Bioinformatics Analyst III

Theiagen Genomics; Northern (KY); Hybrid; USD 110,000 - 120,000; Full time

Benefits offered by this job

Paid Time Off

Fully remote work

Company supplied computer

Medical, Dental, Vision coverage

401(k) with company match

Flexible Spending Accounts

Employee Assistance Program

Employee Discount Program

Job summary

Theiagen Genomics is seeking a Bioinformatics Analyst III to join our Public Health Team in a senior, leadership role. This position will independently lead high-impact pathogen genomics projects and provide scientific oversight for analyses, reports, and partner deliverables.

You will mentor junior staff, collaborate across analysts, developers, and stakeholders, and help scale our cloud-based workflows and services to support public health initiatives.

Qualifications

• Masters or PhD in bioinformatics, biostatistics, computer science, microbiology, or related field.
• 7+ years of bioinformatics experience with NGS and multi-omics.
• Programming in SQL, Python, and R.
• Experience with Nextflow, Snakemake, and WDL.
• Ability to lead complex projects independently.
• Strong communication to diverse audiences.

Responsibilities

• Serve as pathogen genomics SME for public health applications.
• Provide scientific oversight and sign-off for analyses and reports.
• Lead complex projects from initiation through delivery.
• Coordinate across analysts, developers, and managers.
• Mentor junior staff and contribute to SOPs.

Skills

Bioinformatics analysis

SQL/Python/R

Pathogen genomics

Project leadership

Communication

UNIX/Linux

Public health knowledge

Education

Masters or PhD in bioinformatics/related field

Tools

Nextflow

Snakemake

WDL

Terra.bio

Galaxy

Job description

Bioinformatics Analyst III

Department: Bioinformatics

Employment Type: Full Time

Location: Remote-US

Reporting To: Public Health Team Lead

Compensation: $110,000 - $120,000 / year

Description

About the Company:

Theiagen Genomics is an innovative technology company dedicated to transforming public health and pathogen genomics through advanced technology solutions and a collaborative work culture. At Theiagen we aim to work with state IT and bring these computing resources outside the state infrastructure. Leveraging the affordability, scalability, and security of cloud computing environments resulting in cutting edge technology that can drive your public health interventions. We are a team of experts across academia, government and industry careers who have come together to deliver a world-leading service covering a diverse range of microbial genomics applications.

About the Position:

Theiagen is seeking a Bioinformatics Analyst III to serve as a senior scientific and operational leader within our Public Health Team, reporting to the Public Health Team Lead. This role will independently lead complex and high-impact initiatives, serve as a primary owner for select partner engagements and projects, provide scientific oversight and mentorship across teams, and support the continued growth and scalability of Theiagen’s pathogen genomics services and operations.

Key Responsibilities

Technical & Scientific Leadership

• Serve as a pathogen genomics subject matter expert for public health and other applications.
• Provide scientific oversight and sign-off authority for analyses, reports, presentations, and partner deliverables.
• Guide interpretation of complex or non-routine analytical results.
• Ensure scientific rigor, reproducibility, and alignment with partner needs.
• Support development and evaluation of analytical methods, workflows, and tools.

Initiative Ownership & Execution

• Independently lead novel, ambiguous, or high-complexity projects from initiation through delivery.
• Serve as primary owner for partner engagements and specialized initiatives.
• Coordinate across analysts, developers, project managers, and stakeholders to drive execution.
• Develop implementation strategies, design documentation, and operational approaches for new project types.
• Act as escalation point for non-routine analytical and operational challenges.

Partner & Stakeholder Engagement

• Lead partner-facing meetings and communications independently.
• Build trusted relationships with public health and external partners.
• Identify partner needs and translate them into actionable analytical and technical solutions.
• Present findings, recommendations, and project updates to technical and non-technical audiences.
• Support strategic discussions regarding project direction and delivery.

