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Bioinformatics Specialist I, Analytic
4 months ago
The Karczewski Laboratory in the Center for Genomic Medicine (CGM) and Analytic and Translational Genetics Unit (ATGU) at Massachusetts General Hospital (MGH) and the Broad Institute of Harvard and MIT is seeking exceptional computational biology candidates to build tools necessary to visualize and interpret massive data sets of human genetic variation and functional genomic information. The Karczewski Laboratory helped lead the development of gnomAD ), the world's largest public reference dataset of human exomes and genomes. gnomAD has become one of the most widely used resources in the field and is now the default reference database for virtually all clinical interpretation pipelines, as well as a standard analysis resource for a wide variety of genetic and biological studies. We estimate gnomAD has contributed to the clinical diagnosis of over 2 million patients with genetic disorders.
Your role will be to build upon previous iterations of the gnomAD browser to develop a new web-browser to visualize and query the genomic and clinical data from electronic health records for the >50,000 patients in the Mass General Brigham (MGB) Biobank as part of a collaboration with the Brand and Samocha Laboratories, also based at MGH and the Broad Institute. Software engineering skills and an interest in user interface design and data visualization are key. Basic familiarity with genomics and DNA sequencing data is preferred, but not required. Most importantly, the ideal candidate will have enthusiasm for playing a critical role in a team-oriented project and learning new domains. There will also be opportunities to analyze these and other large-scale genomic datasets using deep learning to interpret genetic variants found in patients.
Candidates will have the opportunity to work in a unique translational genomics environment in the CGM that seeks to integrate computational genomics, technology development, and molecular genomics methods. The MGH and the Broad Institute provide a vibrant research environment with close links to top academic institutions across the Boston area and provide the potential for your contributions to be used and recognized worldwide.
This position is hybrid, including both onsite and remote work.
PRINCIPAL DUTIES AND RESPONSIBILITIES: In order of importance, list essential areas of responsibility, major job duties, special projects and key objectives for this position. These items should be evaluated throughout the year and included in the written annual evaluation. This section should be completed as a bulleted list and explain how the role is performed.
• Construct a browser to intuitively display genomic variants
• Apply state-of-the-art front-end libraries, such as TypeScript and React, and cloud-based infrastructure in Hail to store and serve data on the back-end
• Develop new visualization approaches to easily disseminate clinical data
- Evaluate and recommend new emerging tools for use in project
- Collaborate with other bioinformaticians to improve new genetic analysis
- Create scientifically rigorous visualizations, communications, and presentations of results
- Contribute to the generation of pipelines, protocols, publications, and intellectual property
• Bachelors or Masters degree in Computer Science or related field or equivalent experience.
• Experience with React, CSS, D3, GraphQL, Python.
• Experience building web-based applications with a focus on quality and incorporating user feedback.
• Highly collaborative attitude and ability to work well in a team setting.
• Excellent communication skills.
• Demonstrated attention to detail and analytical skills.
• Experience with Docker, Kubernetes, and a major cloud provider (Google Cloud Platform and/or Amazon Web Services) is a plus.
• Experience with bioinformatics datasets and analyses, particularly scalable frameworks such as Hail or Pyspark, is a big plus.
• Solid understanding of machine learning methods, ideally deep learning, with experience using at least one of the following frameworks: Pytorch, TensorFlow, JAX.
EDUCATION: Check boxes that best describe the minimum and preferred education requirements.
BS and/or MS in computational biology, bioinformatics, computer science, or a related field required.
Visa sponsorship available.
EXPERIENCE: Indicate the required and preferred (optional)amount and type of experience.
Minimum 1 year of directly related work experience in bioinformatics required.
WORKING CONDITIONS: Describe the conditions in which the work is performed. Use this section to detail any physical requirements for the position (lifting, carrying, etc). Use this section to also detail any environmental conditions associated with the position (outdoor weather requirements, hazardous materials, etc).
Office space in the Center for Genomic Medicine at the Simches Research Center of MGH.
Massachusetts General Hospital is an Affirmative Action Employer. By embracing diverse skills, perspectives and ideas, we choose to lead. All qualified applicants will receive consideration for employment without regard to race, color, religious creed, national origin, sex, age, gender identity, disability, sexual orientation, military service, genetic information, and/or other status protected under law. We will ensure that all individuals with a disability are provided a reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment.
