BACKGROUND

RESPONSIBILITIES

• You will be involved in research projects that contain large cross-disease cohorts which are being characterized with next-generation sequencing
• This role will have a strong focus on phenotype harmonization and association with genomic variation
• Successful candidates will gain deep knowledge about important clinical and research phenotypes across a number of pediatric diseases
• With this knowledge, this role will utilize controlled vocabularies, ontologies and associated methodologies to develop scalable systems that harmonize, store, and analyze these phenotypes in the context of genomics
• Computational Environment Development and Optimization
• Independently manage and develop large-scale bioinformatics pipelines with NGS data such as Whole Genome Re-sequencing, Whole Exome Sequencing, Transcriptome, Small RNA analysis, Somatic Mutation analysis and Trio based analysis etc
• Facilitate efficient transfer of bioinformatics data from data sources to data users with benchmarking and data quality checks
• Troubleshoot data quality issues or discrepancies
• Generally implement bioinformatics processing, storage, and manipulation of bioinformatics data in a cloud environment
• Independently manage and evolve process for effectively using large-scale, cloud-based, bioinformatics storage frameworks
• Establish and implement integration and testing procedures following industry best practices for production bioinformatics systems integration and deployment
• Provide continuous assessment of commercial and open-source bioinformatics data resources and processing solutions
• Identify and test application/pipeline defects and fixes
• Work with technical team to establish and maintain appropriate levels of availability, response time, and performance of bioinformatics software and systems
• Serve as engineering resource on a variety of bioinformatics-focused projects
• Serve as engineering facilitator by assessing all stakeholders, including bioinformatics management, bioinformatics scientists, information systems staff, and principal investigators
• Mentor lower tier engineering individuals and groups as needed
• Under supervision, contribute to the development of a formal bioinformatics engineering plan and development roadmap
• Adopts and implements policies and standards for data quality, completeness, and reproducibility
• Adopts and implements policies and standards for performance benchmarking and system stability
• Maintain and audit all documentation required for transparency and reproducibility of operations and any relevant regulations
• Documentation may include configuration, processes, service records, asset inventories, topologies, admin manuals, job instructions, support contacts, and bug/issue tracking
• Install, maintain, and provide technical support for all software installations and associated hardware

REQUIREMENTS

• BS/MS in computational discipline required
• Ability to independently plan and execute pipelines and workflows of high complexity required
• Knowledge of phenotype harmonization processes and associated resources such as ontologies required
• Knowledge of common NGS or other high-throughput data formats is required
• Strong UNIX/LINUX expertise required
• Expertise in applications written in common bioinformatics languages such as Python, R, Perl or similar required
• Expertise in support mechanisms for common bioinformatics applications, data sources, and data formats required
• Expertise with resources of genomic data sets and analysis tools, such as NCBI databases, UCSC Genome Browser, ENCODE, and others is required
• Demonstrated ability to develop and implement best practices for bioinformatics systems integration, testing, and deployment is required
• Knowledge with cloud computing concepts and applications is required

LOCATION

HOW TO APPLY