applicable federal, state, or local law. 

Note to Recruiters:

 We value building direct relationships with our candidates and prefer to manage our hiring process internally. While we occasionally partner with select recruitment agencies for specialized roles, we do not accept unsolicited resumes from recruiters or agencies without a written agreement executed by the authorized signatory for Baylor Genetics ("Agreement"). Any resumes submitted to Baylor Genetics in the absence of an Agreement executed by Baylor Genetics' authorized signatory will be considered the property of Baylor Genetics, and Baylor Genetics will not be obligated to pay any associated recruitment fees.