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Associate Director, Clinical Informatics


New York Genome Center

Job Location

101 Avenue of the Americas
New York, NY 10013
United States

Job Description

The New York Genome Center is looking for a highly motivated individual to join our rapidly expanding Clinical Laboratory. As Associate Director, Clinical Informatics you will lead the analysis and interpretation of next-generation sequencing (NGS) data meeting CLIA and CAP guidelines. This work will be done in collaboration with the Clinical Laboratory Director and cross-functional team of Computational Biologists, Software Engineers and Analysts passionate about understanding the genetic basis of rare disease and cancer.

The Associate Director of Clinical Informatics will be responsible for analyzing and managing the clinical next generation sequencing pipeline. The goal will be to test and implement novel tools and methods for analyzing and interpreting human whole genome/exome sequencing data in relation to the available clinical information. The person will be responsible for managing the clinical genome/exome sequencing analysis needs of NYGC’s CLIA laboratory. In addition, the person will be responsible for improving the existing pipelines and analysis workflows to create a scalable solution to handle large clinical volumes. Publication of developed methods and scientific findings is encouraged.

Job duties will include:

  • Setup, improve, manage and maintain next generation sequencing (NGS) data analysis pipeline for constitutional diseases and cancer;
  • Analyze sequencing data using the established pipeline(s);
  • Filter and prioritize sequencing data with the available clinical information and generate priority variant reports;
  • Develop and implement innovative computational approaches for the analysis of large sequence datasets from NGS technologies with special focus on clinical assays;
  • Collaborate and consult with external researchers on the clinical research projects;
  • Perform appropriate quality control measures and implement statistical analyses on NGS data;
  • Interpret and present the results of the computational and statistical analyses to collaborators and coworkers;
  • Assist with data access, analysis, and interpretations;
  • Manage the Clinical Informatics team (currently one bioinformatics analyst);
    • Train bioinformatics analyst(s) to perform data analysis using established workflows
    • Provide technical guidance to bioinformatics analyst(s) in designing and implementing new workflows and analysis pipelines
    • Help bioinformatics analyst(s) in troubleshooting errors in existing pipelines or workflows
    • Train clinical genomics scientist(s) in standard procedures of data mining, biocuration, variant prioritization and interpretation
    • Provide ongoing support to clinical genomics scientist(s) in performing day to day variant analyses
    • Assign duties appropriately and monitor progress of tasks assigned to bioinformatics analysts and clinical genomics scientists.
  • Develop and maintain clinical reporting systems;
  • Assist in new clinical assay development, validation and CLEP submissions;
  • Provide technical support to germline computational biology team as needed;
  • Other duties as assigned.


Please note this job description is not designed to cover or contain a comprehensive listing of activities, duties or responsibilities that are required of the employee for this job. Duties, responsibilities, and activities may change at any time with or without notice.


  • PhD degree in the biological sciences with demonstrable computational skills required;
  • 8 or more years work experience in Bioinformatics, Genomics or Genetics with experience in analyzing data in a CLIA laboratory required;
  • Experience managing and working with next generation sequencing data required;
  • Extensive knowledge and experience in the use of existing bioinformatics tools and biological databases required, as well as familiarity with cloud computing;
  • Proficiency in utilizing data from public resources such as OMIM, EXAC, GNOMAD, ClinVar as part of data analysis or method development required;
  • Experience with running workflows and analyses on AWS and GCP required;
  • Experience writing scalable genomics workflows using Workflow Description Language (WDL) required;
  • Extensive knowledge about variant annotations, including variant annotation tools (e.g. VEP, SnpEff, Nirvana), ClinVr, HGMD, in-silico prediction algorithms and other clinical relevant annotations required.
  • Excellent written and verbal communication skills required; and,
  • Experience working in a Linux environment required, with C++/JAVA and running a cluster using SGE and BASH shell scripting strongly preferred.


