Reference #: 1007821 SHIFT:Day (United States of America)

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We strongly encourage all candidates of diverse backgrounds and lived experiences to apply.

A Brief Overview

The bioinformatics group in the Department of Biomedical and Health Informatics (DBHI) at The Children's Hospital of Philadelphia (CHOP) is seeking a Bioinformatics Scientist to join our team of Bioinformatics Scientists supporting ongoing basic and translational research within the Division of Oncology and Center for Childhood Cancer Research (CCCR). The candidate will be embedded in the CCCR, a highly collaborative environment, and will primarily be focused on supporting scientific teams and projects as a bioinformatics domain expert. The candidate will attend selected lab meetings and interact daily with principal investigators and individual lab members on a project-by-project basis. Additionally, the candidate will work with a principal investigator overseeing the bioinformatics group in the CCCR and our extended bioinformatics group in DBHI to stay current on emerging technologies and algorithms.

The successful candidate will preferably have a PhD degree in Bioinformatics, Computational Biology, or a related field, and must have demonstrable skills in coding in R and/or Python, though both are preferred. The successful candidate will have had biology training, experience with high-performance and/or cloud-based computing environments, experience in the analysis of sequencing data related to cancer (e.g. somatic single nucleotide variants (SNVs), indels, structural variations (SVs), fusion transcripts, copy number analyses, or ATAC sequencing), as well as experience in other types of bioinformatics analyses, particularly those involving next-generation sequencing. The successful candidate will have experience with established algorithms/pipelines for processing genomics data, and the ability to learn and apply new methods. They will also be able to conceive and develop innovative solutions for a variety of computational challenges of these data. Creative data visualization skills are important for this position.

The Bioinformatics Scientist II position is a 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. he 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 knowledge 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 Experience with management and analysis of complex data types. Required At least four (4) years of experience in applied bioinformatics, genomics, and computational work Preferre