Associate Director, Bioinformatics- Medical Informatics- Remote, USA

Ambry Genetics-posted 7 months ago
$175,000 - $220,000/Yr
Full-time • Senior
Remote • Aliso Viejo, CA
Ambulatory Health Care Services
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We seek an Associate Director to lead a team of data engineers, scientists, and wranglers in designing genomic research data platforms. The candidate will provide leadership and hands-on guidance, focusing on high-throughput sequencing data and FAIR-compliant metadata. Collaborate with bioinformaticians, software engineers, lab scientists, and clinicians to improve diagnostic and research workflows. Manage technical solutions with medical informatics and IT teams, participate in scrum ceremonies, and understand stakeholder needs. Oversee medical informatics strategies, align with organizational goals, mentor teams, set performance standards, manage project timelines, resources, budgets, and offer professional development for team members. This individual will play a critical leadership role in designing and managing data models and products that support translational research, clinical development, and real-world data initiatives. The ideal candidate will bridge technical and scientific domains to deliver high-impact data solutions that drive decision-making across the organization.

  • Lead, mentor, and manage a hybrid team of engineers, bioinformaticians, and data scientists, ensuring effective performance.
  • Define and implement long-term technical vision in alignment with enterprise R&D objectives.
  • Promote cross-functional collaboration across R&D, translational research, and clinical development teams.
  • Co-develop robust, containerized (Docker/WDL/CWL) and cloud-optimized (AWS/GCP) environments to support production-level deployment.
  • Implement data CI/CD best practices for platform stability and faster iteration in clinical data.
  • Support the design, development, and maintenance of scalable data pipelines, warehousing solutions, and metadata management systems.
  • Ensure efficient integration of data from internal and external sources (e.g., EHRs, genomics, real-world evidence, OMOP, FHIR and UMLS).
  • Guide the evolution of metadata models and ontologies to support interoperability across internal and external data ecosystems.
  • Align organizational data models with public standards from consortia such as ENCODE, HuBMAP, GREGoR, HGRP, UMLS, OMOP, and FHIR.
  • Collaborate with external research partners to drive data alignment across multi-stakeholder efforts.
  • Manage high-impact initiatives, ensuring strategic alignment, risk management, and resource optimization.
  • Develop executive dashboards and metrics for data quality, project delivery, and long-term data value assessment.
  • Support data quality, governance, and security standards in collaboration with IT, QA, and compliance functions.
  • Facilitate regulatory submissions and audit readiness through reliable data traceability and documentation.
  • Assess and apply emerging technologies in data science and informatics (e.g., AI/ML, cloud-based platforms).
  • Encourage a culture of scientific inquiry, operational efficiency, and interdisciplinary collaboration.
  • Serve as a role model for the team, establishing standards for excellence and mentoring junior engineers.
  • Ph.D., M.D., or Master's in Biomedical Informatics, Data Science, Computer Science, or a related field.
  • 7+ years in medical/clinical informatics, data engineering, or bioinformatics, preferably in biotech or pharma.
  • 3+ years in a leadership or team management role.
  • Proven experience in medical informatics, including the development and implementation of systems such as clinical informatics systems, electronic health records (EHR), or health information exchange (HIE) systems.
  • Experience in managing large-scale projects and cross-functional teams, with a focus on improving clinical workflows and patient outcomes.
  • Strong understanding of data standards (e.g., CDISC, OMOP, HL7, FHIR), privacy regulations (HIPAA, GDPR), and GxP compliance.
  • Deep understanding of FAIR principles, metadata standards, and medical informatics best practices.
  • Proven track record in developing standardized, interoperable data platforms serving large consortia or user communities.
  • Proficient in Python, cloud-native tools (AWS), Docker, GitHub, and workflow engines (WDL, Nextflow, or Snakemake).
  • Proficiency in cloud environments (AWS, Azure, GCP).
  • Experience with modern data stacks (e.g., Snowflake, DBT, Airflow, SQL, Python/R).
  • In-depth knowledge of clinical genetics, mutation analysis, and medical informatics principles, with experience in gene-disease ontologies and databases (HGVS nomenclatures, ClinVar, HGMD).
  • Proficient in molecular biology, and genomics for automated clinical interpretation.
  • Proficiency with medical informatics 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, medical informatics software.
  • Experienced in API development, statistical analysis methods, and use of frameworks/tools like PHP, React, Symfony, and Atlassian suite (Jira, Confluence).
  • Advanced analytical skills focused on creating efficient, reproducible medical informatics solutions for clinical and research applications, with strong statistical analysis expertise.
  • Excellent written and verbal communication skills, with a proven ability to work both independently and collaboratively across teams.
  • 401k
  • medical
  • dental
  • vision
  • FSA
  • paid sick leave
  • generous paid time off (PTO) program
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