Communication & Strategic Alignment

• Support Team Leads in alignment of analytical work with organizational priorities and operational strategy.
• Support Team Leads in scaling operations and distributing leadership responsibilities.
• Contribute to planning discussions regarding current and future services, and idea development for services expansion/improvement.
• Collaborate across teams to improve consistency, coordination, and delivery quality.
• Communicate technical concepts clearly across interdisciplinary teams.

Process Improvement & Technical Mentorship

• Mentor Analyst I and II staff through onboarding, troubleshooting, and professional development.
• Lead training initiatives and contribute to development of best practices and SOPs.
• Identify opportunities for workflow optimization, automation, and operational efficiency.
• Support knowledge-sharing and development of internal technical standards.
• Foster technical excellence and collaborative problem solving across teams.

Product Management & Design

• Define and translate product vision, roadmap, and priorities into actionable initiatives and continuously optimize direction based on user feedback, performance metrics, and organizational goals.
• Define and validate product acceptance criteria, ensuring deliverables meet functional and quality standards while monitoring product performance and user experience to drive continuous improvement.
• Serve as the primary liaison between stakeholders and the development team, ensuring clear communication of requirements, and supporting the team to successfully deliver sprint goals.
• Support refinement and prioritization of the product backlog by defining clear requirements, user stories, and acceptance criteria; collaborate with cross-functional stakeholders to incorporate customer and business feedback; and communicate product priorities, timelines, and risks to ensure delivery aligns with business value.

Skills, Knowledge and Expertise

• Masters or doctoral degree in bioinformatics, biostatistics, computer science, microbiology, molecular biology, or related field.
• 7+ years of professional experience working in bioinformatics analysis, with expertise in NGS and multi-omics data.
• Experience in programming languages such as SQL/Python/R.
• Experience with bioinformatics tools, databases, and workflow management systems (Nextflow, Snakemake, WDL).
• Demonstrated expertise applying bioinformatics tools and workflows to answer complex biological questions, particularly in pathogen genomics.
• Advanced proficiency in using bioinformatics tools for tasks such as genome assembly, annotation, taxonomic classification, and antimicrobial resistance detection.
• Proficiency with genomic epidemiology methods, including phylogenetics, outbreak investigation tools, and MLST typing.
• Proven ability to lead and manage multiple projects independently or within a collaborative team environment.
• Excellent written and verbal communication, with experience presenting technical results to diverse audiences.
• Effective judgment and advanced problem-solving skills with minimal supervision.
• Strong motivation and demonstrated impact in public health initiatives.

Preferred Skills:

• Comprehensive knowledge of public health laboratory processes and workflows, including validation and verification of bioinformatics workflows for decision-making.
• Expertise in interpreting bioinformatics results and providing actionable public health insights.
• Significant experience analyzing pathogen genomics datasets for public health applications (e.g., SARS-CoV-2, Mycobacterium tuberculosis, antimicrobial resistance, or HAIs).
• Advanced experience with cloud-based bioinformatics platforms (e.g., Terra.bio, Galaxy) and workflow orchestration tools (e.g., Nextflow, WDL, or Snakemake).
• Hands-on expertise in using visualization and reporting tools to clearly communicate results to stakeholders.
• Proficiency in shell scripting and working in UNIX/Linux environments.
• Experience mentoring junior team members and fostering technical excellence.

Benefits

• Paid Time Off
• Fully remote work (Must hold citizenship for where you plan to work from, role does not offer sponsorship)
• Company supplied computer
• Medical, Dental, Vision coverage/stipend
• 401(k) with company match
• Flexible Spending Accounts
• Employee Assistance Program
• Employee Discount Program

Why Join Theiagen Genomics?

• Be part of a passionate team driving innovation in the pathogen genomics space.
• Competitive salary, comprehensive benefits, and opportunities for professional development.
• A culture that values diversity, collaboration, and a commitment to excellence.

Theiagen Genomics is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability or veteran status.