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Position Overview

The Associate Director, Bioinformatics Operations is largely a self-directed leader responsible for the reliability, scalability, and compliane of bioinformatics pipelines and data workflows that support a high throughput clinical NGS and other advanced genomic technologies laboratory. This role oversees end-to-end bioinformatics operations from raw data acquisition through report ready outputs, ensuring that production systems meet CLIA/CAP, ISO, and internal quality requirements. The Associate Director partners closely with the Laboratory Director, clinical lab operations, QA/RA, and IT/DevOps to maintain robust day-to-day operations while driving continuous improvement and supporting assay validations and change management.

As a technical and operational subject matter expert, the Associate Director provides guidance and mentorship to a team of bioinformaticians and scientists, develops and enforces SOPs and standards, and leads incident response, capacity planning, and operational readiness for audits and inspections.

Essential Duties

Include, but are not limited to, the following:

• Operational ownership of clinical pipelines
• Provide operational ownership of production bioinformatics pipelines for clinical NGS assays, from BCL/FASTQ through aligned data, variant calls, QC metrics, and report ready outputs.
• Ensure that routine analyses, QC checks, and automated workflows run reliably within defined SLAs for turnaround time and quality.
• Oversee monitoring of sequencing runs and pipeline performance, including review of run-level and sample-level metrics, and lead response to data quality concerns, contamination, discordance, and unexpected error patterns.
• Partner with IT/DevOps/HPC teams to manage compute, storage, and data transfer needs for production, including environment configuration, access control, and backup/restore processes.
• Own bioinformatics components of CLIA/CAP compliance for assigned assays, including documentation, validation reports, and ongoing quality monitoring for pipelines and associated tools.
• Lead or oversee verification and validation studies for new assays, assay updates, software changes, and instrumentation impacting bioinformatics workflows; develop study designs, acceptance criteria, and analysis plans in collaboration with Laboratory Director, R&D, QA and Lab Operations.
• Lead investigation and documentation of nonconformities, QC failures, and incidents involving bioinformatics systems; perform root cause analysis, define and implement corrective and preventive actions, and track effectiveness.
• Ensure that bioinformatics SOPs, work instructions, software design specifications, and change control records are current, complete, and aligned with regulatory requirements and internal QMS.
• Support preparation for and participation in CLIA/CAP, ISO, and other regulatory or client audits, serving as the primary bioinformatics operations representative for assigned areas.
• Provide day‑to‑day leadership to a team of bioinformatics professionals (e.g., Bioinformatician I–Principal), including workload allocation, prioritization, coaching, and performance management.
• Set clear goals and expectations for bioinformatics operations staff, conduct performance reviews, identify development needs, and support career progression consistent with the Bioinformatics Operations career ladder.
• Oversee training, competency assessment, and ongoing education for team members on production pipelines, QC practices, SOPs, and regulatory expectations.
• Foster a collaborative culture that emphasizes quality, accountability, continuous improvement, and effective communication across the lab and broader organization.
• Serve as the primary bioinformatics operations contact for clinical lab leadership, Laboratory Directors, medical directors, QA, IT/DevOps, and other stakeholders.
• Participate in and often lead regular clinical operations meetings, presenting run metrics, incident trends, capacity status, and improvement initiatives.
• Collaborate with R&D bioinformatics and assay development teams to transition new assays and algorithm updates into production, ensuring robust validation, documentation, and change management.
• Communicate complex technical and regulatory topics in a clear, concise way to both technical and non‑technical audiences through written reports, presentations, and live discussions.
• Identify, prioritize, and lead initiatives to improve pipeline robustness, efficiency, and scalability, including automation, monitoring enhancements, standardization, and reduction of manual touchpoints.
• Use operational metrics, dashboards, and retrospective reviews to drive continuous improvement in TAT, failure rates, incident response, and resource utilization.
• Anticipate future operational needs (e.g., new assay launches, increased volume, regulatory changes) and contribute to strategic planning for bioinformatics infrastructure, staffing, and processes.
• Stay current with industry best practices, regulatory expectations, and emerging technologies relevant to clinical bioinformatics operations, and translate them into practical improvements.
• Motivate and inspire employees to do their best work through coaching.
• Maintain morale and support employee engagement initiatives.
• Maintain regular and reliable attendance.
• Ability to act with an inclusion mindset and model these behaviors for the organization.
• Ability to work on a mobile device, tablet, or in front of a computer screen and/or perform typing for approximately 90% of a typical working day.
• Ability to work on a computer and phone simultaneously.
• Ability to travel 10% of working time away from work location, may include overnight/weekend travel.

Minimum Qualifications

• PhD in bioinformatics, computational biology, computer science, mathematics, or related field; or Master’s degree in bioinformatics, computational biology, computer science, mathematics, or related field plus 4 years of experience in lieu of a PhD; or Bachelor’s degree in bioinformatics, computational biology, computer science, mathematics, or related field plus 6 years of experience in lieu of PhD.
• 8+ years of industry or academia experience in bioinformatics.
• 6+ years of experience in medical device/IVD, biotech, life science or pharmaceutical industry.
• 3+ years of direct people leadership and management experience.
• Deep knowledge and thorough understanding of molecular biology and/or biochemistry and/or next-generation sequencing (NGS) and genomics.
• Demonstrated expertise in product/assay research, design, or development
• Basic computer skills to include Internet navigation, Email usage, and word processing. Proficient in Microsoft Office to include Excel, Word, and PowerPoint.
• Authorization to work in the United States without sponsorship.
• Demonstrated ability to perform the Essential Duties of the position with or without accommodation.

Preferred Qualifications

• 10+ years of experience in medical device/IVD, biotech, life science or pharmaceutical industry.
• Previous experience as a project lead for a team of scientists.
• 2+ years of direct people leadership and management experience.
• Experience in a pharmaceutical or biotech manufacturing environment, preferably in a GMP and/or ISO environment.
• Previous industry experience in product development or technical support.
• Experience with genomic databases and software.
• Background containing a substantial amount of bioinformatics work including troubleshooting.
• Previous experience working in a molecular diagnostics/clinical laboratory setting.

Salary Range:

$153,000.00 - $259,000.00

The annual base salary shown is for this position located in US - WI - Madison on a full-time basis. In addition, this position is bonus eligible.

Exact Sciences is proud to offer an employee experience that includes paid time off (including days for vacation, holidays, volunteering, and personal time), paid leave for parents and caregivers, a retirement savings plan, wellness support, and health benefits including medical, prescription drug, dental, and vision coverage. Learn more about our benefits.

Our success relies on the experiences and perspectives of a diverse team, and Exact Sciences fosters a culture where all employees can develop personally and professionally with a sense of respect and belonging. If you require an accommodation, please contact us here.

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We are an equal employment opportunity employer. All qualified applicants will receive consideration for employment without regard to disability, protected veteran status, and any other status protected by applicable local, state, or federal law.

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