  • Technical and Professional Skills: Consistently demonstrates skills and knowledge relevant for current role; strives to expand the depth and breadth of technical and professional skills; works with a high level of integrity; exhibits focus and discipline; appropriately prioritizes, manages expectations and delivers on commitments.
  • Collaborative & Communicative: Models collaboration and teamwork; brings out the best in others; effectively works with all levels, internally and externally; respects and embraces diversity of perspective; communicates clearly and listens carefully; uses good judgment as to what to communicate and when to do so.
  • Adaptable & Innovative: Adaptable and embraces change; develops new insights and pursues improvements and efficiency; fosters exchange of new ideas and willing to challenge the status quo; takes initiative and is solution-oriented; engages in work with passion and curiosity.
  • Leader and Manager: Attracts, develops and retains diverse talent to achieve outstanding results; encourages professional development, coaches and regularly communicates expectations and feedback; aligns and inspires efforts toward our mission; translates organizational vision into action; responsibly utilizes NYGC’s human and financial resources to ensure organizational and financial health; uses good judgment when making decisions; pushes boundaries and generates new ideas.


Work Flexibility

NYGC has established a flexible work policy to give employees and other staff more ability to balance their work, personal commitments, and commuting challenges. The incumbent in this position is eligible for a flexible work schedule or hybrid remote work arrangement with supervisory approval.


FLSA Status – Exempt

This position is eligible for visa sponsorship and relocation assistance

How to Apply

About Our Organization

About the Clinical Lab

The New York Genome Center (NYGC) has a state-of-the-art clinical diagnostic laboratory that utilizes next-generation sequencing technology to perform cutting-edge tests in the areas of genetics and oncology. The Clinical Laboratory is accredited by the Clinical Laboratory Improvement Amendments (CLIA) and the Clinical Laboratory Evaluation Program of the New York State Department of Health (CLEP). It is licensed to perform clinical testing in all fifty (50) of the United States and the District of Columbia. The laboratory participates in the College of American Pathologists (CAP) proficiency testing.

The Lab offers a variety of tests including Whole Genome Sequencing (WGS) and Whole Exome Sequencing (WES). Oncology Testing is available for patients with hematological malignancies and solid tumors. Genetic Testing is available for patients with undiagnosed diseases as well as individuals who are seeking predispositional genetic testing. NYGC is the first clinical laboratory offering New York State-approved clinical whole genome and transcriptome tests for cancer, and the first clinical laboratory offering New York State (NYS)-approved clinical WGS tests for undiagnosed disease and for predispositional genetic screening.


About the New York Genome Center

The New York Genome Center (NYGC) is an independent, nonprofit, academic research organization dedicated to advancing genomic research. NYGC scientists and staff are furthering new approaches to diagnosing and treating neurological diseases and cancer through their unique capabilities in whole genome sequencing, RNA sequencing, state-of-the art analytics, and the development of genomic tools. NYGC concentrates specifically on disease-based research in the following areas: neuropsychiatric disease (autism, schizophrenia, bipolar); neurodegenerative disease (ALS, Alzheimer’s, Parkinson’s, Huntington’s), and cancer.

Located in Lower Manhattan, the New York Genome Center was founded by and remains closely affiliated with the leading academic medical centers and research universities in the New York region, engaging in research projects with and for these institutions. Essential to our collaborative work is an outstanding faculty, whose members typically hold a joint appointment at NYGC and a partner university. They support our scientific mission by conducting independent research in areas of mutual interest to us and the wider scientific community.

Please note: We care greatly about our employees’ wellbeing, so NYGC has moved to a fully COVID-19 vaccinated work environment. You must be vaccinated against COVID-19 to work at NYGC, even if you are working partially remotely. If you are selected to interview for this role, we will explain our vaccination policy (including medical and religious exemptions) and ensure you are comfortable moving forward with further interviews.


Equal Opportunity

Diversity, equity, and inclusion are central to NYGC’s core mission. We strive to create a workplace environment that is welcoming and fair to all regardless of race, ethnicity, gender, sexual orientation, physical ability, or religion. We believe that when people of various backgrounds, life experiences, and perspectives work together in an inclusive and equitable environment we gain new and valuable perspectives that otherwise would have been missed. Valuing and supporting all NYGC employees as individuals while helping them realize their full potential is critical to promoting greater collaboration, innovation, and discovery – fostering a sense of belonging for our greatest strength, our people. We recognize that there is still work to be done that will require sustained commitment from the entire organization.

The New York Genome Center is a VEVRAA Federal Contractor. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, creed, color, gender, religion, national origin, sexual orientation, age, disability, genetic predisposition or carrier status, protected veteran or military status, domestic violence victim status, partnership status, caregiver status, alienage or citizenship status, marital status, or any other characteristic protected by applicable law. NYGC takes affirmative action in support of its policy to hire and advance in employment individuals who are minorities, women, protected veterans, and individuals with disabilities.