Bioinformatics Scientist II

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

About the Department
The Division of Genomic Diagnostics and the Center for Data Driven Biomedicine (D3B) at the Children’s Hospital of Philadelphia are seeking bioinformatics scientists to expand the cancer genomics program. 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 to work with the rest of the team to identify, build and maintain bioinformatics tools pipelines, and algorithms necessary to offer whole exome and whole transcriptome (RNA-Seq) as a clinical test for tumor profiling. Expected areas of expertise include data integration, data management, application/ algorithm development, cancer genomics. Other responsibilities of this position include:

1. Apply sequence analysis methods, clustering algorithms, functional and statistical analysis methods to conduct data mining and in depth data analysis of genomic data to develop pipelines, applications and databases as needed.
2. Leverage existing public and commercial bioinformatics resources and tools
3. Enable integration and construction of scientific databases and applications in a growing clinical genomics environment
4. Design, implement, test, maintain, and support software applications
5. 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
6. Contribute to bioinformatics process optimization and standardization
7. Write protocols and policies as they relate to clinical bioinformatics and required regulations

Position Description
1. 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 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
2. Implement, update and maintain locally stored data resources required for various analysis tasks
3. Writes protocols and documentation for tests in compliance with CAP regulatory standards
4. Develops customized applications or scripts with friendly graphic or form-based user interfaces, full database access functions and other specific features as required by individual projects. 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

5. 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

Requirements

• 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, cancer biology and genetics. 
• Advanced/proven skills utilizing and in depth knowledge of bioinformatics algorithms, tools and resources, e.g. NGS (RNA-seq, whole genome, whole exome) related tools and pipelines (alignment, variant calling, QC, etc.), 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. STAR, BWA, 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) 
• 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.

The Children's Hospital of Philadelphia is committed to providing a safe and healthy environment for its patients, family members, visitors and employees. In an effort to achieve this goal, employment at The Children's Hospital of Philadelphia, other than for positions with regularly scheduled hours in New Jersey, is contingent upon an attestation that the job applicant does not use tobacco products or nicotine in any form and a negative nicotine screen (the latter occurs after a job offer).

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.

About Our Organization

The Children's Hospital of Philadelphia (CHOP) is the nation's first hospital devoted exclusively to the care of children. Since our start in 1855, CHOP has been the birthplace for many dramatic firsts in pediatric medicine. The Hospital has fostered medical discoveries and innovations that have improved pediatric healthcare and saved countless children’s lives. Today, families facing complex conditions come to CHOP from all over the world, and our care and innovation has repeatedly earned us a spot on the U.S. News & World Report's Honor Roll of the nation's best children's hospitals.

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