Senior Bioinformatics Software Engineer

Baylor Genetics; United States; Remote; USD 120,000 - 180,000; Full time

Job summary

Baylor Genetics in the United States is seeking a Senior Bioinformatics Software Engineer to design, develop, and maintain scalable software for bioinformatics pipelines, collaborating with cross-functional teams to deliver data-driven solutions aligned with business needs.

The role focuses on BI development, data modeling, ETL, API and microservices, dashboards and reports, with emphasis on code quality, testing, and thorough documentation.

Qualifications

• Bachelor’s degree in Computer Science, Software Engineering, Bioinformatics or related field; Master’s degree preferred.
• Minimum of 5 years of experience in software development with scalable solutions; production-ready from scratch.

Responsibilities

• Design, develop, and maintain robust BI software solutions for Baylor Genetics’ pipelines.
• Create and optimize data models for accurate, high-performance computations in assembly, mapping, variant calling, and annotation.
• Develop and optimize ETL processes to extract, transform, and load data from diverse sources.
• Analyze and optimize SQL queries; contribute to schema design for high performance.
• Build interactive dashboards and automated reports using BI tools and pipelines.
• Collaborate with data analysts, clinical reviewers, lab personnel, and developers to deliver timely integrations.
• Integrate disparate data sources with minimal code debt; ensure data consistency and reliability.
• Conduct rigorous testing and automate test suites using pytest, doctest, and CI/CD pipelines.
• Document solutions and maintain inline comments, wikis, and README files.

Skills

Python

SQL

CI/CD

Git

Data modeling

APIs

Linux

Docker

Kubernetes

Nextflow

Education

Bachelor's degree in CS/Software Engineering/Bioinformatics

Master’s degree preferred

Tools

Azure

SQL Server

NoSQL/MongoDB

Elasticsearch

Docker

Kubernetes

Git

SNakemake/Nextflow

Job description

The SeniorBioinformatics (BI)Software Engineer holds acriticaltechnical role, responsible for designing, developing, andmaintainingscalable and efficientsoftwaresolutionsforBaylorGenetics’bioinformaticpipelines. This role involves collaborating withand supportingcross-functional teams to deliver data-drivensoftwaresolutionsaligning withbusiness needs.

KEY RESPONSIBILITIES

• BI Development:Design, develop, andmaintainrobustsoftwaresolutions using various tools, databases, and technologies to meet business requirements.
• Data Modeling:Create and optimize data models, ensuring the accuracy, integrity, and performance of theunderlingcomputational algorithms, especially as pertains toassembly, mapping,variantcallingand variant annotation.
• ETL Processes:Develop andoptimizeETL (Extract, Transform, Load) processes to efficiently extract data from various sources, transform it, and load it into the BI system, with an emphasis onutilizingAPIs
• Query Optimization:Analyze andoptimizeSQL queries and database performance to enhance data retrieval and reporting speed.Contributeto schema design and review sessions to ensure high performance and maintainable databases.
• Dashboard & Report Creation:Develop interactive dashboards andautomatedreports using BI tools (e.g.,AzurePipelines, Teams Power Automate,email,Nextflow) to provide actionable insights for stakeholders.
• Collaboration:Workand alignclosely with stakeholders, including data analysts, business users,clinical reviewers, laboratorypersonneland software developers, toscope theirrequirementsand delivertimelyintegrationsof newsoftware.
• Data Integration:Integrate disparate data sources and ensure consistency, accuracy, and reliability of data across the BI system, with a focus on devising systems that have minimal to no code debt and are highly maintainable and flexible.
• Quality Assurance:Conduct rigorous testing of BI solutions to ensure data accuracy, system stability, andoptimalperformance, with the ability to automatetestingsuites using packages(e.g.pytest,doctest,Azure Pipelines)
• Documentation & Maintenance:Create comprehensive documentation for developed solutions and provide support andmaintenanceas necessary.Thisgenerallyincludes: (1)detailed in-line commenting notingJira ticket request numbers, genomic diagrams,reasoning and personal thoughts, TODO comments, docstrings, BG headers, etc.; (2)wikis and README filesinstructing users on how to install and implement the software along withtrace mappings detailing how the software is generally organized.

QUALIFICATIONS

Required

• Education:Bachelor’s degree in Computer Science, Software Engineering,Bioinformaticsora relatedfield;Master’sdegree preferred.
• Experience:Minimum of 5 years of experience in software development, with a proventrack recordof designing and implementing scalable softwaresolutions based on diverse user feature needs. Must have a proventrack recordof implementing production ready software solutions from scratch. Prior experience or domain knowledge from collaborating with laboratory scientists, computational biologists, or clinical reviewers is a nice-to-have.

COMPETENCIES

Technical Skills:

• Deep knowledge andexpertisein at least two programming languages (Python, Perl, R, or Bash, will also consider Java, C++, and Groovy).
• Proficient in a range of database technologies, including SQL Server, NoSQL, MongoDB, MySQL, andElasticSearch,demonstratingcomprehensive skills in database management, optimization, and query development.
• Proficiencyin working in an Agile framework and implementing CI/CD practices using Git. Knowledge of Azure is abonus.Implementationof object orientated programming (OOP) is second nature, which includes building intuitive classes relevant to the science, system, or service.
• Standard software design practices relevant to that languageisintuitive to you. Demonstrated ability to build entire software packages from scratch that are performant and highly maintainable, ensuring they are tested and are production ready. Solid understanding and habitual practice of unit and integration testing of software.
• High regard for documentation and object/variable naming that is explicit, with the ability to relay or distill scientific concepts within supplemental documentation or inline code itself.
• Proficiencyin designing and building APIs and microservices from scratch.
• Familiarity with Linux OS and HPC clusters (SLURM, Kubernetes, GCP, Azure, etc.) is a plus, but not essential.
• Solid understanding of package management practices (PIP, Conda, etc.) and containerization (Docker, Singularity, etc.).
• Proficiencyor knowledge of workflow management or orchestration tools (Nextflow, Airflow,Snakemake, etc.) is a plus, but not essential.

Analytical Thinking:

Strong analytical and problem-solving skills with the ability to translate complex business needs into technical solutions and work independently to solve problems. Also requiresgood communicationskills and flexibility to reach out to stakeholders and SMEs as necessary

• Team Collaboration:Excellent interpersonal and communication skills to collaborate effectively with multidisciplinary teams. Should be open and willing to receive and give criticism and feedback in a measured manner, focused on solving the problem at hand.
• Adaptability:Ability to adapt to evolving technologies, learn new tools, and implement best practices in BI software engineering and development. Should be able to assess situations when a drop-in solution would be preferable to a custom software implementation and run proof-of-concepts as needed. Should be highly familiar with best practices in software development and an advocate of best practices, even under pressure.
• Project Management:Experience in managing individual projects and adhering to timelines while delivering high-quality solutions, ensuringgood communicationin situations where project scopes may fluctuate
• Performs other advanced job-related duties as assigned.

PHYSICAL DEMANDS AND WORK ENVIRONMENT

• Frequently required to sit.
• Frequently required to stand.
• Frequently required toutilizehand and finger dexterity.
• Frequently required to talk or hear.

EEO STATEMENT

Baylor Genetics is proud to be 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.

Equal Opportunity Employer
This employer is required to notify all applicants of their rights pursuant to federal employment laws. For further information, please review the Know Your Rights notice from the Department of Labor.