Bioinformatics Scientist II

Children's Hospital of Philadelphia
Job Location
Philadelphia, PA 19104
Job Description

The Bioinformatics scientist II will join the clinical bioinformatics group at the Division of Genomic Diagnostics (DGD) to provide bioinformatics expertise to integrate and apply latest technologies (including NGS) into clinical diagnostics. The focus of the position is service-level application of bioinformatics tools and methods to bench and clinical problems in genomics. Expected areas of expertise include data integration, data management, application/ algorithm development, genomics. The scientist will work with the bioinformatics group to consult with lab members on high throughput lab test design and optimization and perform project requirement analysis and provide pertinent bioinformatics development. Other responsibilities of this position include:

• Apply sequence analysis methods, clustering algorithms, functional and statistical analysis methods to conduct data mining and in depth data analysis of genomic data in patients. Develop pipeline, application and databases as needed.
• Leverage existing public and commercial bioinformatics resources and tools
• Enable integration and construction of scientific databases and applications in a growing clinical genomics environment
• Design, implement, test, maintain, and support software applications
• Work in a team environment and interact with experts in molecular biology, genetics, bioinformatics and IT to contribute to cutting edge clinical diagnostics at CHOP
• Contribute to bioinformatics process optimization and standardization
• Write protocols and policies as they relate to clinical bioinformatics and required regulations

• Pre/Post Analysis (40%): Works with the DGD to help determine bioinformatics needs. Analyzes user requirements, determines user software, hardware, and data management needs. Based on feedback, implements bioinformatics solutions. 
o Helps to identify and assess demands, requirements, and effective software solutions for the laboratory
o Use standard pipelines for data processing and manipulation in advance of performing analysis in a manner that best enables the analysis plan
o Contribute to the development of additional pipeline functionality and changes by providing knowledge of both project-specific requirements and bioinformatics discipline advances
o Advocate for specific project requirements for continual advancement of shared pipeline and code resources
o Recognizes areas of improvement in software implementation, usage, and performance; implements improvements as appropriate and suitable for the The DGD to implement
o Implement, update and maintain locally stored data resources required for various analysis tasks
o Writes protocols and documentation for tests in compliance with CAP regulatory standards

• Coding (30%): Code and generally support code and applications on behalf of collaborative project and/or team.
o Within the context of the project, develop and apply best practices to code development:
 Establish requirements with the project team
 Review existing applications and code sources (both commercial and open source) and selection of best strategy for development or adoption
 Advocate for chosen strategy to project team by showing value of approach
o Develop best practices for project-based code development, QC, and execution consist with the expectations of specific collaborations
o Develops any customized applications or scripts with friendly graphic or form-based user interfaces, full database access functions and other specific features as required by individual studies. Correctly chooses most efficient programming language(s)
o Regularly seek peer-to-peer code reviews by participating in informal and formal critical code reviews
o Writes documentation of software implementation, maintenance, and customization according to standard programming protocols
o Design, implement, and execute bioinformatics analysis strategies for various bioinformatics analysis tasks as requested by the DGD

• Data Analysis (30%): Perform data analysis for various projects in the Division of Genomics Diagnostics (DGD). Identifies, ports/develops, maintains, and makes accessible all bioinformatics software for the DGD as needed 
o Develop robust analysis plans independently with regular peer-to-peer review in both informal and formal settings
o Incorporate more advanced applications and methods into analysis
o Data analysis for genomics data in the DGD. Includes monitoring and assessment of the data quality, variant prioritization, data modeling, and statistical analysis
o Actively collaborate and communicate with the DGD team, core sequencing lab, and Bioinformatics Team throughout project life-cycles and for pipeline development

The Children's Hospital of Philadelphia is an equal opportunity employer. We do not discriminate on the basis of race, color, gender, gender identity, sexual orientation, age, religion, national or ethnic origin, disability or protected veteran status.


• MS/PhD in bioinformatics, computer science, computational biology or closely related fields
• 4-5 years experience (preferably in a clinical setting) in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation.
• Strong knowledge of molecular biology and genetics. 
• Advanced/proven skills utilizing and in depth knowledge of bioinformatics algorithms, tools and resources, e.g. sequence retrieval, alignment and clustering techniques, expression profiling and protein related analysis, major databases and standards in the field.
• Proficiency commonly used bioinformatics languages: Python, Java, R.
• Experience with pipeline or workflow development frameworks preferred (e.g. common workflow language frameworks).
• Experience with management and analysis of complex data types required.
• Proficiency in various open source and commercial bioinformatics resources and software required (e.g. Novoalign, GATK, Freebayes, etc.) 
• Strong UNIX/LINUX expertise required. 
• Proven experience of using standard software development practices including using version control systems (e.g. Github)
• Fluency in database management systems (MySQL, PostgreSQL, NoSQL databases) 
• Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture preferred.
• Familiarity with resources of genomic data sets and analysis tools, such as UCSC Genome Browser, ENCODE, and NCBI databases is required.
• Ability to correctly select and perform statistical tests for most types of genomic data, and to properly interpret their results in the scenario of a specific study is preferred.
• Ability to interact with clinicians during a clinical/scientific discussion is required. 
• Accountability and attention to timelines. 
• Excellent organization and communication skills with an emphasis on strong presentation skills
• Ability to independently plan and execute analyses of moderate complexity required
• Ability to provide objective validation of results required
• Ability to work in a team environment. 

All CHOP employees who work in a patient building or who provide patient care are required to receive an annual influenza vaccine unless they are granted a medical or religious exemption.

How to Apply
About Our Organization

The Children's Hospital of Philadelphia does more than make a difference in the lives of children — we offer the same endless opportunities for growth, change and support to the professionals who make up our team. Within a unique work environment, complete with exceptional team members, supportive managers, state-of-the-art care and training, our people are empowered to realize their well-defined goals. At CHOP, everyone makes a difference — that's the very foundation on which our hospital is built.

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