Reference #: 1009045 SHIFT:Day (United States of America)

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A Brief Overview The Genomic Diagnostic Laboratory (GDL) of the Children's Hospital of Philadelphia is seeking a highly motivated Bioinformatics Scientist II with an interest in laboratory diagnostics to join our team. This is an exciting opportunity to work collaboratively within the bioinformatics team and together with our laboratory directors, supervisors, analysts, genetic counselors, and wet bench team to develop and improve pipelines and other tools to support our expanding testing menu. Our work focuses on providing accurate, timely diagnostic testing that has a direct impact on establishing the diagnosis, prognosis, treatment, and management plan for our patients. The team also supports cutting edge R&D efforts including new clinical test development and clinical research. The position can be worked in a remote capacity or on-site, according to individual preference. Work hours must align with the core lab hours of 9am-5:30pm EST; some flexibility in work hours is possible after the training period (e.g. 8am-4:30pm). Seasoned professionals with expertise in NGS pipeline development and Python are encouraged to apply. The Bioinformatics Scientist II position is an entry level position for a PhD level professional and a 2nd stage position for those with moderate experience without a PhD. The focus of the position is service-level application of bioinformatics tools and methods to bench and clinical research problems in various biomedical domains. The position allows for a wide variety of activities described within the job responsibilities and encompasses positions within both research and clinical environments. Activities occur with a moderate degree of supervision with some latitude for independent judgment, development of bioinformatics workflows and processes, and presentation of results. The Bioinformatics Scientist II will begin to apply best practices in collaborative science as a bioinformatics domain expert. Academic output, while not a primary focus of this position, is also expected with a moderate degree of supervision. The Bioinformatics Scientist II is primarily focused on supporting scientific teams and projects as a bioinformatics domain expert.

The Bioinformatics Scientist II must be able to perform all responsibilities listed in the Bioinformatics Scientist I job description. All responsibilities listed in this description are additional.

What you will do Pre-Analysis (20%): Contribute to the development of application portfolio by developing knowledge of internally developed systems, open-source programs, and commercial applications. Provide efficient data management support. Use standard pipelines for data processing and manipulation in advance of performing analysis in a manner that best enables the analysis plan. Contribute to the development of additional pipeline functionality and changes by providing nowledge of both collaboration-specific requirements and bioinformatics discipline advances. Advocate for specific collaboration requirements for continual advancement of shared pipeline and code resources. Provide collaboration-specific transparency for data processing and pre-analysis, including sample- and cohort-level status. Coding (20%): Code and generally support code and applications on behalf of collaborative project and/or team. Within the context of the collaboration or 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 Develop best practices for project-based code development, QC, and execution consist with the expectations of specific collaborations. Regularly seek peer-to-peer code reviews by participating in informal and formal critical code reviews. Data Analysis (20%): Analyze data of high complexity by applying sound statistical and commonly accepted bioinformatics methods to -omics data primarily under the direction of the collaborative project team. Develop robust analysis plans independently with regular peer-to-peer review in both informal and formal settings. Incorporate more advanced applications and methods into analysis. Develop at least one specialty analytical or biomedical area that serves the collaborative team. Collaboration (20%): Establish role within collaborative project team as primary bioinformatics resource. Contribute to and influence project-level management by serving as bioinformatics point. Define and promote boundaries of support by assessing all stakeholders, including bioinformatics management, collaborator expectations, and funding levels and mechanisms. Regularly discuss satisfaction and expectations with collaborators; continually advocate for clear understanding of role. Develop new collaborations with high degree of supervision. Academic Output (20%): Develop presentations, grant sections, and manuscript sections with subsequent review by peers and mentors. Regularly contribute to bioinformatics-focused manuscripts and publications. Regularly contribute to podium presentations and posters. Contribute to bioinformatics sections of grant and award proposals. Education Qualifications Bachelor's Degree Required Master's Degree biological or computational discipline Preferred Experience Qualifications At least three (3) years experience in applied bioinformatics, genomics, and computational work Required Four (4) or more years of experience in applied bioinformatics, genomics, and computational work. This experience can be inclusive of a relevant PhD dissertation Preferred Experience with software and algorithms used for NGS data analysis. * Experience with object oriented development Preferred At least four (4) years of experience in applied bioinformatics, genomics, and computational work Preferred Experience with Python, Perl, or other languages Preferred Experience with pipeline or workflow development frameworks Preferred Experience or knowledge of technologies commonly used in biological labs, such as PCR, cloning, electrophoresis gels, and cell culture Preferred Skills and Abilities Strong UNIX/LINUX expertise required. Proficiency in R or similar commonly used bioinformatics language required. Proficiency in various open source and commercial bioinformatics resources and software required. Knowledge of the working mechanis